Starting phenix.real_space_refine
on Wed Sep 17 12:18:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9i6b_52652/09_2025/9i6b_52652.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9i6b_52652/09_2025/9i6b_52652.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9i6b_52652/09_2025/9i6b_52652.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9i6b_52652/09_2025/9i6b_52652.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9i6b_52652/09_2025/9i6b_52652.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9i6b_52652/09_2025/9i6b_52652.map"
  }
  resolution = 2.7
  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=   0.021
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      11      5.49       5
     S      24      5.16       5
     C    5646      2.51       5
     N    1339      2.21       5
     O    1624      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8644
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "C"
      Number of atoms: 451
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 451
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 1, 'TRANS': 55}
    Chain: "E"
      Number of atoms: 326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 326
          Classifications: {'peptide': 43}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 39}
    Chain: "G"
      Number of atoms: 298
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 298
          Classifications: {'peptide': 41}
          Link IDs: {'TRANS': 40}
    Chain: "I"
      Number of atoms: 410
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 410
          Classifications: {'peptide': 51}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 46}
    Chain: "A"
      Number of atoms: 2466
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2466
          Classifications: {'peptide': 318}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 305}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 451
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 451
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 1, 'TRANS': 55}
    Chain: "C"
      Number of atoms: 87
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 87
          Unusual residues: {'PC1': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 21
    Chain: "G"
      Number of atoms: 37
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 37
          Unusual residues: {'DU0': 1}
          Classifications: {'undetermined': 1}
    Chain: "I"
      Number of atoms: 47
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 47
          Unusual residues: {'PC1': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 7
    Chain: "A"
      Number of atoms: 221
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 221
          Unusual residues: {'DU0': 3, 'PC1': 2, 'PLC': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 40
    Chain: "D"
      Number of atoms: 87
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 87
          Unusual residues: {'PC1': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 21
    Chain: "B"
      Number of atoms: 151
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 151
          Unusual residues: {'DU0': 3, 'PC1': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 14
  Restraints were copied for chains:
    B, F, H, J
  Time building chain proxies: 2.65, per 1000 atoms: 0.31
  Number of scatterers: 8644
  At special positions: 0
  Unit cell: (135.801, 115.173, 91.107, 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      24     16.00
     P      11     15.00
     O    1624      8.00
     N    1339      7.00
     C    5646      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: 0.92
  Conformation dependent library (CDL) restraints added in 349.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1888

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 2 sheets defined
      40.0% alpha, 33.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'C' and resid 62 through 117
      Proline residue:  C 100  - end of helix
    Processing helix  chain 'E' and resid 11 through 50
      removed outlier: 3.733A  pdb=" N   ARG E  16 " --> pdb=" O   PRO E  12 " (cutoff:3.500A)
      Proline residue:  E  40  - end of helix
    Processing helix  chain 'G' and resid 17 through 26
      removed outlier: 3.993A  pdb=" N   ALA G  23 " --> pdb=" O   GLY G  19 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU G  24 " --> pdb=" O   ALA G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 48
    Processing helix  chain 'G' and resid 49 through 56
    Processing helix  chain 'I' and resid 23 through 57
      removed outlier: 5.587A  pdb=" N   LEU I  46 " --> pdb=" O   HIS I  42 " (cutoff:3.500A)
      Proline residue:  I  47  - end of helix
    Processing helix  chain 'I' and resid 64 through 68
    Processing helix  chain 'A' and resid 22 through 34
      removed outlier: 3.608A  pdb=" N   ALA A  27 " --> pdb=" O   ASP A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 46
    Processing helix  chain 'A' and resid 47 through 52
    Processing helix  chain 'A' and resid 332 through 337
      removed outlier: 3.826A  pdb=" N   LEU A 336 " --> pdb=" O   GLY A 332 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 117
      Proline residue:  D 100  - end of helix
    Processing helix  chain 'F' and resid 11 through 50
      removed outlier: 3.733A  pdb=" N   ARG F  16 " --> pdb=" O   PRO F  12 " (cutoff:3.500A)
      Proline residue:  F  40  - end of helix
    Processing helix  chain 'H' and resid 17 through 26
      removed outlier: 3.993A  pdb=" N   ALA H  23 " --> pdb=" O   GLY H  19 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU H  24 " --> pdb=" O   ALA H  20 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 29 through 48
    Processing helix  chain 'H' and resid 49 through 56
    Processing helix  chain 'J' and resid 23 through 57
      removed outlier: 5.587A  pdb=" N   LEU J  46 " --> pdb=" O   HIS J  42 " (cutoff:3.500A)
      Proline residue:  J  47  - end of helix
    Processing helix  chain 'J' and resid 64 through 68
    Processing helix  chain 'B' and resid 22 through 34
      removed outlier: 3.608A  pdb=" N   ALA B  27 " --> pdb=" O   ASP B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 46
    Processing helix  chain 'B' and resid 47 through 52
    Processing helix  chain 'B' and resid 332 through 337
      removed outlier: 3.826A  pdb=" N   LEU B 336 " --> pdb=" O   GLY B 332 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 73
      removed outlier: 6.401A  pdb=" N   PHE A  78 " --> pdb=" O   PHE A  72 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   ALA A 146 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   THR A 174 " --> pdb=" O   PRO A 166 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   LYS A 293 " --> pdb=" O   ASP A 289 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 63 through 73
      removed outlier: 6.401A  pdb=" N   PHE B  78 " --> pdb=" O   PHE B  72 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   ALA B 146 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   THR B 174 " --> pdb=" O   PRO B 166 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   LYS B 293 " --> pdb=" O   ASP B 289 " (cutoff:3.500A)

    590 hydrogen bonds defined for protein.
