Starting phenix.real_space_refine
on Tue Mar 11 15:43:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sks_40566/03_2025/8sks_40566.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sks_40566/03_2025/8sks_40566.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sks_40566/03_2025/8sks_40566.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sks_40566/03_2025/8sks_40566.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sks_40566/03_2025/8sks_40566.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sks_40566/03_2025/8sks_40566.cif"
  }
  resolution = 2.91
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.019
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
     Mn      4      7.51       5
     S      16      5.16       5
     C    3992      2.51       5
     N    1092      2.21       5
     O    1128      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6232
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1557
          Classifications: {'peptide': 198}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 187}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 3.29, per 1000 atoms: 0.53
  Number of scatterers: 6232
  At special positions: 0
  Unit cell: (71.69, 86.67, 86.67, 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)
     Mn      4     24.99
     S      16     16.00
     O    1128      8.00
     N    1092      7.00
     C    3992      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.69
  Conformation dependent library (CDL) restraints added in 876.3 milliseconds
  

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1432

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 4 sheets defined
      69.2% alpha, 10.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 39
      removed outlier: 4.275A  pdb=" N   LEU A  38 " --> pdb=" O   TYR A  35 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLU A  39 " --> pdb=" O   GLY A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 76
      removed outlier: 3.915A  pdb=" N   HIS A  55 " --> pdb=" O   HIS A  51 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   ALA A  56 " --> pdb=" O   SER A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 105
      Proline residue:  A  86  - end of helix
      removed outlier: 3.627A  pdb=" N   THR A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 126
    Processing helix  chain 'A' and resid 127 through 142
    Processing helix  chain 'A' and resid 169 through 174
    Processing helix  chain 'A' and resid 185 through 188
    Processing helix  chain 'A' and resid 189 through 194
    Processing helix  chain 'A' and resid 196 through 205
      removed outlier: 3.517A  pdb=" N   TYR A 200 " --> pdb=" O   VAL A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 222
    Processing helix  chain 'B' and resid 34 through 39
      removed outlier: 4.276A  pdb=" N   LEU B  38 " --> pdb=" O   TYR B  35 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLU B  39 " --> pdb=" O   GLY B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 76
      removed outlier: 3.914A  pdb=" N   HIS B  55 " --> pdb=" O   HIS B  51 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   ALA B  56 " --> pdb=" O   SER B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 105
      Proline residue:  B  86  - end of helix
      removed outlier: 3.628A  pdb=" N   THR B 103 " --> pdb=" O   SER B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 126
    Processing helix  chain 'B' and resid 127 through 142
    Processing helix  chain 'B' and resid 169 through 174
    Processing helix  chain 'B' and resid 185 through 188
    Processing helix  chain 'B' and resid 189 through 194
    Processing helix  chain 'B' and resid 196 through 205
      removed outlier: 3.516A  pdb=" N   TYR B 200 " --> pdb=" O   VAL B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 222
    Processing helix  chain 'C' and resid 34 through 39
      removed outlier: 4.276A  pdb=" N   LEU C  38 " --> pdb=" O   TYR C  35 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLU C  39 " --> pdb=" O   GLY C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 76
      removed outlier: 3.915A  pdb=" N   HIS C  55 " --> pdb=" O   HIS C  51 " (cutoff:3.500A)
      removed outlier: 4.588A  pdb=" N   ALA C  56 " --> pdb=" O   SER C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 77 through 105
      Proline residue:  C  86  - end of helix
      removed outlier: 3.627A  pdb=" N   THR C 103 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 126
    Processing helix  chain 'C' and resid 127 through 142
    Processing helix  chain 'C' and resid 169 through 174
    Processing helix  chain 'C' and resid 185 through 188
    Processing helix  chain 'C' and resid 189 through 194
    Processing helix  chain 'C' and resid 196 through 205
      removed outlier: 3.517A  pdb=" N   TYR C 200 " --> pdb=" O   VAL C 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 222
    Processing helix  chain 'D' and resid 34 through 39
      removed outlier: 4.275A  pdb=" N   LEU D  38 " --> pdb=" O   TYR D  35 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLU D  39 " --> pdb=" O   GLY D  36 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 43 through 76
      removed outlier: 3.915A  pdb=" N   HIS D  55 " --> pdb=" O   HIS D  51 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   ALA D  56 " --> pdb=" O   SER D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 77 through 105
      Proline residue:  D  86  - end of helix
      removed outlier: 3.628A  pdb=" N   THR D 103 " --> pdb=" O   SER D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 126
    Processing helix  chain 'D' and resid 127 through 142
    Processing helix  chain 'D' and resid 169 through 174
    Processing helix  chain 'D' and resid 185 through 188
    Processing helix  chain 'D' and resid 189 through 194
    Processing helix  chain 'D' and resid 196 through 205
      removed outlier: 3.517A  pdb=" N   TYR D 200 " --> pdb=" O   VAL D 196 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 222
    Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 165
      removed outlier: 7.322A  pdb=" N   GLY A 146 " --> pdb=" O   ASP A 183 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   ASP A 183 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   GLY A 148 " --> pdb=" O   GLY A 181 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   GLY A 181 " --> pdb=" O   GLY A 148 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU A 150 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 158 through 165
      removed outlier: 7.323A  pdb=" N   GLY B 146 " --> pdb=" O   ASP B 183 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   ASP B 183 " --> pdb=" O   GLY B 146 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   GLY B 148 " --> pdb=" O   GLY B 181 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   GLY B 181 " --> pdb=" O   GLY B 148 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU B 150 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 158 through 165
      removed outlier: 7.323A  pdb=" N   GLY C 146 " --> pdb=" O   ASP C 183 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   ASP C 183 " --> pdb=" O   GLY C 146 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   GLY C 148 " --> pdb=" O   GLY C 181 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   GLY C 181 " --> pdb=" O   GLY C 148 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU C 150 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 158 through 165
      removed outlier: 7.322A  pdb=" N   GLY D 146 " --> pdb=" O   ASP D 183 " (cutoff:3.500A)
      removed outlier: 5.342A  pdb=" N   ASP D 183 " --> pdb=" O   GLY D 146 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   GLY D 148 " --> pdb=" O   GLY D 181 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   GLY D 181 " --> pdb=" O   GLY D 148 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU D 150 " --> pdb=" O   LEU D 179 " (cutoff:3.500A)

