Starting phenix.real_space_refine
on Wed Mar  4 17:45:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pfd_13372/03_2026/7pfd_13372.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pfd_13372/03_2026/7pfd_13372.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pfd_13372/03_2026/7pfd_13372.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pfd_13372/03_2026/7pfd_13372.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pfd_13372/03_2026/7pfd_13372.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pfd_13372/03_2026/7pfd_13372.map"
  }
  resolution = 4.4
  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=   0.001 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic.
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     344      5.49       5
     S      10      5.16       5
     C    7520      2.51       5
     N    2563      2.21       5
     O    3238      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13675
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "J"
      Number of atoms: 3541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 3541
          Classifications: {'DNA': 172}
          Link IDs: {'rna3p': 171}
    Chain: "I"
      Number of atoms: 3511
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 3511
          Classifications: {'DNA': 172}
          Link IDs: {'rna3p': 171}
    Chain: "U"
      Number of atoms: 535
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 535
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
  Time building chain proxies: 2.89, per 1000 atoms: 0.21
  Number of scatterers: 13675
  At special positions: 0
  Unit cell: (111.3, 160.65, 114.45, 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      10     16.00
     P     344     15.00
     O    3238      8.00
     N    2563      7.00
     C    7520      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.97
  Conformation dependent library (CDL) restraints added in 323.4 milliseconds
  

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1566

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      68.8% alpha, 2.8% beta
      169 base pairs and 294 stacking pairs defined.
    Time for finding SS restraints: 2.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.842A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.537A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.533A  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 46 through 73
    Processing helix  chain 'C' and resid 79 through 89
      removed outlier: 3.507A  pdb=" N   ASN C  89 " --> pdb=" O   LEU C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.564A  pdb=" N   VAL D  41 " --> pdb=" O   TYR D  37 " (cutoff:3.500A)
    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: 3.796A  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
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.544A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.641A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.313A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.573A  pdb=" N   VAL H  41 " --> pdb=" O   TYR H  37 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 123
    Processing helix  chain 'U' and resid 38 through 49
      removed outlier: 3.967A  pdb=" N   LEU U  42 " --> pdb=" O   PRO U  38 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 57 through 69
    Processing helix  chain 'U' and resid 75 through 90
      removed outlier: 3.971A  pdb=" N   LYS U  84 " --> pdb=" O   LYS U  80 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   VAL U  87 " --> pdb=" O   LEU U  83 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.283A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97
      removed outlier: 6.192A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 6.846A  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: 6.967A  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: 7.503A  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 'U' and resid 92 through 94

    429 hydrogen bonds defined for protein.
    1284 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      431 hydrogen bonds
      862 hydrogen bond angles
      0 basepair planarities
      169 basepair parallelities
      294 stacking parallelities
  Total time for adding SS restraints: 3.13