    1698 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.11

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1342
        1.32 -     1.44: 2320
        1.44 -     1.56: 5103
        1.56 -     1.68: 28
        1.68 -     1.80: 46
  Bond restraints: 8839
  Sorted by residual:
  bond pdb=" CB  PRO F   8 "
       pdb=" CG  PRO F   8 "
    ideal  model  delta    sigma   weight residual
    1.492  1.583 -0.091 5.00e-02 4.00e+02 3.31e+00
  bond pdb=" CB  PRO E   8 "
       pdb=" CG  PRO E   8 "
    ideal  model  delta    sigma   weight residual
    1.492  1.583 -0.091 5.00e-02 4.00e+02 3.31e+00
  bond pdb=" CG1 ILE B 327 "
       pdb=" CD1 ILE B 327 "
    ideal  model  delta    sigma   weight residual
    1.513  1.452  0.061 3.90e-02 6.57e+02 2.41e+00
  bond pdb=" CG1 ILE A 327 "
       pdb=" CD1 ILE A 327 "
    ideal  model  delta    sigma   weight residual
    1.513  1.452  0.061 3.90e-02 6.57e+02 2.41e+00
  bond pdb=" CG  LEU B 193 "
       pdb=" CD1 LEU B 193 "
    ideal  model  delta    sigma   weight residual
    1.521  1.471  0.050 3.30e-02 9.18e+02 2.31e+00
  ... (remaining 8834 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 11296
        1.71 -     3.42: 557
        3.42 -     5.12: 92
        5.12 -     6.83: 36
        6.83 -     8.54: 10
  Bond angle restraints: 11991
  Sorted by residual:
  angle pdb=" CA  PRO E  12 "
        pdb=" N   PRO E  12 "
        pdb=" CD  PRO E  12 "
      ideal   model   delta    sigma   weight residual
     112.00  105.51    6.49 1.40e+00 5.10e-01 2.15e+01
  angle pdb=" CA  PRO F  12 "
        pdb=" N   PRO F  12 "
        pdb=" CD  PRO F  12 "
      ideal   model   delta    sigma   weight residual
     112.00  105.51    6.49 1.40e+00 5.10e-01 2.15e+01
  angle pdb=" N   GLY A 332 "
        pdb=" CA  GLY A 332 "
        pdb=" C   GLY A 332 "
      ideal   model   delta    sigma   weight residual
     112.73  118.18   -5.45 1.20e+00 6.94e-01 2.06e+01
  angle pdb=" N   GLY B 332 "
        pdb=" CA  GLY B 332 "
        pdb=" C   GLY B 332 "
      ideal   model   delta    sigma   weight residual
     112.73  118.18   -5.45 1.20e+00 6.94e-01 2.06e+01
  angle pdb=" CA  PRO F  40 "
        pdb=" N   PRO F  40 "
        pdb=" CD  PRO F  40 "
      ideal   model   delta    sigma   weight residual
     112.00  106.13    5.87 1.40e+00 5.10e-01 1.76e+01
  ... (remaining 11986 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.58: 5418
       27.58 -    55.15: 347
       55.15 -    82.73: 96
       82.73 -   110.30: 34
      110.30 -   137.87: 18
  Dihedral angle restraints: 5913
    sinusoidal: 2975
      harmonic: 2938
  Sorted by residual:
  dihedral pdb=" CD  ARG E  16 "
           pdb=" NE  ARG E  16 "
           pdb=" CZ  ARG E  16 "
           pdb=" NH1 ARG E  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   68.09  -68.09     1      1.00e+01 1.00e-02 6.02e+01
  dihedral pdb=" CD  ARG F  16 "
           pdb=" NE  ARG F  16 "
           pdb=" CZ  ARG F  16 "
           pdb=" NH1 ARG F  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   68.09  -68.09     1      1.00e+01 1.00e-02 6.02e+01
  dihedral pdb=" C26 DU0 A 403 "
           pdb=" C24 DU0 A 403 "
           pdb=" C25 DU0 A 403 "
           pdb=" O23 DU0 A 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     189.32   51.45  137.87     1      3.00e+01 1.11e-03 1.86e+01
  ... (remaining 5910 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 975
       0.055 -    0.111: 278
       0.111 -    0.166: 62
       0.166 -    0.221: 8
       0.221 -    0.277: 6
  Chirality restraints: 1329
  Sorted by residual:
  chirality pdb=" CB  VAL A 249 "
            pdb=" CA  VAL A 249 "
            pdb=" CG1 VAL A 249 "
            pdb=" CG2 VAL A 249 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CB  VAL B 249 "
            pdb=" CA  VAL B 249 "
            pdb=" CG1 VAL B 249 "
            pdb=" CG2 VAL B 249 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.35   -0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" CA  PRO F  40 "
            pdb=" N   PRO F  40 "
            pdb=" C   PRO F  40 "
            pdb=" CB  PRO F  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.45    0.27 2.00e-01 2.50e+01 1.85e+00
  ... (remaining 1326 not shown)

  Planarity restraints: 1428
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG E  16 "   -0.843 9.50e-02 1.11e+02   3.79e-01 1.01e+02
        pdb=" NE  ARG E  16 "    0.074 2.00e-02 2.50e+03
        pdb=" CZ  ARG E  16 "   -0.054 2.00e-02 2.50e+03
        pdb=" NH1 ARG E  16 "    0.018 2.00e-02 2.50e+03
        pdb=" NH2 ARG E  16 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG F  16 "    0.843 9.50e-02 1.11e+02   3.79e-01 1.01e+02
        pdb=" NE  ARG F  16 "   -0.074 2.00e-02 2.50e+03
        pdb=" CZ  ARG F  16 "    0.054 2.00e-02 2.50e+03
        pdb=" NH1 ARG F  16 "   -0.018 2.00e-02 2.50e+03
        pdb=" NH2 ARG F  16 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E  11 "   -0.083 5.00e-02 4.00e+02   1.22e-01 2.37e+01