    404 hydrogen bonds defined for protein.
    1164 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: 1.55

  Time building geometry restraints manager: 1.84 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2041
        1.34 -     1.46: 1253
        1.46 -     1.57: 3094
        1.57 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 6412
  Sorted by residual:
  bond pdb=" CA  LYS D 221 "
       pdb=" C   LYS D 221 "
    ideal  model  delta    sigma   weight residual
    1.524  1.508  0.016 1.28e-02 6.10e+03 1.61e+00
  bond pdb=" CA  VAL A 196 "
       pdb=" CB  VAL A 196 "
    ideal  model  delta    sigma   weight residual
    1.527  1.543 -0.016 1.31e-02 5.83e+03 1.45e+00
  bond pdb=" CA  LYS C 221 "
       pdb=" C   LYS C 221 "
    ideal  model  delta    sigma   weight residual
    1.524  1.509  0.015 1.28e-02 6.10e+03 1.45e+00
  bond pdb=" CA  LYS B 221 "
       pdb=" C   LYS B 221 "
    ideal  model  delta    sigma   weight residual
    1.524  1.509  0.015 1.28e-02 6.10e+03 1.45e+00
  bond pdb=" CA  VAL B 196 "
       pdb=" CB  VAL B 196 "
    ideal  model  delta    sigma   weight residual
    1.527  1.542 -0.016 1.31e-02 5.83e+03 1.41e+00
  ... (remaining 6407 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 8176
        0.98 -     1.97: 419
        1.97 -     2.95: 89
        2.95 -     3.93: 28
        3.93 -     4.92: 12
  Bond angle restraints: 8724
  Sorted by residual:
  angle pdb=" C   VAL A 196 "
        pdb=" N   ARG A 197 "
        pdb=" CA  ARG A 197 "
      ideal   model   delta    sigma   weight residual
     120.09  124.62   -4.53 1.25e+00 6.40e-01 1.31e+01
  angle pdb=" C   VAL B 196 "
        pdb=" N   ARG B 197 "
        pdb=" CA  ARG B 197 "
      ideal   model   delta    sigma   weight residual
     120.09  124.61   -4.52 1.25e+00 6.40e-01 1.31e+01
  angle pdb=" C   VAL D 196 "
        pdb=" N   ARG D 197 "
        pdb=" CA  ARG D 197 "
      ideal   model   delta    sigma   weight residual
     120.09  124.61   -4.52 1.25e+00 6.40e-01 1.31e+01
  angle pdb=" C   VAL C 196 "
        pdb=" N   ARG C 197 "
        pdb=" CA  ARG C 197 "
      ideal   model   delta    sigma   weight residual
     120.09  124.58   -4.49 1.25e+00 6.40e-01 1.29e+01
  angle pdb=" N   VAL C 184 "
        pdb=" CA  VAL C 184 "
        pdb=" C   VAL C 184 "
      ideal   model   delta    sigma   weight residual
     112.29  109.52    2.77 9.40e-01 1.13e+00 8.66e+00
  ... (remaining 8719 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.49: 3408
       16.49 -    32.99: 256
       32.99 -    49.48: 28
       49.48 -    65.98: 8
       65.98 -    82.47: 4
  Dihedral angle restraints: 3704
    sinusoidal: 1448
      harmonic: 2256
  Sorted by residual:
  dihedral pdb=" CA  TRP B 149 "
           pdb=" C   TRP B 149 "
           pdb=" N   LEU B 150 "
           pdb=" CA  LEU B 150 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.65   18.35     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  TRP C 149 "
           pdb=" C   TRP C 149 "
           pdb=" N   LEU C 150 "
           pdb=" CA  LEU C 150 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.70   18.30     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  TRP D 149 "
           pdb=" C   TRP D 149 "
           pdb=" N   LEU D 150 "
           pdb=" CA  LEU D 150 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.71   18.29     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 3701 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 467
       0.026 -    0.052: 286
       0.052 -    0.078: 111
       0.078 -    0.104: 24
       0.104 -    0.131: 16
  Chirality restraints: 904
  Sorted by residual:
  chirality pdb=" CA  ILE A 182 "
            pdb=" N   ILE A 182 "
            pdb=" C   ILE A 182 "
            pdb=" CB  ILE A 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.26e-01
  chirality pdb=" CA  ILE C 182 "
            pdb=" N   ILE C 182 "
            pdb=" C   ILE C 182 "
            pdb=" CB  ILE C 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.07e-01
  chirality pdb=" CA  ILE D 182 "
            pdb=" N   ILE D 182 "
            pdb=" C   ILE D 182 "
            pdb=" CB  ILE D 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.06e-01
  ... (remaining 901 not shown)

