Starting phenix.real_space_refine
on Wed Feb  4 03:17:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qv5_53386/02_2026/9qv5_53386.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qv5_53386/02_2026/9qv5_53386.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qv5_53386/02_2026/9qv5_53386.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qv5_53386/02_2026/9qv5_53386.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qv5_53386/02_2026/9qv5_53386.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qv5_53386/02_2026/9qv5_53386.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     240      5.49       5
     S      12      5.16       5
     C    4551      2.51       5
     N    1659      2.21       5
     O    2166      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8628
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 527
          Classifications: {'peptide': 68}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 67}
    Chain: "B"
      Number of atoms: 527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 527
          Classifications: {'peptide': 68}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 67}
    Chain: "C"
      Number of atoms: 527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 527
          Classifications: {'peptide': 68}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 67}
    Chain: "D"
      Number of atoms: 527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 527
          Classifications: {'peptide': 68}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 67}
    Chain: "E"
      Number of atoms: 527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 527
          Classifications: {'peptide': 68}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 67}
    Chain: "F"
      Number of atoms: 527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 527
          Classifications: {'peptide': 68}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 67}
    Chain: "G"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 273
          Classifications: {'peptide': 68}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 63}
          Link IDs: {'TRANS': 67}
          Unresolved non-hydrogen bonds: 259
          Unresolved non-hydrogen angles: 371
          Unresolved non-hydrogen dihedrals: 161
          Unresolved non-hydrogen chiralities: 79
          Planarities with less than four sites: {'ASN:plan1': 5, 'PHE:plan': 1, 'ARG:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 3, 'ASP:plan': 4, 'TRP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 120
    Chain: "H"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 68, 273
          Classifications: {'peptide': 68}
          Modifications used: {'COO': 1}
          Incomplete info: {'backbone_only': 63}
          Link IDs: {'TRANS': 67}
          Unresolved non-hydrogen bonds: 259
          Unresolved non-hydrogen angles: 371
          Unresolved non-hydrogen dihedrals: 161
          Unresolved non-hydrogen chiralities: 79
          Planarities with less than four sites: {'ASN:plan1': 5, 'PHE:plan': 1, 'ARG:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 3, 'ASP:plan': 4, 'TRP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 120
    Chain: "X"
      Number of atoms: 2446
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 2446
          Classifications: {'DNA': 120}
          Link IDs: {'rna3p': 119}
    Chain: "Y"
      Number of atoms: 2474
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 2474
          Classifications: {'DNA': 120}
          Link IDs: {'rna3p': 119}
  Time building chain proxies: 2.08, per 1000 atoms: 0.24
  Number of scatterers: 8628
  At special positions: 0
  Unit cell: (86.505, 113.88, 112.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     P     240     15.00
     O    2166      8.00
     N    1659      7.00
     C    4551      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: 0.75
  Conformation dependent library (CDL) restraints added in 178.5 milliseconds
  

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  768

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 8 sheets defined
      77.2% alpha, 2.9% beta
      118 base pairs and 205 stacking pairs defined.