        pdb=" N   PRO E  12 "    0.210 5.00e-02 4.00e+02
        pdb=" CA  PRO E  12 "   -0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO E  12 "   -0.066 5.00e-02 4.00e+02
  ... (remaining 1425 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2093
        2.81 -     3.33: 7421
        3.33 -     3.86: 13932
        3.86 -     4.38: 16811
        4.38 -     4.90: 29427
  Nonbonded interactions: 69684
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 237 "
            pdb=" OE1 GLN A 239 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OH  TYR B 237 "
            pdb=" OE1 GLN B 239 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OE2 GLU A  88 "
            pdb=" NH1 ARG A  89 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" OE2 GLU B  88 "
            pdb=" NH1 ARG B  89 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" OG  SER A  73 "
            pdb=" O   PRO A  76 "
     model   vdw
     2.296 3.040
  ... (remaining 69679 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 21 through 347 or resid 403 or resid 405))
  selection = (chain 'B' and (resid 21 through 347 or resid 403 or resid 405))
}
ncs_group {
  reference = (chain 'C' and (resid 62 through 118 or (resid 201 through 202 and (name N or na \ 
me C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C2 or  \ 
name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 \ 
 or name C28 or name C29 or name C2A or name C2B or name C3 or name C31 or name  \ 
C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or n \ 
ame C39 or name C3A or name O11 or name O12 or name O13 or name O14 or name O21  \ 
or name O22 or name O31 or name O32 or name P ))))
  selection = (chain 'D' and (resid 62 through 201 or (resid 202 and (name N or name C1 or nam \ 
e C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or  \ 
name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ 
 or name C29 or name C2A or name C2B or name C3 or name C31 or name C32 or name  \ 
C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or n \ 
ame C3A or name O11 or name O12 or name O13 or name O14 or name O21 or name O22  \ 
or name O31 or name O32 or name P ))))
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             14.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.630
  Find NCS groups from input model:        0.160
  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:6.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
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      :  0.007   0.091   8839  Z= 0.302
  Angle     :  0.904   8.540  11991  Z= 0.464
  Chirality :  0.056   0.277   1329
  Planarity :  0.017   0.379   1428
  Dihedral  : 21.113 137.875   4025
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.25), residues: 996
  helix:  0.28 (0.23), residues: 368
  sheet:  1.43 (0.25), residues: 396
  loop : -0.11 (0.43), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.064   0.004   ARG E  16 
 TYR   0.014   0.002   TYR J  43 
 PHE   0.018   0.002   PHE G  45 
 TRP   0.032   0.004   TRP B 197 
 HIS   0.004   0.002   HIS C  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00735 ( 8839)
  covalent geometry    : angle       0.90362 (11991)
  hydrogen bonds       : bond        0.17739 (  590)
  hydrogen bonds       : angle       7.19866 ( 1698)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.232 
Fit side-chains
REVERT: C  109 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7838 (mm-40)
REVERT: E   49 MET cc_start: 0.5807 (mmm) cc_final: 0.5485 (mtm)
REVERT: A   48 LYS cc_start: 0.7919 (tttt) cc_final: 0.7643 (ttpp)
REVERT: A  145 MET cc_start: 0.7625 (mtm) cc_final: 0.7390 (mmm)
REVERT: A  151 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7490 (tt0)
REVERT: A  217 LYS cc_start: 0.8700 (tttp) cc_final: 0.8322 (tttp)
REVERT: A  308 MET cc_start: 0.8375 (mmm) cc_final: 0.7553 (tmt)
REVERT: D  109 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7834 (mm-40)
REVERT: F   49 MET cc_start: 0.5806 (mmm) cc_final: 0.5485 (mtm)
REVERT: B   48 LYS cc_start: 0.7922 (tttt) cc_final: 0.7644 (ttpp)
REVERT: B  145 MET cc_start: 0.7627 (mtm) cc_final: 0.7392 (mmm)
REVERT: B  151 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7491 (tt0)
REVERT: B  217 LYS cc_start: 0.8700 (tttp) cc_final: 0.8322 (tttp)
REVERT: B  308 MET cc_start: 0.8378 (mmm) cc_final: 0.7552 (tmt)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.7975
  time to fit residues: 110.3174
Evaluate side-chains
  80 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.1980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A  83 GLN
A 135 GLN
B  29 GLN
B  83 GLN
B 135 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.181070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.131570 restraints weight = 7995.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.75
r_work: 0.3247 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8839  Z= 0.163
  Angle     :  0.652   6.737  11991  Z= 0.331
  Chirality :  0.043   0.168   1329
  Planarity :  0.005   0.052   1428