  Planarity restraints: 1140
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG D 197 "    0.026 5.00e-02 4.00e+02   3.92e-02 2.46e+00
        pdb=" N   PRO D 198 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D 198 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 198 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 197 "    0.026 5.00e-02 4.00e+02   3.90e-02 2.43e+00
        pdb=" N   PRO B 198 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO B 198 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 198 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 197 "   -0.026 5.00e-02 4.00e+02   3.89e-02 2.42e+00
        pdb=" N   PRO C 198 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO C 198 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C 198 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1137 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.48: 36
        2.48 -     3.09: 4537
        3.09 -     3.69: 9955
        3.69 -     4.30: 15215
        4.30 -     4.90: 25365
  Nonbonded interactions: 55108
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP C 183 "
            pdb="MN    MN C 301 "
     model   vdw
     1.880 2.320
  nonbonded pdb=" OD2 ASP B 183 "
            pdb="MN    MN B 301 "
     model   vdw
     1.881 2.320
  nonbonded pdb=" OD2 ASP D 183 "
            pdb="MN    MN D 301 "
     model   vdw
     1.881 2.320
  nonbonded pdb=" OD2 ASP A 183 "
            pdb="MN    MN A 301 "
     model   vdw
     1.881 2.320
  nonbonded pdb=" NE2 HIS D  50 "
            pdb="MN    MN D 301 "
     model   vdw
     2.017 2.400
  ... (remaining 55103 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

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:             0.660
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     16.940
  Find NCS groups from input model:        0.120
  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:10.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6412  Z= 0.246
  Angle     :  0.551   4.917   8724  Z= 0.324
  Chirality :  0.039   0.131    904
  Planarity :  0.004   0.039   1140
  Dihedral  : 11.977  82.471   2272
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.29), residues: 784
  helix:  0.78 (0.23), residues: 504
  sheet:  1.20 (0.52), residues: 72
  loop : -0.02 (0.44), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 147 
 HIS   0.004   0.001   HIS D 187 
 PHE   0.005   0.001   PHE B  90 
 TYR   0.023   0.002   TYR C  69 
 ARG   0.002   0.000   ARG A 197 

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.754 
Fit side-chains
REVERT: A   70 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7843 (tm-30)
REVERT: A  124 ASP cc_start: 0.8531 (m-30) cc_final: 0.8160 (m-30)
REVERT: A  200 TYR cc_start: 0.9364 (t80) cc_final: 0.9120 (t80)
REVERT: B   70 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7815 (tm-30)
REVERT: B  124 ASP cc_start: 0.8508 (m-30) cc_final: 0.8105 (m-30)
REVERT: B  200 TYR cc_start: 0.9356 (t80) cc_final: 0.9143 (t80)
REVERT: C   70 GLN cc_start: 0.8389 (tm-30) cc_final: 0.7924 (tm-30)
REVERT: C  124 ASP cc_start: 0.8491 (m-30) cc_final: 0.8071 (m-30)
REVERT: C  200 TYR cc_start: 0.9358 (t80) cc_final: 0.9097 (t80)
REVERT: D   70 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7850 (tm-30)
REVERT: D  124 ASP cc_start: 0.8481 (m-30) cc_final: 0.8072 (m-30)
REVERT: D  200 TYR cc_start: 0.9355 (t80) cc_final: 0.9142 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 1.1904
  time to fit residues: 162.3089
Evaluate side-chains
  105 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
B  81 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.083509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.075145 restraints weight = 12182.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 2.01
r_work: 0.2884 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2764 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   6412  Z= 0.326
  Angle     :  0.571   5.103   8724  Z= 0.309
  Chirality :  0.042   0.119    904
  Planarity :  0.004   0.038   1140
  Dihedral  :  7.239  84.175    844
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  8.07 %
    Favored  : 90.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.30), residues: 784
  helix:  0.83 (0.23), residues: 508
  sheet:  1.75 (0.60), residues: 72
  loop :  0.30 (0.45), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 147 
 HIS   0.004   0.001   HIS D 187 
 PHE   0.007   0.002   PHE D 101 
 TYR   0.010   0.002   TYR A  33 
 ARG   0.002   0.000   ARG D 197 