    Time for finding SS restraints: 1.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 17
    Processing helix  chain 'A' and resid 23 through 52
    Processing helix  chain 'A' and resid 58 through 67
    Processing helix  chain 'B' and resid 6 through 17
    Processing helix  chain 'B' and resid 23 through 52
    Processing helix  chain 'B' and resid 58 through 67
    Processing helix  chain 'C' and resid 6 through 17
    Processing helix  chain 'C' and resid 23 through 53
    Processing helix  chain 'C' and resid 58 through 67
    Processing helix  chain 'D' and resid 6 through 17
    Processing helix  chain 'D' and resid 23 through 52
    Processing helix  chain 'D' and resid 58 through 67
    Processing helix  chain 'E' and resid 6 through 17
    Processing helix  chain 'E' and resid 23 through 52
    Processing helix  chain 'E' and resid 58 through 67
    Processing helix  chain 'F' and resid 6 through 17
    Processing helix  chain 'F' and resid 23 through 52
    Processing helix  chain 'F' and resid 58 through 67
    Processing helix  chain 'G' and resid 6 through 17
    Processing helix  chain 'G' and resid 23 through 53
      removed outlier: 4.135A  pdb=" N   TYR G  44 " --> pdb=" O   ASN G  40 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 58 through 68
      removed outlier: 3.581A  pdb=" N   GLN G  67 " --> pdb=" O   LYS G  63 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 6 through 17
    Processing helix  chain 'H' and resid 23 through 52
      removed outlier: 3.553A  pdb=" N   ASP H  28 " --> pdb=" O   ALA H  24 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   TYR H  44 " --> pdb=" O   ASN H  40 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 58 through 68
      removed outlier: 3.528A  pdb=" N   ILE H  62 " --> pdb=" O   LYS H  58 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22
      removed outlier: 7.030A  pdb=" N   ARG A  21 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57
    Processing sheet with id=AA3, first strand: chain 'C' and resid 21 through 22
      removed outlier: 7.068A  pdb=" N   ARG C  21 " --> pdb=" O   VAL D  57 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 56 through 57
    Processing sheet with id=AA5, first strand: chain 'E' and resid 21 through 22
      removed outlier: 7.104A  pdb=" N   ARG E  21 " --> pdb=" O   VAL F  57 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 56 through 57
    Processing sheet with id=AA7, first strand: chain 'G' and resid 21 through 22
      removed outlier: 7.261A  pdb=" N   ARG G  21 " --> pdb=" O   VAL H  57 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 56 through 57

    323 hydrogen bonds defined for protein.
    969 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      295 hydrogen bonds
      590 hydrogen bond angles
      0 basepair planarities
      118 basepair parallelities
      205 stacking parallelities
  Total time for adding SS restraints: 1.43

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1104
        1.32 -     1.44: 3277
        1.44 -     1.56: 4365
        1.56 -     1.69: 478
        1.69 -     1.81: 24
  Bond restraints: 9248
  Sorted by residual:
  bond pdb=" CA  SER D  23 "
       pdb=" CB  SER D  23 "
    ideal  model  delta    sigma   weight residual
    1.529  1.459  0.070 1.53e-02 4.27e+03 2.09e+01
  bond pdb=" CA  SER F  23 "
       pdb=" CB  SER F  23 "
    ideal  model  delta    sigma   weight residual
    1.529  1.470  0.060 1.58e-02 4.01e+03 1.42e+01
  bond pdb=" C   ASP D  61 "
       pdb=" O   ASP D  61 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.043 1.15e-02 7.56e+03 1.40e+01
  bond pdb=" CA  SER E  23 "
       pdb=" CB  SER E  23 "
    ideal  model  delta    sigma   weight residual
    1.528  1.467  0.061 1.66e-02 3.63e+03 1.35e+01
  bond pdb=" CA  SER A  23 "
       pdb=" CB  SER A  23 "
    ideal  model  delta    sigma   weight residual
    1.528  1.469  0.060 1.66e-02 3.63e+03 1.30e+01
  ... (remaining 9243 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 9870
        1.81 -     3.62: 2993
        3.62 -     5.43: 555
        5.43 -     7.23: 28
        7.23 -     9.04: 4
  Bond angle restraints: 13450
  Sorted by residual:
  angle pdb=" N   VAL H  10 "
        pdb=" CA  VAL H  10 "
        pdb=" C   VAL H  10 "
      ideal   model   delta    sigma   weight residual
     111.00  101.96    9.04 1.09e+00 8.42e-01 6.88e+01
  angle pdb=" N   VAL H  27 "
        pdb=" CA  VAL H  27 "
        pdb=" C   VAL H  27 "
      ideal   model   delta    sigma   weight residual
     110.42  104.00    6.42 9.60e-01 1.09e+00 4.47e+01
  angle pdb=" CA  ASP D  61 "
        pdb=" C   ASP D  61 "
        pdb=" O   ASP D  61 "
      ideal   model   delta    sigma   weight residual
     120.90  115.10    5.80 1.07e+00 8.73e-01 2.94e+01
  angle pdb=" C   GLU D  59 "
        pdb=" CA  GLU D  59 "
        pdb=" CB  GLU D  59 "
      ideal   model   delta    sigma   weight residual
     110.81  102.33    8.48 1.60e+00 3.91e-01 2.81e+01
  angle pdb=" N   VAL G  10 "
        pdb=" CA  VAL G  10 "
        pdb=" C   VAL G  10 "
      ideal   model   delta    sigma   weight residual
     110.72  105.71    5.01 1.01e+00 9.80e-01 2.46e+01