  Dihedral  : 17.875 139.656   2227
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  8.25 %
    Favored  : 90.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.06 (0.27), residues: 996
  helix:  2.03 (0.26), residues: 370
  sheet:  1.41 (0.25), residues: 394
  loop :  0.27 (0.46), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 215 
 TYR   0.009   0.001   TYR I  43 
 PHE   0.011   0.001   PHE A  72 
 TRP   0.014   0.002   TRP B 197 
 HIS   0.002   0.001   HIS B 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 8839)
  covalent geometry    : angle       0.65172 (11991)
  hydrogen bonds       : bond        0.04383 (  590)
  hydrogen bonds       : angle       5.07158 ( 1698)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.312 
Fit side-chains
REVERT: C  109 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7340 (mm-40)
REVERT: E   49 MET cc_start: 0.5738 (mmm) cc_final: 0.5347 (mtp)
REVERT: A   48 LYS cc_start: 0.7966 (tttt) cc_final: 0.7530 (ttpp)
REVERT: A  145 MET cc_start: 0.8008 (mtm) cc_final: 0.7759 (mmm)
REVERT: A  301 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7085 (tpt170)
REVERT: A  308 MET cc_start: 0.8766 (mmm) cc_final: 0.7722 (tmt)
REVERT: D  109 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7344 (mm-40)
REVERT: F   49 MET cc_start: 0.5739 (mmm) cc_final: 0.5345 (mtp)
REVERT: B   48 LYS cc_start: 0.7965 (tttt) cc_final: 0.7530 (ttpp)
REVERT: B  145 MET cc_start: 0.8023 (mtm) cc_final: 0.7771 (mmm)
REVERT: B  301 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7116 (tpt170)
REVERT: B  308 MET cc_start: 0.8756 (mmm) cc_final: 0.7685 (tmt)
  outliers start: 8
  outliers final: 2
  residues processed: 100
  average time/residue: 0.7683
  time to fit residues: 80.7769
Evaluate side-chains
  88 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  301 ARG
Chi-restraints excluded: chain B residue  198 GLN
Chi-restraints excluded: chain B residue  301 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 95 optimal weight:    5.9990
   chunk 73 optimal weight:    0.5980
   chunk 53 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 90 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0570
   overall best weight:    0.6898

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.181846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.132943 restraints weight = 7998.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 1.73
r_work: 0.3250 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8839  Z= 0.134
  Angle     :  0.556   5.592  11991  Z= 0.287
  Chirality :  0.040   0.147   1329
  Planarity :  0.004   0.044   1428
  Dihedral  : 16.091 133.463   2227
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 11.04 %
    Favored  : 87.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.07 (0.27), residues: 996
  helix:  2.51 (0.26), residues: 372
  sheet:  1.13 (0.25), residues: 404
  loop : -0.11 (0.45), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 133 
 TYR   0.009   0.001   TYR I  45 
 PHE   0.010   0.001   PHE H  45 
 TRP   0.014   0.001   TRP A 197 
 HIS   0.002   0.001   HIS C  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 8839)
  covalent geometry    : angle       0.55561 (11991)
  hydrogen bonds       : bond        0.03600 (  590)
  hydrogen bonds       : angle       4.68224 ( 1698)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.356 
Fit side-chains
REVERT: C  109 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7332 (mm-40)
REVERT: E   49 MET cc_start: 0.5749 (mmm) cc_final: 0.5346 (mtp)
REVERT: A   48 LYS cc_start: 0.7870 (tttt) cc_final: 0.7434 (ttpp)
REVERT: A  151 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7501 (tt0)
REVERT: A  215 ARG cc_start: 0.8704 (ttp-170) cc_final: 0.8346 (ttm-80)
REVERT: A  308 MET cc_start: 0.8756 (mmm) cc_final: 0.7700 (tmt)
REVERT: D  109 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7358 (mm-40)
REVERT: F   49 MET cc_start: 0.5742 (mmm) cc_final: 0.5341 (mtp)
REVERT: B   48 LYS cc_start: 0.7864 (tttt) cc_final: 0.7429 (ttpp)
REVERT: B  151 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7509 (tt0)
REVERT: B  215 ARG cc_start: 0.8708 (ttp-170) cc_final: 0.8351 (ttm-80)
REVERT: B  308 MET cc_start: 0.8732 (mmm) cc_final: 0.7693 (tmt)
  outliers start: 10
  outliers final: 2
  residues processed: 102
  average time/residue: 0.7442
  time to fit residues: 79.9423
Evaluate side-chains
  94 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain B residue  129 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    0.3980
   chunk 29 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 24 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
I  27 GLN
A  58 ASN
J  27 GLN
B  58 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.181643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.132447 restraints weight = 8182.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.75
r_work: 0.3249 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8839  Z= 0.128