  Time building geometry restraints manager: 1.32 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: 2420
        1.33 -     1.45: 5050
        1.45 -     1.57: 6440
        1.57 -     1.69: 686
        1.69 -     1.82: 20
  Bond restraints: 14616
  Sorted by residual:
  bond pdb=" C3'  DG J 763 "
       pdb=" O3'  DG J 763 "
    ideal  model  delta    sigma   weight residual
    1.422  1.497 -0.075 3.00e-02 1.11e+03 6.24e+00
  bond pdb=" CG  GLU H 113 "
       pdb=" CD  GLU H 113 "
    ideal  model  delta    sigma   weight residual
    1.516  1.456  0.060 2.50e-02 1.60e+03 5.76e+00
  bond pdb=" C3'  DG I 119 "
       pdb=" O3'  DG I 119 "
    ideal  model  delta    sigma   weight residual
    1.422  1.478 -0.056 3.00e-02 1.11e+03 3.47e+00
  bond pdb=" C3'  DT I 133 "
       pdb=" O3'  DT I 133 "
    ideal  model  delta    sigma   weight residual
    1.422  1.474 -0.052 3.00e-02 1.11e+03 3.04e+00
  bond pdb=" CG  GLU F  63 "
       pdb=" CD  GLU F  63 "
    ideal  model  delta    sigma   weight residual
    1.516  1.475  0.041 2.50e-02 1.60e+03 2.68e+00
  ... (remaining 14611 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.99: 20936
        2.99 -     5.98: 237
        5.98 -     8.97: 30
        8.97 -    11.96: 2
       11.96 -    14.95: 3
  Bond angle restraints: 21208
  Sorted by residual:
  angle pdb=" N   GLU H 113 "
        pdb=" CA  GLU H 113 "
        pdb=" CB  GLU H 113 "
      ideal   model   delta    sigma   weight residual
     110.28  119.29   -9.01 1.55e+00 4.16e-01 3.38e+01
  angle pdb=" N   GLU F  63 "
        pdb=" CA  GLU F  63 "
        pdb=" CB  GLU F  63 "
      ideal   model   delta    sigma   weight residual
     110.16  118.40   -8.24 1.48e+00 4.57e-01 3.10e+01
  angle pdb=" N   GLY D 104 "
        pdb=" CA  GLY D 104 "
        pdb=" C   GLY D 104 "
      ideal   model   delta    sigma   weight residual
     110.77  121.25  -10.48 1.93e+00 2.68e-01 2.95e+01
  angle pdb=" C   THR A  80 "
        pdb=" N   ASP A  81 "
        pdb=" CA  ASP A  81 "
      ideal   model   delta    sigma   weight residual
     121.54  129.78   -8.24 1.91e+00 2.74e-01 1.86e+01
  angle pdb=" CA  LEU F  62 "
        pdb=" CB  LEU F  62 "
        pdb=" CG  LEU F  62 "
      ideal   model   delta    sigma   weight residual
     116.30  131.25  -14.95 3.50e+00 8.16e-02 1.82e+01
  ... (remaining 21203 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.86: 6098
       35.86 -    71.73: 1769
       71.73 -   107.59: 49
      107.59 -   143.46: 1
      143.46 -   179.32: 2
  Dihedral angle restraints: 7919
    sinusoidal: 5488
      harmonic: 2431
  Sorted by residual:
  dihedral pdb=" CA  LEU B  22 "
           pdb=" C   LEU B  22 "
           pdb=" N   ARG B  23 "
           pdb=" CA  ARG B  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.60  -20.40     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" C4'  DG I 119 "
           pdb=" C3'  DG I 119 "
           pdb=" O3'  DG I 119 "
           pdb=" P    DC I 120 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.68  179.32     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  PHE A  84 "
           pdb=" C   PHE A  84 "
           pdb=" N   GLN A  85 "
           pdb=" CA  GLN A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.32   19.68     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 7916 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1705
       0.047 -    0.094: 575
       0.094 -    0.142: 107
       0.142 -    0.189: 21
       0.189 -    0.236: 8
  Chirality restraints: 2416
  Sorted by residual:
  chirality pdb=" CB  THR G  59 "
            pdb=" CA  THR G  59 "
            pdb=" OG1 THR G  59 "
            pdb=" CG2 THR G  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  PHE E 104 "
            pdb=" N   PHE E 104 "
            pdb=" C   PHE E 104 "
            pdb=" CB  PHE E 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.37e+00
  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    2.30    0.21 2.00e-01 2.50e+01 1.14e+00
  ... (remaining 2413 not shown)

  Planarity restraints: 1488
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "    0.052 5.00e-02 4.00e+02   7.88e-02 9.94e+00
        pdb=" N   PRO G  80 "   -0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU H 113 "    0.015 2.00e-02 2.50e+03   3.14e-02 9.87e+00
        pdb=" CD  GLU H 113 "   -0.054 2.00e-02 2.50e+03