  ... (remaining 13445 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.48: 3669
       35.48 -    70.96: 1025
       70.96 -   106.44: 21
      106.44 -   141.92: 0
      141.92 -   177.40: 3
  Dihedral angle restraints: 4718
    sinusoidal: 3408
      harmonic: 1310
  Sorted by residual:
  dihedral pdb=" CD  ARG F  54 "
           pdb=" NE  ARG F  54 "
           pdb=" CZ  ARG F  54 "
           pdb=" NH1 ARG F  54 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.25  -86.25     1      1.00e+01 1.00e-02 8.97e+01
  dihedral pdb=" CD  ARG C   9 "
           pdb=" NE  ARG C   9 "
           pdb=" CZ  ARG C   9 "
           pdb=" NH1 ARG C   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   41.72  -41.72     1      1.00e+01 1.00e-02 2.43e+01
  dihedral pdb=" CD  ARG F   9 "
           pdb=" NE  ARG F   9 "
           pdb=" CZ  ARG F   9 "
           pdb=" NH1 ARG F   9 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   38.05  -38.05     1      1.00e+01 1.00e-02 2.04e+01
  ... (remaining 4715 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.133: 1130
       0.133 -    0.266: 161
       0.266 -    0.399: 139
       0.399 -    0.531: 2
       0.531 -    0.664: 2
  Chirality restraints: 1434
  Sorted by residual:
  chirality pdb=" P    DT Y   1 "
            pdb=" OP1  DT Y   1 "
            pdb=" OP2  DT Y   1 "
            pdb=" O5'  DT Y   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -3.01   -0.66 2.00e-01 2.50e+01 1.10e+01
  chirality pdb=" P    DG X   1 "
            pdb=" OP1  DG X   1 "
            pdb=" OP2  DG X   1 "
            pdb=" O5'  DG X   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -3.01   -0.66 2.00e-01 2.50e+01 1.10e+01
  chirality pdb=" P    DC X  96 "
            pdb=" OP1  DC X  96 "
            pdb=" OP2  DC X  96 "
            pdb=" O5'  DC X  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.76   -0.41 2.00e-01 2.50e+01 4.28e+00
  ... (remaining 1431 not shown)

  Planarity restraints: 934
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG F  54 "    1.139 9.50e-02 1.11e+02   5.11e-01 1.57e+02
        pdb=" NE  ARG F  54 "   -0.064 2.00e-02 2.50e+03
        pdb=" CZ  ARG F  54 "   -0.025 2.00e-02 2.50e+03
        pdb=" NH1 ARG F  54 "    0.018 2.00e-02 2.50e+03
        pdb=" NH2 ARG F  54 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C   9 "    0.717 9.50e-02 1.11e+02   3.21e-01 6.30e+01
        pdb=" NE  ARG C   9 "   -0.044 2.00e-02 2.50e+03
        pdb=" CZ  ARG C   9 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG C   9 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG C   9 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C  37 "    0.087 2.00e-02 2.50e+03   4.73e-02 5.59e+01
        pdb=" CG  TRP C  37 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TRP C  37 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TRP C  37 "   -0.055 2.00e-02 2.50e+03
        pdb=" NE1 TRP C  37 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE2 TRP C  37 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE3 TRP C  37 "   -0.068 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C  37 "    0.028 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C  37 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP C  37 "    0.071 2.00e-02 2.50e+03
  ... (remaining 931 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 725
        2.74 -     3.28: 7403
        3.28 -     3.82: 14782
        3.82 -     4.36: 20397
        4.36 -     4.90: 28093
  Nonbonded interactions: 71400
  Sorted by model distance:
  nonbonded pdb=" N2   DG X  58 "
            pdb=" N2   DG Y  64 "
     model   vdw
     2.202 3.200
  nonbonded pdb=" N6   DA X  93 "
            pdb=" O6   DG Y  27 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" O6   DG X  42 "
            pdb=" O6   DG Y  78 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" N4   DC X  68 "
            pdb=" O6   DG Y  52 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" C2   DG X  58 "
            pdb=" N2   DG Y  64 "
     model   vdw
     2.252 3.340
  ... (remaining 71395 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' and ((resid 1 through 67 and (name N or name CA or name C or name O ) \ 
) or (resid 68 and (name N or name CA or name C or name O or name OXT))))
  selection = (chain 'B' and ((resid 1 through 67 and (name N or name CA or name C or name O ) \ 
) or (resid 68 and (name N or name CA or name C or name O or name OXT))))
  selection = (chain 'C' and ((resid 1 through 67 and (name N or name CA or name C or name O ) \ 
) or (resid 68 and (name N or name CA or name C or name O or name OXT))))
  selection = (chain 'D' and ((resid 1 through 67 and (name N or name CA or name C or name O ) \ 
) or (resid 68 and (name N or name CA or name C or name O or name OXT))))
  selection = (chain 'E' and ((resid 1 through 67 and (name N or name CA or name C or name O ) \ 
) or (resid 68 and (name N or name CA or name C or name O or name OXT))))
  selection = (chain 'F' and ((resid 1 through 67 and (name N or name CA or name C or name O ) \ 
) or (resid 68 and (name N or name CA or name C or name O or name OXT))))
  selection = chain 'G'
  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:             32.580