  Angle     :  0.530   5.624  11991  Z= 0.274
  Chirality :  0.039   0.138   1329
  Planarity :  0.004   0.046   1428
  Dihedral  : 15.258 122.244   2227
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 12.50 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.27), residues: 996
  helix:  2.84 (0.26), residues: 372
  sheet:  1.09 (0.25), residues: 404
  loop : -0.06 (0.45), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG J  56 
 TYR   0.008   0.001   TYR I  45 
 PHE   0.008   0.001   PHE B  72 
 TRP   0.012   0.001   TRP A 197 
 HIS   0.002   0.001   HIS D  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8839)
  covalent geometry    : angle       0.53034 (11991)
  hydrogen bonds       : bond        0.03163 (  590)
  hydrogen bonds       : angle       4.50147 ( 1698)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.347 
Fit side-chains
REVERT: C  109 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7301 (mm-40)
REVERT: E   49 MET cc_start: 0.5685 (mmm) cc_final: 0.5276 (mtp)
REVERT: A   48 LYS cc_start: 0.7858 (tttt) cc_final: 0.7428 (ttpp)
REVERT: A  151 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7492 (tt0)
REVERT: A  161 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7806 (tp)
REVERT: A  301 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7273 (tpt170)
REVERT: A  308 MET cc_start: 0.8693 (mmm) cc_final: 0.7601 (tmt)
REVERT: D  109 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7362 (mm-40)
REVERT: F   49 MET cc_start: 0.5680 (mmm) cc_final: 0.5275 (mtp)
REVERT: B   48 LYS cc_start: 0.7855 (tttt) cc_final: 0.7426 (ttpp)
REVERT: B  151 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7499 (tt0)
REVERT: B  161 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7805 (tp)
REVERT: B  301 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7269 (tpt170)
REVERT: B  308 MET cc_start: 0.8649 (mmm) cc_final: 0.7574 (tmt)
  outliers start: 11
  outliers final: 2
  residues processed: 102
  average time/residue: 0.6489
  time to fit residues: 69.9855
Evaluate side-chains
  96 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  301 ARG
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  301 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 94 optimal weight:    0.3980
   chunk 41 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 60 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.180982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.131679 restraints weight = 8173.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 1.76
r_work: 0.3240 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8839  Z= 0.135
  Angle     :  0.530   5.607  11991  Z= 0.274
  Chirality :  0.039   0.135   1329
  Planarity :  0.004   0.046   1428
  Dihedral  : 14.811 114.182   2227
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.14 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.29 (0.27), residues: 996
  helix:  2.95 (0.26), residues: 372
  sheet:  1.04 (0.26), residues: 404
  loop : -0.09 (0.45), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG J  56 
 TYR   0.008   0.001   TYR J  45 
 PHE   0.010   0.001   PHE D 101 
 TRP   0.012   0.001   TRP A 197 
 HIS   0.002   0.001   HIS D  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8839)
  covalent geometry    : angle       0.52958 (11991)
  hydrogen bonds       : bond        0.03142 (  590)
  hydrogen bonds       : angle       4.46128 ( 1698)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.286 
Fit side-chains
REVERT: C  109 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7279 (mm-40)
REVERT: E   49 MET cc_start: 0.5681 (mmm) cc_final: 0.5269 (mtp)
REVERT: A   48 LYS cc_start: 0.7853 (tttt) cc_final: 0.7399 (ttpp)
REVERT: A  151 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7499 (tt0)
REVERT: A  161 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7800 (tp)
REVERT: A  215 ARG cc_start: 0.8715 (ttp-170) cc_final: 0.8400 (ttm-80)
REVERT: A  308 MET cc_start: 0.8674 (mmm) cc_final: 0.7673 (tmt)
REVERT: D  109 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7285 (mm-40)
REVERT: F   49 MET cc_start: 0.5675 (mmm) cc_final: 0.5266 (mtp)
REVERT: B   48 LYS cc_start: 0.7846 (tttt) cc_final: 0.7392 (ttpp)
REVERT: B  151 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7502 (tt0)
REVERT: B  161 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7800 (tp)
REVERT: B  215 ARG cc_start: 0.8716 (ttp-170) cc_final: 0.8403 (ttm-80)
REVERT: B  308 MET cc_start: 0.8613 (mmm) cc_final: 0.7629 (tmt)
  outliers start: 14
  outliers final: 8
  residues processed: 100
  average time/residue: 0.5834
  time to fit residues: 62.0542
Evaluate side-chains
  114 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  208 THR
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  249 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   chunk 68 optimal weight:    0.1980
   chunk 76 optimal weight:    0.9980