        pdb=" OE1 GLU H 113 "    0.019 2.00e-02 2.50e+03
        pdb=" OE2 GLU H 113 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL F  70 "   -0.015 2.00e-02 2.50e+03   2.91e-02 8.49e+00
        pdb=" C   VAL F  70 "    0.050 2.00e-02 2.50e+03
        pdb=" O   VAL F  70 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   THR F  71 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1485 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 2628
        2.78 -     3.31: 12748
        3.31 -     3.84: 30087
        3.84 -     4.37: 33559
        4.37 -     4.90: 45685
  Nonbonded interactions: 124707
  Sorted by model distance:
  nonbonded pdb=" O   VAL D 118 "
            pdb=" OG1 THR D 122 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   LYS G  15 "
            pdb=" NH1 ARG G  20 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" NH1 ARG C  81 "
            pdb=" O   VAL C 107 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" OH  TYR C  39 "
            pdb=" OE1 GLU D  71 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" NH2 ARG D  33 "
            pdb=" O2   DC I  51 "
     model   vdw
     2.296 3.120
  ... (remaining 124702 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     14.490
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075  14616  Z= 0.266
  Angle     :  0.915  14.946  21208  Z= 0.523
  Chirality :  0.049   0.236   2416
  Planarity :  0.007   0.079   1488
  Dihedral  : 29.935 179.324   6353
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.26), residues: 825
  helix:  0.04 (0.20), residues: 560
  sheet: -3.84 (0.84), residues: 10
  loop : -0.91 (0.32), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  67 
 TYR   0.023   0.003   TYR G  50 
 PHE   0.020   0.003   PHE C  25 
 HIS   0.010   0.003   HIS D 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 (14616)
  covalent geometry    : angle       0.91530 (21208)
  hydrogen bonds       : bond        0.11370 (  860)
  hydrogen bonds       : angle       4.75167 ( 2146)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.8488 (t80) cc_final: 0.8221 (t80)
REVERT: A  104 PHE cc_start: 0.9578 (m-10) cc_final: 0.9329 (m-80)
REVERT: E  105 GLU cc_start: 0.9361 (mt-10) cc_final: 0.8961 (mm-30)
REVERT: G   34 LEU cc_start: 0.8427 (mt) cc_final: 0.8216 (mt)
REVERT: H   98 VAL cc_start: 0.9711 (t) cc_final: 0.9467 (p)
REVERT: H  102 LEU cc_start: 0.8816 (mp) cc_final: 0.8425 (tp)
REVERT: H  106 LEU cc_start: 0.9767 (mt) cc_final: 0.9410 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0989
  time to fit residues: 15.7504
Evaluate side-chains
  70 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    8.9990
   chunk 106 optimal weight:   20.0000
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
E 108 ASN
G 112 GLN
H  47 GLN
H  82 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.036806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.029602 restraints weight = 196919.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.030591 restraints weight = 114345.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.031297 restraints weight = 79372.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.031761 restraints weight = 60546.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.032132 restraints weight = 49786.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  14616  Z= 0.236
  Angle     :  0.689   8.682  21208  Z= 0.407
  Chirality :  0.038   0.158   2416
  Planarity :  0.006   0.066   1488
  Dihedral  : 33.400 178.682   4701
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 17.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  4.04 %
    Favored  : 95.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.27), residues: 825
  helix:  0.84 (0.21), residues: 586
  sheet: -4.12 (0.96), residues: 10
  loop : -0.78 (0.35), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  33 
 TYR   0.016   0.002   TYR D  40 
 PHE   0.013   0.002   PHE B 100 
 HIS   0.006   0.002   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 (14616)
  covalent geometry    : angle       0.68946 (21208)
  hydrogen bonds       : bond        0.07581 (  860)
  hydrogen bonds       : angle       3.58831 ( 2146)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.8040 (t80) cc_final: 0.7823 (t80)
REVERT: E  104 PHE cc_start: 0.8919 (m-80) cc_final: 0.8676 (m-80)