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 0.721 
Fit side-chains
REVERT: A   48 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8220 (tm-30)
REVERT: A   70 GLN cc_start: 0.8286 (tm-30) cc_final: 0.7792 (tm-30)
REVERT: A  200 TYR cc_start: 0.9406 (t80) cc_final: 0.9136 (t80)
REVERT: A  202 LYS cc_start: 0.9043 (ttmt) cc_final: 0.8822 (tptm)
REVERT: A  218 MET cc_start: 0.8074 (tpp) cc_final: 0.7845 (mpp)
REVERT: B   70 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7811 (tm-30)
REVERT: B  200 TYR cc_start: 0.9422 (t80) cc_final: 0.9198 (t80)
REVERT: B  202 LYS cc_start: 0.9060 (ttmt) cc_final: 0.8826 (tptm)
REVERT: C   48 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8226 (tm-30)
REVERT: C   70 GLN cc_start: 0.8302 (tm-30) cc_final: 0.7809 (tm-30)
REVERT: C  200 TYR cc_start: 0.9422 (t80) cc_final: 0.9196 (t80)
REVERT: C  202 LYS cc_start: 0.9061 (ttmt) cc_final: 0.8828 (tptm)
REVERT: D   48 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8219 (tm-30)
REVERT: D   70 GLN cc_start: 0.8222 (tm-30) cc_final: 0.7703 (tm-30)
REVERT: D  200 TYR cc_start: 0.9404 (t80) cc_final: 0.9177 (t80)
REVERT: D  202 LYS cc_start: 0.9057 (ttmt) cc_final: 0.8821 (tptm)
  outliers start: 11
  outliers final: 7
  residues processed: 139
  average time/residue: 1.3050
  time to fit residues: 189.5272
Evaluate side-chains
  107 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue  106 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 206 ASN
B 206 ASN
C 206 ASN
D 206 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.086808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.078615 restraints weight = 12391.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 1.99
r_work: 0.2998 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8560
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6412  Z= 0.217
  Angle     :  0.510   5.020   8724  Z= 0.274
  Chirality :  0.040   0.121    904
  Planarity :  0.004   0.037   1140
  Dihedral  :  7.116  83.774    844
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 10.13 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.30), residues: 784
  helix:  0.84 (0.22), residues: 508
  sheet:  1.72 (0.63), residues: 72
  loop :  0.25 (0.45), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 147 
 HIS   0.002   0.001   HIS D 187 
 PHE   0.005   0.001   PHE D 101 
 TYR   0.009   0.001   TYR D  33 
 ARG   0.001   0.000   ARG D 216 

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.717 
Fit side-chains
REVERT: A   48 GLN cc_start: 0.8971 (tm-30) cc_final: 0.8544 (tm-30)
REVERT: A   70 GLN cc_start: 0.8487 (tm-30) cc_final: 0.7932 (tm-30)
REVERT: A  200 TYR cc_start: 0.9561 (t80) cc_final: 0.9334 (t80)
REVERT: A  211 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8308 (tp30)
REVERT: B   48 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8551 (tm-30)
REVERT: B   70 GLN cc_start: 0.8494 (tm-30) cc_final: 0.7937 (tm-30)
REVERT: B  200 TYR cc_start: 0.9561 (t80) cc_final: 0.9332 (t80)
REVERT: B  211 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8282 (tp30)
REVERT: B  218 MET cc_start: 0.8487 (tpp) cc_final: 0.8286 (mpp)
REVERT: C   48 GLN cc_start: 0.8976 (tm-30) cc_final: 0.8554 (tm-30)
REVERT: C   70 GLN cc_start: 0.8500 (tm-30) cc_final: 0.7952 (tm-30)
REVERT: C  200 TYR cc_start: 0.9556 (t80) cc_final: 0.9329 (t80)
REVERT: C  211 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8297 (tp30)
REVERT: C  218 MET cc_start: 0.8474 (tpp) cc_final: 0.8271 (mpp)
REVERT: D   48 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8543 (tm-30)
REVERT: D   70 GLN cc_start: 0.8474 (tm-30) cc_final: 0.7916 (tm-30)
REVERT: D  200 TYR cc_start: 0.9560 (t80) cc_final: 0.9320 (t80)
REVERT: D  211 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8303 (tp30)
  outliers start: 22
  outliers final: 13
  residues processed: 123
  average time/residue: 1.2767
  time to fit residues: 164.3168
Evaluate side-chains
  116 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  199 ASP
Chi-restraints excluded: chain D residue  103 THR
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  199 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 74 optimal weight:    0.4980
   chunk 53 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0070
   chunk 59 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.4998