   chunk 86 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.181485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.132570 restraints weight = 8116.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 1.74
r_work: 0.3250 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3079 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8839  Z= 0.127
  Angle     :  0.520   5.616  11991  Z= 0.269
  Chirality :  0.039   0.136   1329
  Planarity :  0.004   0.047   1428
  Dihedral  : 14.416 105.726   2227
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.38 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.35 (0.28), residues: 996
  helix:  3.06 (0.26), residues: 372
  sheet:  0.99 (0.26), residues: 404
  loop :  0.01 (0.46), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG I  56 
 TYR   0.008   0.001   TYR J  45 
 PHE   0.008   0.001   PHE D 101 
 TRP   0.012   0.001   TRP A 197 
 HIS   0.001   0.001   HIS C  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8839)
  covalent geometry    : angle       0.52006 (11991)
  hydrogen bonds       : bond        0.03002 (  590)
  hydrogen bonds       : angle       4.40539 ( 1698)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.268 
Fit side-chains
REVERT: C  109 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7245 (mm-40)
REVERT: E   49 MET cc_start: 0.5676 (mmm) cc_final: 0.5251 (mtp)
REVERT: A   48 LYS cc_start: 0.7837 (tttt) cc_final: 0.7394 (ttpp)
REVERT: A  151 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7460 (tt0)
REVERT: A  161 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7797 (tp)
REVERT: A  215 ARG cc_start: 0.8700 (ttp-170) cc_final: 0.8374 (ttm-80)
REVERT: A  308 MET cc_start: 0.8677 (mmm) cc_final: 0.7604 (tmt)
REVERT: D  109 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7296 (mm-40)
REVERT: F   49 MET cc_start: 0.5673 (mmm) cc_final: 0.5249 (mtp)
REVERT: B   48 LYS cc_start: 0.7835 (tttt) cc_final: 0.7393 (ttpp)
REVERT: B  151 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7463 (tt0)
REVERT: B  161 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7801 (tp)
REVERT: B  215 ARG cc_start: 0.8701 (ttp-170) cc_final: 0.8375 (ttm-80)
REVERT: B  308 MET cc_start: 0.8598 (mmm) cc_final: 0.7566 (tmt)
  outliers start: 14
  outliers final: 6
  residues processed: 96
  average time/residue: 0.6392
  time to fit residues: 65.1334
Evaluate side-chains
  97 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  198 GLN
Chi-restraints excluded: chain B residue  249 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 49 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.180068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.130745 restraints weight = 8336.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 1.82
r_work: 0.3249 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8188
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8839  Z= 0.140
  Angle     :  0.533   5.637  11991  Z= 0.275
  Chirality :  0.040   0.136   1329
  Planarity :  0.004   0.047   1428
  Dihedral  : 14.167  98.880   2227
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.50 %
    Favored  : 85.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.35 (0.28), residues: 996
  helix:  3.08 (0.26), residues: 372
  sheet:  1.01 (0.26), residues: 404
  loop : -0.07 (0.46), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG I  56 
 TYR   0.008   0.001   TYR I  45 
 PHE   0.011   0.001   PHE D 101 
 TRP   0.012   0.001   TRP B 197 
 HIS   0.002   0.001   HIS C  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8839)
  covalent geometry    : angle       0.53274 (11991)
  hydrogen bonds       : bond        0.03095 (  590)
  hydrogen bonds       : angle       4.42440 ( 1698)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  109 GLN cc_start: 0.7663 (mm-40) cc_final: 0.7322 (mm-40)
REVERT: E   49 MET cc_start: 0.5655 (mmm) cc_final: 0.5218 (mtp)
REVERT: A   48 LYS cc_start: 0.7899 (tttt) cc_final: 0.7455 (ttpp)
REVERT: A  151 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7525 (tt0)
REVERT: A  161 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7816 (tp)
REVERT: A  215 ARG cc_start: 0.8695 (ttp-170) cc_final: 0.8363 (ttm-80)
REVERT: A  308 MET cc_start: 0.8668 (mmm) cc_final: 0.7682 (tmt)
REVERT: D  109 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7359 (mm-40)
REVERT: F   49 MET cc_start: 0.5655 (mmm) cc_final: 0.5219 (mtp)
REVERT: B   48 LYS cc_start: 0.7894 (tttt) cc_final: 0.7450 (ttpp)
REVERT: B  151 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7523 (tt0)
REVERT: B  161 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7815 (tp)
REVERT: B  215 ARG cc_start: 0.8694 (ttp-170) cc_final: 0.8366 (ttm-80)
REVERT: B  308 MET cc_start: 0.8564 (mmm) cc_final: 0.7631 (tmt)
  outliers start: 15
  outliers final: 10
  residues processed: 101
  average time/residue: 0.6700
  time to fit residues: 71.6009
Evaluate side-chains
  112 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  198 GLN
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  249 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 9 optimal weight:    0.1980