REVERT: E  105 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8790 (mm-30)
REVERT: F   97 LEU cc_start: 0.7843 (tp) cc_final: 0.7617 (tp)
REVERT: G   38 ASN cc_start: 0.7179 (m-40) cc_final: 0.6969 (m-40)
REVERT: H   98 VAL cc_start: 0.9448 (t) cc_final: 0.9158 (t)
REVERT: H  102 LEU cc_start: 0.6790 (mp) cc_final: 0.6425 (tp)
  outliers start: 3
  outliers final: 1
  residues processed: 103
  average time/residue: 0.0931
  time to fit residues: 14.7822
Evaluate side-chains
  71 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 4 optimal weight:    0.2980
   chunk 50 optimal weight:    3.9990
   chunk 45 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 25 optimal weight:    9.9990
   chunk 93 optimal weight:   10.0000
   chunk 86 optimal weight:    8.9990
   chunk 10 optimal weight:    5.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    3.4588

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  76 GLN
E 108 ASN
F  93 GLN
G  84 GLN
H  47 GLN
H  82 HIS
H 109 HIS
U  75 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.037003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.029473 restraints weight = 205361.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.030418 restraints weight = 122682.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.031104 restraints weight = 86507.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.031588 restraints weight = 67028.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.031932 restraints weight = 55313.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.3068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  14616  Z= 0.226
  Angle     :  0.666   7.602  21208  Z= 0.397
  Chirality :  0.037   0.165   2416
  Planarity :  0.005   0.066   1488
  Dihedral  : 33.355 179.651   4701
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 15.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.04 %
    Favored  : 95.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.28), residues: 825
  helix:  1.10 (0.21), residues: 584
  sheet: -3.44 (1.28), residues: 10
  loop : -0.89 (0.35), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  86 
 TYR   0.022   0.002   TYR D  42 
 PHE   0.024   0.003   PHE A 104 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 (14616)
  covalent geometry    : angle       0.66620 (21208)
  hydrogen bonds       : bond        0.07135 (  860)
  hydrogen bonds       : angle       3.57906 ( 2146)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.8103 (t80) cc_final: 0.7859 (t80)
REVERT: A  104 PHE cc_start: 0.8949 (m-80) cc_final: 0.8487 (m-80)
REVERT: F   97 LEU cc_start: 0.8174 (tp) cc_final: 0.7923 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1223
  time to fit residues: 16.7099
Evaluate side-chains
  70 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 101 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   chunk 70 optimal weight:    0.6980
   chunk 103 optimal weight:    7.9990
   chunk 44 optimal weight:    0.1980
   chunk 86 optimal weight:    8.9990
   chunk 21 optimal weight:    3.9990
   chunk 30 optimal weight:    9.9990
   chunk 18 optimal weight:    7.9990
   chunk 8 optimal weight:    7.9990
   chunk 87 optimal weight:    8.9990
   overall best weight:    3.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  76 GLN
E 108 ASN
H  82 HIS
H  95 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.034364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.027564 restraints weight = 210430.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.028470 restraints weight = 121846.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.029093 restraints weight = 84401.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.029554 restraints weight = 64970.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.029867 restraints weight = 53143.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.4008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  14616  Z= 0.244
  Angle     :  0.672   8.235  21208  Z= 0.399
  Chirality :  0.038   0.207   2416
  Planarity :  0.005   0.060   1488
  Dihedral  : 33.384 177.692   4701
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 18.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.62 %
    Favored  : 95.24 %
  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 are not related in a simple way.