-------------------------------------------------------------------------------
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 = 0.3272 r_free = 0.3272 target = 0.088390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.079987 restraints weight = 12512.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 2.02
r_work: 0.3024 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.1853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6412  Z= 0.178
  Angle     :  0.494   4.962   8724  Z= 0.265
  Chirality :  0.039   0.121    904
  Planarity :  0.004   0.038   1140
  Dihedral  :  7.089  83.719    844
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 12.82 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.29), residues: 784
  helix:  0.86 (0.22), residues: 508
  sheet:  1.49 (0.58), residues: 80
  loop :  0.30 (0.45), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 147 
 HIS   0.002   0.001   HIS B  54 
 PHE   0.004   0.001   PHE D 101 
 TYR   0.007   0.001   TYR A  33 
 ARG   0.001   0.000   ARG D 216 

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.752 
Fit side-chains
REVERT: A   70 GLN cc_start: 0.8449 (tm-30) cc_final: 0.7923 (tm-30)
REVERT: A  211 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8296 (tp30)
REVERT: A  218 MET cc_start: 0.8521 (tpp) cc_final: 0.8255 (mpp)
REVERT: B   48 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8566 (tm-30)
REVERT: B   70 GLN cc_start: 0.8462 (tm-30) cc_final: 0.7935 (tm-30)
REVERT: B  211 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8268 (tp30)
REVERT: C   48 GLN cc_start: 0.8993 (tm-30) cc_final: 0.8555 (tm-30)
REVERT: C   70 GLN cc_start: 0.8510 (tm-30) cc_final: 0.7991 (tm-30)
REVERT: C  211 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8264 (tp30)
REVERT: D   70 GLN cc_start: 0.8460 (tm-30) cc_final: 0.7943 (tm-30)
REVERT: D  200 TYR cc_start: 0.9551 (t80) cc_final: 0.9343 (t80)
REVERT: D  211 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8287 (tp30)
  outliers start: 19
  outliers final: 17
  residues processed: 138
  average time/residue: 1.1046
  time to fit residues: 160.6512
Evaluate side-chains
  121 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  199 ASP
Chi-restraints excluded: chain D residue  103 THR
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  133 GLU
Chi-restraints excluded: chain D residue  199 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 15 optimal weight:    0.3980
   chunk 66 optimal weight:    0.4980
   chunk 70 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3268 r_free = 0.3268 target = 0.088061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.079767 restraints weight = 12402.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 2.00
r_work: 0.3012 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.2013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6412  Z= 0.195
  Angle     :  0.506   4.994   8724  Z= 0.269
  Chirality :  0.039   0.121    904
  Planarity :  0.004   0.037   1140
  Dihedral  :  7.057  83.579    844
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 13.61 %
    Favored  : 83.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.29), residues: 784
  helix:  0.92 (0.22), residues: 508
  sheet:  1.69 (0.63), residues: 72
  loop :  0.27 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 147 
 HIS   0.002   0.001   HIS D 187 
 PHE   0.005   0.001   PHE D 101 
 TYR   0.008   0.001   TYR D  33 
 ARG   0.001   0.000   ARG C 156 

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.787 
Fit side-chains
REVERT: A   70 GLN cc_start: 0.8519 (tm-30) cc_final: 0.7991 (tm-30)
REVERT: A  211 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8356 (tp30)
REVERT: A  218 MET cc_start: 0.8586 (tpp) cc_final: 0.8341 (mpp)
REVERT: B   70 GLN cc_start: 0.8523 (tm-30) cc_final: 0.7997 (tm-30)
REVERT: B  211 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8313 (tp30)
REVERT: B  218 MET cc_start: 0.8592 (tpp) cc_final: 0.8274 (mpp)
REVERT: C   70 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8008 (tm-30)
REVERT: C  211 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8295 (tp30)
REVERT: C  218 MET cc_start: 0.8594 (tpp) cc_final: 0.8272 (mpp)
REVERT: D   70 GLN cc_start: 0.8510 (tm-30) cc_final: 0.7990 (tm-30)
REVERT: D  211 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8321 (tp30)
REVERT: D  218 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8402 (mpp)
  outliers start: 21
  outliers final: 19
  residues processed: 127
  average time/residue: 1.1852
  time to fit residues: 158.1475
Evaluate side-chains
  124 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  199 ASP
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  133 GLU
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  199 ASP
Chi-restraints excluded: chain D residue  218 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0060
   chunk 9 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 28 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0370
   overall best weight:    0.4274