   chunk 55 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.181617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.132488 restraints weight = 8134.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.76
r_work: 0.3245 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8839  Z= 0.127
  Angle     :  0.520   5.626  11991  Z= 0.269
  Chirality :  0.039   0.136   1329
  Planarity :  0.004   0.048   1428
  Dihedral  : 13.870  92.990   2227
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 12.74 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.35 (0.28), residues: 996
  helix:  3.12 (0.26), residues: 372
  sheet:  0.99 (0.26), residues: 404
  loop : -0.11 (0.45), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG J  56 
 TYR   0.008   0.001   TYR J  45 
 PHE   0.008   0.001   PHE D 101 
 TRP   0.012   0.001   TRP B 197 
 HIS   0.002   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8839)
  covalent geometry    : angle       0.52022 (11991)
  hydrogen bonds       : bond        0.02952 (  590)
  hydrogen bonds       : angle       4.37581 ( 1698)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  109 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7258 (mm-40)
REVERT: E   49 MET cc_start: 0.5637 (mmm) cc_final: 0.5203 (mtp)
REVERT: A   48 LYS cc_start: 0.7845 (tttt) cc_final: 0.7403 (ttpp)
REVERT: A  144 ASP cc_start: 0.7694 (m-30) cc_final: 0.7476 (m-30)
REVERT: A  151 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7477 (tt0)
REVERT: A  161 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7807 (tp)
REVERT: A  215 ARG cc_start: 0.8710 (ttp-170) cc_final: 0.8383 (ttm-80)
REVERT: A  301 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7575 (tpm170)
REVERT: A  308 MET cc_start: 0.8660 (mmm) cc_final: 0.7605 (tmt)
REVERT: D  109 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7304 (mm-40)
REVERT: F   49 MET cc_start: 0.5630 (mmm) cc_final: 0.5202 (mtp)
REVERT: B   48 LYS cc_start: 0.7833 (tttt) cc_final: 0.7390 (ttpp)
REVERT: B  144 ASP cc_start: 0.7690 (m-30) cc_final: 0.7469 (m-30)
REVERT: B  151 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7475 (tt0)
REVERT: B  161 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7806 (tp)
REVERT: B  215 ARG cc_start: 0.8711 (ttp-170) cc_final: 0.8387 (ttm-80)
REVERT: B  308 MET cc_start: 0.8579 (mmm) cc_final: 0.7574 (tmt)
  outliers start: 15
  outliers final: 10
  residues processed: 105
  average time/residue: 0.6007
  time to fit residues: 67.2489
Evaluate side-chains
  104 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  198 GLN
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  301 ARG
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  198 GLN
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  249 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 71 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0980
   chunk 90 optimal weight:    0.2980
   chunk 37 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0870
   overall best weight:    0.3958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.184280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.135379 restraints weight = 8101.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 1.75
r_work: 0.3285 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3115 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8839  Z= 0.098
  Angle     :  0.484   5.630  11991  Z= 0.251
  Chirality :  0.038   0.137   1329
  Planarity :  0.004   0.049   1428
  Dihedral  : 13.197  88.518   2227
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 12.74 %
    Favored  : 85.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.48 (0.28), residues: 996
  helix:  3.32 (0.26), residues: 370
  sheet:  0.97 (0.26), residues: 404
  loop :  0.02 (0.45), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I  56 
 TYR   0.008   0.001   TYR I  45 
 PHE   0.007   0.001   PHE G  45 
 TRP   0.013   0.001   TRP B 197 
 HIS   0.001   0.000   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 8839)
  covalent geometry    : angle       0.48361 (11991)
  hydrogen bonds       : bond        0.02606 (  590)
  hydrogen bonds       : angle       4.19349 ( 1698)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  109 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7331 (mm-40)
REVERT: E   49 MET cc_start: 0.5608 (mmm) cc_final: 0.5138 (mtp)
REVERT: A   48 LYS cc_start: 0.7819 (tttt) cc_final: 0.7390 (ttpp)
REVERT: A  130 THR cc_start: 0.8687 (m) cc_final: 0.8453 (t)
REVERT: A  144 ASP cc_start: 0.7673 (m-30) cc_final: 0.7441 (m-30)
REVERT: A  151 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7475 (tt0)
REVERT: A  215 ARG cc_start: 0.8688 (ttp-170) cc_final: 0.8379 (ttm-80)
REVERT: A  308 MET cc_start: 0.8620 (mmm) cc_final: 0.7601 (tmt)
REVERT: D  109 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7461 (mm-40)
REVERT: F   49 MET cc_start: 0.5604 (mmm) cc_final: 0.5141 (mtp)
REVERT: B   48 LYS cc_start: 0.7812 (tttt) cc_final: 0.7384 (ttpp)