  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:             0.000
  Extract box with map and model:          0.730
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.440
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
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      :  0.012   0.070   9248  Z= 0.722
  Angle     :  1.672   9.044  13450  Z= 1.088
  Chirality :  0.132   0.664   1434
  Planarity :  0.040   0.511    934
  Dihedral  : 29.238 177.397   3950
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  4.17 %
    Favored  : 95.19 %
  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 are not related in a simple way.
  whole: -1.48 (0.32), residues: 528
  helix: -0.69 (0.23), residues: 424
  sheet:  None (None), residues: 0
  loop : -1.47 (0.43), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.002   ARG F   9 
 TYR   0.016   0.005   TYR E  44 
 PHE   0.035   0.014   PHE B   5 
 TRP   0.087   0.034   TRP C  37 
 HIS   0.007   0.003   HIS E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.01164 ( 9248)
  covalent geometry    : angle       1.67222 (13450)
  hydrogen bonds       : bond        0.20001 (  618)
  hydrogen bonds       : angle       7.48568 ( 1559)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 87
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 MET cc_start: 0.8491 (tpt) cc_final: 0.8267 (tpp)
REVERT: B   41 ILE cc_start: 0.8661 (mt) cc_final: 0.8393 (tt)
REVERT: C    1 MET cc_start: 0.3939 (ttt) cc_final: 0.3530 (ttt)
REVERT: F   52 SER cc_start: 0.8765 (t) cc_final: 0.8551 (m)
REVERT: F   56 THR cc_start: 0.9195 (m) cc_final: 0.8813 (p)
REVERT: F   64 LEU cc_start: 0.9345 (tp) cc_final: 0.9003 (mp)
  outliers start: 2
  outliers final: 0
  residues processed: 89
  average time/residue: 0.1356
  time to fit residues: 15.2920
Evaluate side-chains
  68 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:   20.0000
   chunk 27 optimal weight:    0.8980
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
B  16 GLN
C   4 ASN
D   4 ASN
** D  51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  67 GLN
E   4 ASN
F   4 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.168598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.115755 restraints weight = 14225.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.120877 restraints weight = 7699.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.120980 restraints weight = 4805.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.121270 restraints weight = 4593.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.121381 restraints weight = 4254.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   9248  Z= 0.262
  Angle     :  0.674   4.504  13450  Z= 0.413
  Chirality :  0.038   0.142   1434
  Planarity :  0.004   0.034    934
  Dihedral  : 32.392 178.589   3170
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 10.90 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.34), residues: 528
  helix:  1.38 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop : -0.85 (0.50), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F  50 
 TYR   0.010   0.002   TYR A  44 
 PHE   0.013   0.003   PHE D   5 
 TRP   0.031   0.006   TRP C  37 
 HIS   0.003   0.001   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00588 ( 9248)
  covalent geometry    : angle       0.67435 (13450)
  hydrogen bonds       : bond        0.05155 (  618)
  hydrogen bonds       : angle       3.08587 ( 1559)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.9184 (ttmm) cc_final: 0.8793 (ttmt)
REVERT: E   47 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7666 (mm-30)
  outliers start: 7
  outliers final: 7
  residues processed: 88
  average time/residue: 0.1312
  time to fit residues: 14.4530
Evaluate side-chains
  79 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain B residue   67 GLN
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   51 HIS
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   67 GLN
Chi-restraints excluded: chain E residue   23 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 59 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 53 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
C   4 ASN
D  51 HIS
** D  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   4 ASN
F  51 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.165171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.109743 restraints weight = 14080.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.114586 restraints weight = 6404.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.116376 restraints weight = 3866.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.116694 restraints weight = 3148.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.117048 restraints weight = 3189.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7558
moved from start:          0.3964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9248  Z= 0.215
  Angle     :  0.594   5.306  13450  Z= 0.365
  Chirality :  0.033   0.119   1434
  Planarity :  0.004   0.029    934
  Dihedral  : 32.102 174.274   3170
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 13.14 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.71 (0.36), residues: 528