-------------------------------------------------------------------------------
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 = 0.3216 r_free = 0.3216 target = 0.086455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.076595 restraints weight = 12388.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 2.36
r_work: 0.2925 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6412  Z= 0.173
  Angle     :  0.503   4.931   8724  Z= 0.268
  Chirality :  0.038   0.119    904
  Planarity :  0.004   0.037   1140
  Dihedral  :  7.039  83.416    844
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 12.97 %
    Favored  : 82.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.29), residues: 784
  helix:  0.93 (0.22), residues: 508
  sheet:  1.59 (0.58), residues: 80
  loop :  0.26 (0.45), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 147 
 HIS   0.002   0.001   HIS D 187 
 PHE   0.004   0.001   PHE D 101 
 TYR   0.007   0.001   TYR A  33 
 ARG   0.001   0.000   ARG B 197 

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 126
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A   70 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7665 (tm-30)
REVERT: A  119 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8356 (mp0)
REVERT: A  200 TYR cc_start: 0.9420 (t80) cc_final: 0.9181 (t80)
REVERT: A  211 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8008 (tp30)
REVERT: A  218 MET cc_start: 0.8100 (tpp) cc_final: 0.7867 (mpp)
REVERT: B   70 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7656 (tm-30)
REVERT: B  119 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8404 (mp0)
REVERT: B  200 TYR cc_start: 0.9420 (t80) cc_final: 0.9179 (t80)
REVERT: B  211 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7947 (tp30)
REVERT: B  218 MET cc_start: 0.8083 (tpp) cc_final: 0.7735 (mpp)
REVERT: C   70 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7724 (tm-30)
REVERT: C  119 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8391 (mp0)
REVERT: C  200 TYR cc_start: 0.9426 (t80) cc_final: 0.9190 (t80)
REVERT: C  211 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7946 (tp30)
REVERT: C  218 MET cc_start: 0.8018 (tpp) cc_final: 0.7637 (mpp)
REVERT: D   70 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7709 (tm-30)
REVERT: D  119 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8418 (mp0)
REVERT: D  211 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7958 (tp30)
REVERT: D  218 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7855 (mpp)
  outliers start: 29
  outliers final: 18
  residues processed: 142
  average time/residue: 1.1215
  time to fit residues: 167.5121
Evaluate side-chains
  130 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  199 ASP
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue  103 THR
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  199 ASP
Chi-restraints excluded: chain D residue  218 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 56 optimal weight:    0.3980
   chunk 26 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 68 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3213 r_free = 0.3213 target = 0.086690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.077581 restraints weight = 12179.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 2.24
r_work: 0.2937 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6412  Z= 0.197
  Angle     :  0.505   5.009   8724  Z= 0.267
  Chirality :  0.039   0.121    904
  Planarity :  0.004   0.037   1140
  Dihedral  :  7.015  83.400    844
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.03 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.29), residues: 784
  helix:  1.00 (0.22), residues: 508
  sheet:  1.62 (0.63), residues: 72
  loop :  0.23 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 147 
 HIS   0.002   0.001   HIS D 187 
 PHE   0.005   0.001   PHE C 101 
 TYR   0.008   0.001   TYR B  33 
 ARG   0.001   0.000   ARG D 197 

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.808 
Fit side-chains
REVERT: A   70 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7659 (tm-30)
REVERT: A  200 TYR cc_start: 0.9415 (t80) cc_final: 0.9163 (t80)
REVERT: A  211 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8075 (tp30)
REVERT: A  218 MET cc_start: 0.8000 (tpp) cc_final: 0.7734 (mpp)
REVERT: B   70 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7663 (tm-30)
REVERT: B  119 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8408 (mp0)
REVERT: B  200 TYR cc_start: 0.9430 (t80) cc_final: 0.9211 (t80)
REVERT: B  211 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8026 (tp30)
REVERT: B  218 MET cc_start: 0.7961 (tpp) cc_final: 0.7676 (mpp)
REVERT: C   70 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7710 (tm-30)
REVERT: C  119 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8399 (mp0)
REVERT: C  200 TYR cc_start: 0.9421 (t80) cc_final: 0.9167 (t80)
REVERT: C  211 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8031 (tp30)
REVERT: D   70 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7700 (tm-30)
REVERT: D  119 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8395 (mp0)
REVERT: D  200 TYR cc_start: 0.9424 (t80) cc_final: 0.9223 (t80)
REVERT: D  211 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8060 (tp30)
REVERT: D  218 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7631 (mpp)
  outliers start: 19
  outliers final: 18
  residues processed: 122
  average time/residue: 1.2041
  time to fit residues: 154.4106
Evaluate side-chains
  127 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  199 ASP
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue  103 THR
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  199 ASP
Chi-restraints excluded: chain D residue  218 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 70 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 47 optimal weight:    0.2980
   chunk 15 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0770
   chunk 55 optimal weight:    0.3980
   chunk 57 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.3938