REVERT: B  130 THR cc_start: 0.8695 (m) cc_final: 0.8463 (t)
REVERT: B  144 ASP cc_start: 0.7666 (m-30) cc_final: 0.7431 (m-30)
REVERT: B  151 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7479 (tt0)
REVERT: B  215 ARG cc_start: 0.8689 (ttp-170) cc_final: 0.8382 (ttm-80)
REVERT: B  308 MET cc_start: 0.8534 (mmm) cc_final: 0.7577 (tmt)
  outliers start: 13
  outliers final: 8
  residues processed: 103
  average time/residue: 0.6143
  time to fit residues: 67.2430
Evaluate side-chains
  96 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ILE
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  249 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 48 optimal weight:    8.9990
   chunk 84 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 49 optimal weight:   10.0000
   chunk 73 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 89 optimal weight:    0.4980
   chunk 20 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.182459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.133388 restraints weight = 8141.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 1.75
r_work: 0.3258 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8839  Z= 0.123
  Angle     :  0.509   5.610  11991  Z= 0.263
  Chirality :  0.039   0.136   1329
  Planarity :  0.004   0.047   1428
  Dihedral  : 13.029  86.871   2227
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 13.11 %
    Favored  : 85.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.45 (0.28), residues: 996
  helix:  3.26 (0.25), residues: 370
  sheet:  1.00 (0.26), residues: 404
  loop : -0.02 (0.45), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG J  56 
 TYR   0.008   0.001   TYR J  45 
 PHE   0.009   0.001   PHE D 101 
 TRP   0.010   0.001   TRP A 197 
 HIS   0.001   0.001   HIS A  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8839)
  covalent geometry    : angle       0.50866 (11991)
  hydrogen bonds       : bond        0.02825 (  590)
  hydrogen bonds       : angle       4.27995 ( 1698)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.380 
Fit side-chains
REVERT: C  109 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7313 (mm-40)
REVERT: E   49 MET cc_start: 0.5610 (mmm) cc_final: 0.5182 (mtp)
REVERT: A   48 LYS cc_start: 0.7857 (tttt) cc_final: 0.7421 (ttpp)
REVERT: A  151 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7504 (tt0)
REVERT: A  215 ARG cc_start: 0.8703 (ttp-170) cc_final: 0.8390 (ttm-80)
REVERT: A  301 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7528 (tpm170)
REVERT: A  308 MET cc_start: 0.8625 (mmm) cc_final: 0.7615 (tmt)
REVERT: D  109 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7357 (mm-40)
REVERT: F   49 MET cc_start: 0.5602 (mmm) cc_final: 0.5181 (mtp)
REVERT: B   48 LYS cc_start: 0.7853 (tttt) cc_final: 0.7416 (ttpp)
REVERT: B  151 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7506 (tt0)
REVERT: B  215 ARG cc_start: 0.8704 (ttp-170) cc_final: 0.8393 (ttm-80)
REVERT: B  301 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7454 (tpm170)
REVERT: B  308 MET cc_start: 0.8580 (mmm) cc_final: 0.7584 (tmt)
  outliers start: 10
  outliers final: 6
  residues processed: 90
  average time/residue: 0.6806
  time to fit residues: 64.9894
Evaluate side-chains
  94 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain A residue  301 ARG
Chi-restraints excluded: chain B residue  129 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  301 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0970
   chunk 2 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0670
   chunk 73 optimal weight:    2.9990
   chunk 94 optimal weight:    0.1980
   chunk 55 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.4516

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.184018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.135096 restraints weight = 8077.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 1.75
r_work: 0.3279 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.3108 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8839  Z= 0.102
  Angle     :  0.487   5.608  11991  Z= 0.253
  Chirality :  0.038   0.137   1329
  Planarity :  0.004   0.049   1428
  Dihedral  : 12.359  80.538   2227
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 13.59 %
    Favored  : 85.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.50 (0.28), residues: 996
  helix:  3.33 (0.26), residues: 370
  sheet:  0.99 (0.26), residues: 404
  loop :  0.01 (0.45), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG I  56 
 TYR   0.008   0.001   TYR J  45 
 PHE   0.006   0.001   PHE H  45 
 TRP   0.012   0.001   TRP B 197 
 HIS   0.001   0.000   HIS B  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 8839)
  covalent geometry    : angle       0.48711 (11991)
  hydrogen bonds       : bond        0.02630 (  590)
  hydrogen bonds       : angle       4.19859 ( 1698)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4283.17 seconds
wall clock time: 73 minutes 35.81 seconds (4415.81 seconds total)