  helix:  2.33 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop : -0.76 (0.53), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  15 
 TYR   0.012   0.001   TYR A  44 
 PHE   0.015   0.003   PHE D   5 
 TRP   0.018   0.003   TRP A  37 
 HIS   0.003   0.001   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 9248)
  covalent geometry    : angle       0.59372 (13450)
  hydrogen bonds       : bond        0.04413 (  618)
  hydrogen bonds       : angle       2.72972 ( 1559)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 73
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.8693 (ttmm) cc_final: 0.8440 (ttmt)
REVERT: A   47 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7724 (pt0)
REVERT: D   20 GLN cc_start: 0.8070 (mp10) cc_final: 0.7754 (mp10)
REVERT: D   30 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8260 (tpt)
REVERT: D   47 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8159 (tp30)
REVERT: D   50 ARG cc_start: 0.8183 (ttp80) cc_final: 0.7903 (ttm170)
  outliers start: 10
  outliers final: 7
  residues processed: 78
  average time/residue: 0.1225
  time to fit residues: 12.0915
Evaluate side-chains
  80 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain C residue   51 HIS
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   30 MET
Chi-restraints excluded: chain D residue   67 GLN
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain F residue    1 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 56 optimal weight:    5.9990
   chunk 19 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0980
   chunk 22 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
C   4 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.169931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.116811 restraints weight = 14534.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.121928 restraints weight = 6724.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.123555 restraints weight = 4084.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.123994 restraints weight = 3253.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.124247 restraints weight = 3328.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.4602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9248  Z= 0.152
  Angle     :  0.522   5.242  13450  Z= 0.327
  Chirality :  0.030   0.115   1434
  Planarity :  0.002   0.016    934
  Dihedral  : 31.580 172.652   3170
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 14.74 %
    Favored  : 82.69 %
  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:  3.89 (0.36), residues: 528
  helix:  3.20 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop : -0.64 (0.56), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  50 
 TYR   0.008   0.001   TYR C  44 
 PHE   0.006   0.001   PHE D   5 
 TRP   0.013   0.002   TRP F  37 
 HIS   0.003   0.001   HIS C  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 9248)
  covalent geometry    : angle       0.52176 (13450)
  hydrogen bonds       : bond        0.03872 (  618)
  hydrogen bonds       : angle       2.20180 ( 1559)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.8804 (ttmm) cc_final: 0.8506 (ttmt)
REVERT: A   55 LYS cc_start: 0.8561 (mtpt) cc_final: 0.8168 (ttmt)
REVERT: D   47 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8033 (tp30)
REVERT: D   50 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7722 (ttm170)
REVERT: E   47 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7907 (mm-30)
REVERT: F   64 LEU cc_start: 0.9346 (tp) cc_final: 0.9011 (mp)
  outliers start: 8
  outliers final: 5
  residues processed: 74
  average time/residue: 0.1108
  time to fit residues: 10.6136
Evaluate side-chains
  73 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain C residue   51 HIS
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   41 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 46 optimal weight:    9.9990
   chunk 45 optimal weight:   20.0000
   chunk 44 optimal weight:    9.9990
   chunk 28 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 36 optimal weight:   10.0000
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A   4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  67 GLN
C   4 ASN
D  67 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.164770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.110327 restraints weight = 14039.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.114283 restraints weight = 7363.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.115702 restraints weight = 5109.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.116797 restraints weight = 3949.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.117001 restraints weight = 4001.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.4819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   9248  Z= 0.247
  Angle     :  0.585   5.213  13450  Z= 0.354
  Chirality :  0.033   0.118   1434
  Planarity :  0.003   0.025    934
  Dihedral  : 32.191 175.815   3170
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 14.42 %
    Favored  : 81.73 %
  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:  3.40 (0.36), residues: 528
  helix:  2.85 (0.24), residues: 431
  sheet:  None (None), residues: 0