-------------------------------------------------------------------------------
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 = 0.3235 r_free = 0.3235 target = 0.088023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.078983 restraints weight = 11999.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 2.23
r_work: 0.2938 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2812 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6412  Z= 0.169
  Angle     :  0.511   4.927   8724  Z= 0.271
  Chirality :  0.038   0.119    904
  Planarity :  0.004   0.037   1140
  Dihedral  :  7.013  83.577    844
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 14.72 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.29), residues: 784
  helix:  1.01 (0.22), residues: 508
  sheet:  1.64 (0.63), residues: 72
  loop :  0.26 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 147 
 HIS   0.002   0.001   HIS C 187 
 PHE   0.004   0.001   PHE C 101 
 TYR   0.007   0.001   TYR D 200 
 ARG   0.001   0.000   ARG B 197 

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 0.703 
Fit side-chains
REVERT: A   70 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7758 (tm-30)
REVERT: A  119 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8437 (mp0)
REVERT: A  200 TYR cc_start: 0.9441 (t80) cc_final: 0.9193 (t80)
REVERT: A  211 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8170 (tp30)
REVERT: A  218 MET cc_start: 0.8150 (tpp) cc_final: 0.7795 (mpp)
REVERT: B   70 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7768 (tm-30)
REVERT: B  119 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8455 (mp0)
REVERT: B  200 TYR cc_start: 0.9433 (t80) cc_final: 0.9222 (t80)
REVERT: B  211 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8130 (tp30)
REVERT: C   70 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7772 (tm-30)
REVERT: C  119 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8443 (mp0)
REVERT: C  200 TYR cc_start: 0.9441 (t80) cc_final: 0.9191 (t80)
REVERT: C  211 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8137 (tp30)
REVERT: C  218 MET cc_start: 0.8077 (mpp) cc_final: 0.7750 (mpp)
REVERT: D   70 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7776 (tm-30)
REVERT: D  119 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8459 (mp0)
REVERT: D  200 TYR cc_start: 0.9449 (t80) cc_final: 0.9246 (t80)
REVERT: D  211 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8136 (tp30)
REVERT: D  218 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7828 (mpp)
  outliers start: 23
  outliers final: 26
  residues processed: 131
  average time/residue: 1.1110
  time to fit residues: 153.1249
Evaluate side-chains
  142 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue   34 ASP
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue   34 ASP
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  199 ASP
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue   34 ASP
Chi-restraints excluded: chain D residue  103 THR
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  133 GLU
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  199 ASP
Chi-restraints excluded: chain D residue  218 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   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 = 0.3194 r_free = 0.3194 target = 0.085410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.076190 restraints weight = 12247.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 2.28
r_work: 0.2892 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6412  Z= 0.228
  Angle     :  0.527   5.027   8724  Z= 0.278
  Chirality :  0.040   0.117    904
  Planarity :  0.004   0.036   1140
  Dihedral  :  6.978  82.788    844
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 15.19 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.30), residues: 784
  helix:  1.09 (0.23), residues: 508
  sheet:  1.57 (0.62), residues: 72
  loop :  0.29 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 147 
 HIS   0.003   0.001   HIS D 187 
 PHE   0.006   0.001   PHE D 101 
 TYR   0.009   0.002   TYR D  33 
 ARG   0.001   0.000   ARG B 123 

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.754 
Fit side-chains
REVERT: A   70 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7704 (tm-30)
REVERT: A  200 TYR cc_start: 0.9416 (t80) cc_final: 0.9192 (t80)
REVERT: A  211 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8071 (tp30)
REVERT: B   70 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7716 (tm-30)
REVERT: B  200 TYR cc_start: 0.9400 (t80) cc_final: 0.9154 (t80)
REVERT: B  211 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8040 (tp30)
REVERT: B  218 MET cc_start: 0.8022 (tpp) cc_final: 0.7610 (mpp)
REVERT: C   70 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7721 (tm-30)
REVERT: C  200 TYR cc_start: 0.9415 (t80) cc_final: 0.9191 (t80)
REVERT: C  211 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8023 (tp30)
REVERT: C  218 MET cc_start: 0.8034 (tpp) cc_final: 0.7750 (mpp)
REVERT: D   70 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7717 (tm-30)
REVERT: D  200 TYR cc_start: 0.9416 (t80) cc_final: 0.9180 (t80)
REVERT: D  211 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8026 (tp30)
  outliers start: 25
  outliers final: 24
  residues processed: 124
  average time/residue: 1.1621
  time to fit residues: 151.5058
Evaluate side-chains
  132 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  199 ASP
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue  103 THR
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  133 GLU
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  199 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 57 optimal weight:    0.0020
   chunk 59 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   chunk 18 optimal weight:    0.2980
   chunk 58 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 64 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.4988