  whole:  0.55 (0.28), residues: 825
  helix:  1.01 (0.21), residues: 582
  sheet: -2.78 (1.68), residues: 10
  loop : -1.01 (0.35), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG F  35 
 TYR   0.021   0.002   TYR H  42 
 PHE   0.014   0.002   PHE B 100 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 (14616)
  covalent geometry    : angle       0.67182 (21208)
  hydrogen bonds       : bond        0.07861 (  860)
  hydrogen bonds       : angle       3.69942 ( 2146)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   53 GLU cc_start: 0.9194 (tp30) cc_final: 0.8988 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 93
  average time/residue: 0.1021
  time to fit residues: 14.2793
Evaluate side-chains
  65 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 79 optimal weight:    9.9990
   chunk 84 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 62 optimal weight:    8.9990
   chunk 20 optimal weight:    9.9990
   chunk 31 optimal weight:    1.9990
   chunk 50 optimal weight:    9.9990
   chunk 47 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 HIS
E  76 GLN
E 108 ASN
F  64 ASN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 HIS
H 109 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.042390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.031320 restraints weight = 157285.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.032456 restraints weight = 104967.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.033312 restraints weight = 78956.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.033914 restraints weight = 63758.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.034380 restraints weight = 54596.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.4346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  14616  Z= 0.187
  Angle     :  0.637   8.358  21208  Z= 0.378
  Chirality :  0.036   0.153   2416
  Planarity :  0.004   0.060   1488
  Dihedral  : 33.122 177.508   4701
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.89 %
    Favored  : 96.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.28), residues: 825
  helix:  1.05 (0.21), residues: 590
  sheet: -2.18 (1.99), residues: 10
  loop : -0.91 (0.36), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  79 
 TYR   0.013   0.001   TYR B  72 
 PHE   0.009   0.002   PHE B 100 
 HIS   0.006   0.001   HIS H 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (14616)
  covalent geometry    : angle       0.63688 (21208)
  hydrogen bonds       : bond        0.05586 (  860)
  hydrogen bonds       : angle       3.48908 ( 2146)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  104 PHE cc_start: 0.8550 (m-80) cc_final: 0.8205 (m-80)
REVERT: E  105 GLU cc_start: 0.8984 (mt-10) cc_final: 0.8654 (mm-30)
REVERT: F   52 GLU cc_start: 0.9825 (tp30) cc_final: 0.9602 (pm20)
REVERT: F   53 GLU cc_start: 0.9187 (tp30) cc_final: 0.8901 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1039
  time to fit residues: 14.3706
Evaluate side-chains
  65 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 102 optimal weight:   10.0000
   chunk 108 optimal weight:    5.9990
   chunk 73 optimal weight:    8.9990
   chunk 18 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 53 optimal weight:   10.0000
   chunk 95 optimal weight:   10.0000
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  47 GLN
E  76 GLN
E 108 ASN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.032650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.026112 restraints weight = 217334.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.026974 restraints weight = 125557.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.027595 restraints weight = 86813.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.028039 restraints weight = 66315.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.028338 restraints weight = 54211.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.5311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  14616  Z= 0.282
  Angle     :  0.700   7.822  21208  Z= 0.414
  Chirality :  0.039   0.159   2416
  Planarity :  0.006   0.065   1488
  Dihedral  : 33.587 177.674   4701
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 22.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.17 %
    Favored  : 96.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.28), residues: 825
  helix:  0.80 (0.21), residues: 590
  sheet: -2.09 (2.03), residues: 10
  loop : -1.17 (0.36), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  35 
 TYR   0.029   0.003   TYR H  42 
 PHE   0.041   0.003   PHE A 104 
 HIS   0.007   0.002   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00602 (14616)
  covalent geometry    : angle       0.69971 (21208)
  hydrogen bonds       : bond        0.09638 (  860)
  hydrogen bonds       : angle       3.86934 ( 2146)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   53 GLU cc_start: 0.9013 (tp30) cc_final: 0.8810 (tm-30)
REVERT: G   72 ASP cc_start: 0.9547 (t70) cc_final: 0.9338 (m-30)
  outliers start: 1
  outliers final: 1
  residues processed: 84
  average time/residue: 0.0973
  time to fit residues: 12.4826
Evaluate side-chains
  65 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 96 optimal weight:    7.9990
   chunk 21 optimal weight:    6.9990
   chunk 58 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 54 optimal weight:    7.9990