  loop : -0.71 (0.54), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  15 
 TYR   0.004   0.001   TYR E  44 
 PHE   0.015   0.003   PHE D   5 
 TRP   0.010   0.002   TRP C  37 
 HIS   0.003   0.001   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 ( 9248)
  covalent geometry    : angle       0.58459 (13450)
  hydrogen bonds       : bond        0.04543 (  618)
  hydrogen bonds       : angle       2.81416 ( 1559)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.8936 (ttmm) cc_final: 0.8602 (ttmt)
REVERT: D   30 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8276 (tpt)
  outliers start: 12
  outliers final: 9
  residues processed: 78
  average time/residue: 0.1051
  time to fit residues: 10.6025
Evaluate side-chains
  78 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain B residue   67 GLN
Chi-restraints excluded: chain C residue   51 HIS
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   30 MET
Chi-restraints excluded: chain D residue   67 GLN
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain E residue   51 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 46 optimal weight:   50.0000
   chunk 35 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
A  20 GLN
B  67 GLN
D  67 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.165317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.111514 restraints weight = 13989.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.115159 restraints weight = 7000.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.116807 restraints weight = 4835.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.117262 restraints weight = 3845.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.117606 restraints weight = 3830.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.5005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9248  Z= 0.212
  Angle     :  0.556   4.425  13450  Z= 0.339
  Chirality :  0.031   0.119   1434
  Planarity :  0.003   0.018    934
  Dihedral  : 31.894 179.474   3170
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.06 %
    Favored  : 82.05 %
  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:  3.60 (0.36), residues: 528
  helix:  2.98 (0.24), residues: 431
  sheet:  None (None), residues: 0
  loop : -0.61 (0.56), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  50 
 TYR   0.004   0.001   TYR C  44 
 PHE   0.013   0.002   PHE D   5 
 TRP   0.011   0.002   TRP D  37 
 HIS   0.002   0.001   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 9248)
  covalent geometry    : angle       0.55611 (13450)
  hydrogen bonds       : bond        0.04222 (  618)
  hydrogen bonds       : angle       2.62216 ( 1559)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.8929 (ttmm) cc_final: 0.8603 (ttmt)
  outliers start: 9
  outliers final: 9
  residues processed: 76
  average time/residue: 0.1210
  time to fit residues: 11.7860
Evaluate side-chains
  78 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain B residue   67 GLN
Chi-restraints excluded: chain C residue   51 HIS
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   55 LYS
Chi-restraints excluded: chain D residue   67 GLN
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain E residue   51 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 42 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 48 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 47 optimal weight:   50.0000
   chunk 17 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B  67 GLN
D  67 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.169204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.116249 restraints weight = 13993.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.120360 restraints weight = 6634.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.121588 restraints weight = 4570.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.122267 restraints weight = 3688.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.122709 restraints weight = 3637.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.5287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9248  Z= 0.158
  Angle     :  0.512   4.080  13450  Z= 0.319
  Chirality :  0.029   0.118   1434
  Planarity :  0.002   0.013    934
  Dihedral  : 31.476 175.785   3170
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.71 %
    Favored  : 81.41 %
  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:  4.15 (0.36), residues: 528
  helix:  3.41 (0.24), residues: 431
  sheet:  None (None), residues: 0
  loop : -0.69 (0.56), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  50 
 TYR   0.006   0.001   TYR D  44 
 PHE   0.008   0.001   PHE D   5 
 TRP   0.015   0.002   TRP D  37 
 HIS   0.001   0.000   HIS E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 9248)
  covalent geometry    : angle       0.51241 (13450)
  hydrogen bonds       : bond        0.03723 (  618)
  hydrogen bonds       : angle       2.25928 ( 1559)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.8890 (ttmm) cc_final: 0.8602 (ttmt)
REVERT: D   47 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7884 (mm-30)
REVERT: F   64 LEU cc_start: 0.9417 (tp) cc_final: 0.9047 (mp)
  outliers start: 9
  outliers final: 8
  residues processed: 77