-------------------------------------------------------------------------------
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 = 0.3236 r_free = 0.3236 target = 0.087486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.077129 restraints weight = 12676.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 2.38
r_work: 0.2941 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6412  Z= 0.194
  Angle     :  0.538   6.074   8724  Z= 0.284
  Chirality :  0.039   0.119    904
  Planarity :  0.004   0.037   1140
  Dihedral  :  6.978  82.866    844
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 15.19 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.29), residues: 784
  helix:  1.08 (0.22), residues: 508
  sheet:  1.55 (0.63), residues: 72
  loop :  0.30 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 147 
 HIS   0.002   0.001   HIS C 187 
 PHE   0.004   0.001   PHE D 101 
 TYR   0.007   0.001   TYR B  33 
 ARG   0.001   0.000   ARG A 156 

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

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

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1568 Ramachandran restraints generated.
    784 Oldfield, 0 Emsley, 784 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.761 
Fit side-chains
REVERT: A   70 GLN cc_start: 0.8357 (tm-30) cc_final: 0.7816 (tm-30)
REVERT: A  119 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8471 (mp0)
REVERT: A  200 TYR cc_start: 0.9484 (t80) cc_final: 0.9270 (t80)
REVERT: A  211 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8151 (tp30)
REVERT: A  218 MET cc_start: 0.8248 (tpp) cc_final: 0.7921 (mpp)
REVERT: B   70 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7820 (tm-30)
REVERT: B  119 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8540 (mp0)
REVERT: B  200 TYR cc_start: 0.9471 (t80) cc_final: 0.9229 (t80)
REVERT: B  211 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8111 (tp30)
REVERT: B  218 MET cc_start: 0.8272 (tpp) cc_final: 0.7992 (mpp)
REVERT: C   70 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7813 (tm-30)
REVERT: C  119 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8528 (mp0)
REVERT: C  200 TYR cc_start: 0.9487 (t80) cc_final: 0.9273 (t80)
REVERT: C  211 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8112 (tp30)
REVERT: C  218 MET cc_start: 0.8309 (tpp) cc_final: 0.8085 (mpp)
REVERT: D   70 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7815 (tm-30)
REVERT: D  119 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8494 (mp0)
REVERT: D  200 TYR cc_start: 0.9472 (t80) cc_final: 0.9233 (t80)
REVERT: D  211 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8111 (tp30)
  outliers start: 24
  outliers final: 24
  residues processed: 130
  average time/residue: 1.0565
  time to fit residues: 144.8089
Evaluate side-chains
  140 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 SER
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  106 SER
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain A residue  196 VAL
Chi-restraints excluded: chain A residue  199 ASP
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  103 THR
Chi-restraints excluded: chain B residue  106 SER
Chi-restraints excluded: chain B residue  133 GLU
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  199 ASP
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue  103 THR
Chi-restraints excluded: chain C residue  106 SER
Chi-restraints excluded: chain C residue  133 GLU
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  199 ASP
Chi-restraints excluded: chain D residue   27 SER
Chi-restraints excluded: chain D residue  103 THR
Chi-restraints excluded: chain D residue  106 SER
Chi-restraints excluded: chain D residue  133 GLU
Chi-restraints excluded: chain D residue  196 VAL
Chi-restraints excluded: chain D residue  199 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 158 HIS
A 160 GLN
C 158 HIS
C 160 GLN
D 158 HIS
D 160 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.083716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.074351 restraints weight = 12707.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 2.33
r_work: 0.2898 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.2281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6412  Z= 0.247
  Angle     :  0.561   9.246   8724  Z= 0.293
  Chirality :  0.040   0.118    904
  Planarity :  0.004   0.036   1140
  Dihedral  :  6.949  82.022    844
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 14.87 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.30), residues: 784
  helix:  1.08 (0.23), residues: 508
  sheet:  1.34 (0.62), residues: 72
  loop :  0.22 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 147 
 HIS   0.003   0.001   HIS C 187 
 PHE   0.005   0.001   PHE C 101 
 TYR   0.009   0.001   TYR B 190 
 ARG   0.001   0.000   ARG D 123 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4340.73 seconds
wall clock time: 75 minutes 1.39 seconds (4501.39 seconds total)