   chunk 17 optimal weight:    0.8980
   chunk 43 optimal weight:   20.0000
   overall best weight:    3.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  76 GLN
E 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.033470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.026804 restraints weight = 211808.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.027728 restraints weight = 119974.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.028394 restraints weight = 82261.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.028851 restraints weight = 62478.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.029168 restraints weight = 50787.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.5651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  14616  Z= 0.219
  Angle     :  0.667   7.161  21208  Z= 0.396
  Chirality :  0.038   0.172   2416
  Planarity :  0.005   0.063   1488
  Dihedral  : 33.421 177.359   4701
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 17.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.28), residues: 825
  helix:  0.88 (0.21), residues: 590
  sheet: -1.98 (2.07), residues: 10
  loop : -1.07 (0.36), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G  35 
 TYR   0.016   0.002   TYR D  42 
 PHE   0.014   0.002   PHE A 104 
 HIS   0.004   0.001   HIS H 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 (14616)
  covalent geometry    : angle       0.66718 (21208)
  hydrogen bonds       : bond        0.06657 (  860)
  hydrogen bonds       : angle       3.72971 ( 2146)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   52 GLU cc_start: 0.9815 (tp30) cc_final: 0.9567 (pm20)
REVERT: F   53 GLU cc_start: 0.9122 (tp30) cc_final: 0.8865 (tm-30)
REVERT: G   72 ASP cc_start: 0.9550 (t70) cc_final: 0.9327 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0993
  time to fit residues: 12.4120
Evaluate side-chains
  63 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 100 optimal weight:    7.9990
   chunk 55 optimal weight:    7.9990
   chunk 25 optimal weight:    8.9990
   chunk 51 optimal weight:    5.9990
   chunk 12 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 64 optimal weight:    7.9990
   chunk 85 optimal weight:   10.0000
   chunk 109 optimal weight:   30.0000
   chunk 112 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  67 ASN
E  76 GLN
E 108 ASN
H  82 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.032457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.027602 restraints weight = 242046.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.028341 restraints weight = 144672.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.028813 restraints weight = 100424.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.029209 restraints weight = 77348.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.029448 restraints weight = 62864.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.6868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061  14616  Z= 0.333
  Angle     :  0.770   8.342  21208  Z= 0.450
  Chirality :  0.043   0.181   2416
  Planarity :  0.006   0.061   1488
  Dihedral  : 34.189 178.261   4701
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 28.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.27), residues: 825
  helix:  0.40 (0.20), residues: 580
  sheet: -2.11 (2.02), residues: 10
  loop : -1.29 (0.36), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  79 
 TYR   0.036   0.003   TYR H  42 
 PHE   0.017   0.003   PHE E  78 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00711 (14616)
  covalent geometry    : angle       0.76993 (21208)
  hydrogen bonds       : bond        0.11024 (  860)
  hydrogen bonds       : angle       4.24164 ( 2146)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.9648 (m-80) cc_final: 0.9381 (m-80)
REVERT: E  104 PHE cc_start: 0.9639 (m-10) cc_final: 0.9315 (m-80)
REVERT: F   53 GLU cc_start: 0.9511 (tp30) cc_final: 0.9300 (tm-30)
REVERT: G   72 ASP cc_start: 0.9562 (t70) cc_final: 0.9286 (m-30)
REVERT: G   73 ASN cc_start: 0.9136 (t0) cc_final: 0.8892 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1062
  time to fit residues: 13.3574
Evaluate side-chains
  65 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 27 optimal weight:    8.9990
   chunk 100 optimal weight:    6.9990
   chunk 102 optimal weight:    6.9990
   chunk 92 optimal weight:    6.9990
   chunk 83 optimal weight:    7.9990
   chunk 77 optimal weight:    8.9990
   chunk 87 optimal weight:    7.9990
   chunk 35 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 79 optimal weight:    7.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS
E  76 GLN
E 108 ASN
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.031227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.026587 restraints weight = 244605.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.027303 restraints weight = 147745.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.027763 restraints weight = 102524.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.028146 restraints weight = 79040.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.028380 restraints weight = 64101.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.8201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051  14616  Z= 0.340
  Angle     :  0.801   9.428  21208  Z= 0.468
  Chirality :  0.044   0.226   2416