  average time/residue: 0.1278
  time to fit residues: 12.6398
Evaluate side-chains
  78 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain B residue   67 GLN
Chi-restraints excluded: chain C residue   51 HIS
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   67 GLN
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain E residue   51 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 25 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 65 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B  67 GLN
D  67 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.169022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.115897 restraints weight = 13909.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.119452 restraints weight = 6611.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.121587 restraints weight = 4603.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.121732 restraints weight = 3683.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.122232 restraints weight = 3643.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.5326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9248  Z= 0.160
  Angle     :  0.509   4.219  13450  Z= 0.317
  Chirality :  0.029   0.120   1434
  Planarity :  0.002   0.014    934
  Dihedral  : 31.517 175.462   3170
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 15.38 %
    Favored  : 81.09 %
  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 are not related in a simple way.
  whole:  4.29 (0.36), residues: 528
  helix:  3.52 (0.24), residues: 431
  sheet:  None (None), residues: 0
  loop : -0.69 (0.56), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  50 
 TYR   0.006   0.001   TYR D  44 
 PHE   0.009   0.001   PHE D   5 
 TRP   0.013   0.001   TRP D  37 
 HIS   0.002   0.000   HIS E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 9248)
  covalent geometry    : angle       0.50934 (13450)
  hydrogen bonds       : bond        0.03725 (  618)
  hydrogen bonds       : angle       2.27273 ( 1559)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A   12 LYS cc_start: 0.8889 (ttmm) cc_final: 0.8618 (ttmt)
REVERT: B   55 LYS cc_start: 0.8852 (mttt) cc_final: 0.8514 (mtpp)
REVERT: D   47 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7842 (mm-30)
REVERT: D   50 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7631 (ttm110)
REVERT: F   64 LEU cc_start: 0.9430 (tp) cc_final: 0.9050 (mp)
  outliers start: 11
  outliers final: 9
  residues processed: 74
  average time/residue: 0.1257
  time to fit residues: 11.8926
Evaluate side-chains
  77 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain B residue   67 GLN
Chi-restraints excluded: chain C residue   51 HIS
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   55 LYS
Chi-restraints excluded: chain D residue   67 GLN
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain E residue   51 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 64 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 60 optimal weight:   20.0000
   chunk 15 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 59 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
B  67 GLN
D  67 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.168478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.115256 restraints weight = 13910.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.118948 restraints weight = 6787.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.120811 restraints weight = 4667.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.121201 restraints weight = 3712.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.121542 restraints weight = 3687.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.5383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9248  Z= 0.166
  Angle     :  0.513   4.004  13450  Z= 0.318
  Chirality :  0.029   0.121   1434
  Planarity :  0.002   0.023    934
  Dihedral  : 31.529 175.004   3170
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 16.03 %
    Favored  : 80.77 %
  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:  4.27 (0.36), residues: 528
  helix:  3.50 (0.24), residues: 431
  sheet:  None (None), residues: 0
  loop : -0.66 (0.56), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  50 
 TYR   0.006   0.001   TYR D  44 
 PHE   0.010   0.002   PHE D   5 
 TRP   0.013   0.001   TRP D  37 
 HIS   0.002   0.001   HIS E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 9248)
  covalent geometry    : angle       0.51326 (13450)
  hydrogen bonds       : bond        0.03747 (  618)
  hydrogen bonds       : angle       2.32698 ( 1559)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A   12 LYS cc_start: 0.8900 (ttmm) cc_final: 0.8628 (ttmt)
REVERT: B   55 LYS cc_start: 0.8846 (mttt) cc_final: 0.8511 (mtpp)
REVERT: D   47 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7840 (mm-30)
REVERT: D   50 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7646 (ttm110)
  outliers start: 10
  outliers final: 9
  residues processed: 71
  average time/residue: 0.1323
  time to fit residues: 12.0966
Evaluate side-chains
  76 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain B residue   67 GLN
Chi-restraints excluded: chain C residue   51 HIS
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   55 LYS
Chi-restraints excluded: chain D residue   67 GLN
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain E residue   51 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 17 optimal weight:    4.9990
   chunk 16 optimal weight:    0.6980
   chunk 69 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   chunk 3 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 70 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B  67 GLN
D  67 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.168994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.115710 restraints weight = 13800.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.119812 restraints weight = 6808.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.121059 restraints weight = 4655.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.121622 restraints weight = 3755.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.121853 restraints weight = 3715.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.5467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9248  Z= 0.161
  Angle     :  0.511   3.983  13450  Z= 0.316
  Chirality :  0.029   0.122   1434
  Planarity :  0.002   0.024    934
  Dihedral  : 31.501 174.234   3170
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 16.35 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.31 (0.36), residues: 528
  helix:  3.52 (0.24), residues: 431
  sheet:  None (None), residues: 0
  loop : -0.63 (0.56), residues: 97

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  50 
 TYR   0.006   0.001   TYR D  44 
 PHE   0.009   0.002   PHE D   5 
 TRP   0.013   0.001   TRP D  37 
 HIS   0.002   0.001   HIS E  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 9248)
  covalent geometry    : angle       0.51070 (13450)
  hydrogen bonds       : bond        0.03706 (  618)
  hydrogen bonds       : angle       2.30548 ( 1559)

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

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

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1056 Ramachandran restraints generated.
    528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A   12 LYS cc_start: 0.8896 (ttmm) cc_final: 0.8635 (ttmt)
REVERT: B   55 LYS cc_start: 0.8825 (mttt) cc_final: 0.8503 (mtpp)
REVERT: D   47 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7945 (mm-30)
  outliers start: 10
  outliers final: 9
  residues processed: 71
  average time/residue: 0.1243
  time to fit residues: 11.3523
Evaluate side-chains
  76 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   51 HIS
Chi-restraints excluded: chain B residue   67 GLN
Chi-restraints excluded: chain C residue   51 HIS
Chi-restraints excluded: chain D residue    1 MET
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain D residue   55 LYS
Chi-restraints excluded: chain D residue   67 GLN
Chi-restraints excluded: chain E residue   23 SER
Chi-restraints excluded: chain E residue   41 ILE
Chi-restraints excluded: chain E residue   51 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   chunk 38 optimal weight:   30.0000
   chunk 39 optimal weight:   10.0000
   chunk 27 optimal weight:    0.4980
   chunk 55 optimal weight:    4.9990
   chunk 17 optimal weight:    0.3980
   chunk 50 optimal weight:    6.9990
   chunk 57 optimal weight:    7.9990
   chunk 60 optimal weight:   20.0000
   chunk 54 optimal weight:    4.9990
   overall best weight:    2.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A   4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  67 GLN
D  67 GLN
E   4 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.165738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.110612 restraints weight = 13777.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.114383 restraints weight = 7386.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.115908 restraints weight = 5071.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.116228 restraints weight = 4083.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.116659 restraints weight = 4054.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.5458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   9248  Z= 0.265
  Angle     :  0.595   5.937  13450  Z= 0.356
  Chirality :  0.033   0.125   1434
  Planarity :  0.003   0.023    934
  Dihedral  : 31.980 174.438   3170
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 15.38 %
    Favored  : 81.09 %
  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 are not related in a simple way.
  whole:  3.53 (0.36), residues: 528
  helix:  2.92 (0.24), residues: 432
  sheet:  None (None), residues: 0
  loop : -0.56 (0.57), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E  50 
 TYR   0.006   0.001   TYR E  44 
 PHE   0.016   0.003   PHE D   5 
 TRP   0.012   0.001   TRP D  37 
 HIS   0.003   0.001   HIS B  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00603 ( 9248)
  covalent geometry    : angle       0.59452 (13450)
  hydrogen bonds       : bond        0.04657 (  618)
  hydrogen bonds       : angle       2.93912 ( 1559)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2009.51 seconds
wall clock time: 35 minutes 16.21 seconds (2116.21 seconds total)