  Planarity :  0.006   0.064   1488
  Dihedral  : 34.675 177.140   4701
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 27.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.27), residues: 825
  helix:  0.24 (0.20), residues: 554
  sheet: -2.51 (1.80), residues: 10
  loop : -1.03 (0.36), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  95 
 TYR   0.024   0.003   TYR D  40 
 PHE   0.012   0.002   PHE B 100 
 HIS   0.013   0.002   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00724 (14616)
  covalent geometry    : angle       0.80051 (21208)
  hydrogen bonds       : bond        0.10638 (  860)
  hydrogen bonds       : angle       4.34596 ( 2146)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 PHE cc_start: 0.9635 (m-80) cc_final: 0.9400 (m-80)
REVERT: E  104 PHE cc_start: 0.9428 (m-10) cc_final: 0.9183 (m-10)
REVERT: G   72 ASP cc_start: 0.9567 (t70) cc_final: 0.9298 (m-30)
REVERT: G   73 ASN cc_start: 0.9261 (t0) cc_final: 0.8997 (t0)
REVERT: H   42 TYR cc_start: 0.9411 (m-80) cc_final: 0.9185 (m-80)
REVERT: H  109 HIS cc_start: 0.9476 (m90) cc_final: 0.8856 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0943
  time to fit residues: 11.9146
Evaluate side-chains
  59 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 47 optimal weight:    8.9990
   chunk 16 optimal weight:    0.5980
   chunk 67 optimal weight:    0.6980
   chunk 80 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9990
   chunk 99 optimal weight:    6.9990
   chunk 93 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  76 GLN
E 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.031004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.025082 restraints weight = 207424.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.026016 restraints weight = 112520.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.026673 restraints weight = 74646.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.027135 restraints weight = 55140.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.027455 restraints weight = 43755.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.8175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  14616  Z= 0.206
  Angle     :  0.705   8.734  21208  Z= 0.412
  Chirality :  0.040   0.196   2416
  Planarity :  0.005   0.058   1488
  Dihedral  : 34.141 175.262   4701
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 16.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.00 (0.27), residues: 825
  helix:  0.67 (0.21), residues: 576
  sheet: -2.47 (1.86), residues: 10
  loop : -1.43 (0.35), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG E 116 
 TYR   0.013   0.002   TYR D  40 
 PHE   0.019   0.002   PHE D  65 
 HIS   0.004   0.001   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (14616)
  covalent geometry    : angle       0.70495 (21208)
  hydrogen bonds       : bond        0.06143 (  860)
  hydrogen bonds       : angle       3.92709 ( 2146)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.9644 (tp40) cc_final: 0.9298 (mm-40)
REVERT: D  100 LEU cc_start: 0.6759 (mt) cc_final: 0.6021 (mt)
REVERT: F   52 GLU cc_start: 0.9731 (tp30) cc_final: 0.9504 (pm20)
REVERT: G   72 ASP cc_start: 0.9585 (t70) cc_final: 0.9361 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.1040
  time to fit residues: 14.2585
Evaluate side-chains
  68 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 112 optimal weight:   20.0000
   chunk 97 optimal weight:   10.0000
   chunk 59 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 2 optimal weight:    5.9990
   chunk 21 optimal weight:    7.9990
   chunk 87 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 55 optimal weight:    7.9990
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
E  76 GLN
E 108 ASN
H  82 HIS
H 109 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.029203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.023593 restraints weight = 218729.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.024420 restraints weight = 122004.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.024976 restraints weight = 82599.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.025386 restraints weight = 63084.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.025668 restraints weight = 51102.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.8603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  14616  Z= 0.274
  Angle     :  0.730   8.068  21208  Z= 0.428
  Chirality :  0.040   0.161   2416
  Planarity :  0.005   0.060   1488
  Dihedral  : 34.349 175.563   4701
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 22.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.30 %
    Favored  : 98.56 %
  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 are not related in a simple way.
  whole: -0.02 (0.27), residues: 825
  helix:  0.63 (0.20), residues: 570
  sheet:  None (None), residues: 0
  loop : -1.38 (0.35), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  92 
 TYR   0.015   0.002   TYR D  42 
 PHE   0.050   0.003   PHE E 104 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00586 (14616)
  covalent geometry    : angle       0.73028 (21208)
  hydrogen bonds       : bond        0.08906 (  860)
  hydrogen bonds       : angle       4.07221 ( 2146)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2022.85 seconds
wall clock time: 35 minutes 53.81 seconds (2153.81 seconds total)