Starting phenix.real_space_refine
on Wed Jul 23 23:13:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ixu_60977/07_2025/9ixu_60977.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ixu_60977/07_2025/9ixu_60977.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ixu_60977/07_2025/9ixu_60977.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ixu_60977/07_2025/9ixu_60977.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ixu_60977/07_2025/9ixu_60977.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ixu_60977/07_2025/9ixu_60977.cif"
  }
  resolution = 3.19
  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=  -0.056 sd=   0.405
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: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    3010      2.51       5
     N     770      2.21       5
     O     834      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 4642
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1054
          Classifications: {'peptide': 138}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 133}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 32
    Chain: "B"
      Number of atoms: 898
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 898
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 2, 'TRANS': 116}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "E"
      Number of atoms: 182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 182
          Classifications: {'peptide': 23}
          Link IDs: {'TRANS': 22}
    Chain: "F"
      Number of atoms: 187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 187
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
    Chain: "C"
      Number of atoms: 1054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 138, 1054
          Classifications: {'peptide': 138}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 133}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 32
    Chain: "D"
      Number of atoms: 898
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 898
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 2, 'TRANS': 116}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 59
          Unresolved non-hydrogen angles: 75
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 32
    Chain: "G"
      Number of atoms: 182
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 182
          Classifications: {'peptide': 23}
          Link IDs: {'TRANS': 22}
    Chain: "H"
      Number of atoms: 187
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 187
          Classifications: {'peptide': 24}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 23}
  Time building chain proxies: 3.74, per 1000 atoms: 0.81
  Number of scatterers: 4642
  At special positions: 0
  Unit cell: (101.65, 82.65, 76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O     834      8.00
     N     770      7.00
     C    3010      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: 1.36
  Conformation dependent library (CDL) restraints added in 615.1 milliseconds
  

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1144

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 0 sheets defined
      89.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 54 through 73
    Processing helix  chain 'A' and resid 73 through 81
    Processing helix  chain 'A' and resid 87 through 100
      removed outlier: 3.656A  pdb=" N   VAL A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 128
    Processing helix  chain 'A' and resid 130 through 153
    Processing helix  chain 'A' and resid 157 through 162
    Processing helix  chain 'A' and resid 163 through 165
      No H-bonds generated for 'chain 'A' and resid 163 through 165'
    Processing helix  chain 'A' and resid 170 through 187
      removed outlier: 3.730A  pdb=" N   ILE A 187 " --> pdb=" O   ALA A 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 72
    Processing helix  chain 'B' and resid 73 through 82
    Processing helix  chain 'B' and resid 87 through 100
      removed outlier: 3.685A  pdb=" N   VAL B  91 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 128
    Processing helix  chain 'B' and resid 128 through 149
      removed outlier: 3.764A  pdb=" N   LEU B 149 " --> pdb=" O   ARG B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 190
    Processing helix  chain 'E' and resid 170 through 191
    Processing helix  chain 'F' and resid 170 through 192
    Processing helix  chain 'C' and resid 55 through 73
    Processing helix  chain 'C' and resid 73 through 81
    Processing helix  chain 'C' and resid 87 through 100
      removed outlier: 3.607A  pdb=" N   VAL C  91 " --> pdb=" O   SER C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 128
    Processing helix  chain 'C' and resid 130 through 153
    Processing helix  chain 'C' and resid 157 through 162
    Processing helix  chain 'C' and resid 163 through 165
      No H-bonds generated for 'chain 'C' and resid 163 through 165'
    Processing helix  chain 'C' and resid 170 through 187
      removed outlier: 3.730A  pdb=" N   ILE C 187 " --> pdb=" O   ALA C 183 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 54 through 72
    Processing helix  chain 'D' and resid 73 through 82
    Processing helix  chain 'D' and resid 87 through 100
      removed outlier: 3.685A  pdb=" N   VAL D  91 " --> pdb=" O   SER D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 106 through 128
    Processing helix  chain 'D' and resid 128 through 149
      removed outlier: 3.764A  pdb=" N   LEU D 149 " --> pdb=" O   ARG D 145 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 190
    Processing helix  chain 'G' and resid 170 through 191
    Processing helix  chain 'H' and resid 170 through 192

    407 hydrogen bonds defined for protein.
    1221 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: 1.24

  Time building geometry restraints manager: 1.59 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 754
        1.32 -     1.44: 1264
        1.44 -     1.56: 2658
        1.56 -     1.68: 4
        1.68 -     1.81: 48
  Bond restraints: 4728
  Sorted by residual:
  bond pdb=" C   ASN A 106 "
       pdb=" O   ASN A 106 "
    ideal  model  delta    sigma   weight residual
    1.234  1.283 -0.049 1.22e-02 6.72e+03 1.63e+01
  bond pdb=" C   ASN C 106 "
       pdb=" O   ASN C 106 "
    ideal  model  delta    sigma   weight residual
    1.234  1.283 -0.048 1.22e-02 6.72e+03 1.58e+01
  bond pdb=" C   TRP C 158 "
       pdb=" O   TRP C 158 "
    ideal  model  delta    sigma   weight residual
    1.236  1.281 -0.045 1.15e-02 7.56e+03 1.55e+01
  bond pdb=" C   TRP A 158 "
       pdb=" O   TRP A 158 "
    ideal  model  delta    sigma   weight residual
    1.236  1.281 -0.045 1.15e-02 7.56e+03 1.54e+01
  bond pdb=" C   LEU C  76 "
       pdb=" O   LEU C  76 "
    ideal  model  delta    sigma   weight residual
    1.237  1.194  0.043 1.17e-02 7.31e+03 1.36e+01
  ... (remaining 4723 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 5682
        1.57 -     3.13: 589
        3.13 -     4.70: 109
        4.70 -     6.27: 28
        6.27 -     7.84: 10
  Bond angle restraints: 6418
  Sorted by residual:
  angle pdb=" N   MET B  74 "
        pdb=" CA  MET B  74 "
        pdb=" C   MET B  74 "
      ideal   model   delta    sigma   weight residual
     111.11  118.85   -7.74 1.20e+00 6.94e-01 4.16e+01
  angle pdb=" N   MET D  74 "
        pdb=" CA  MET D  74 "
        pdb=" C   MET D  74 "
      ideal   model   delta    sigma   weight residual
     111.11  118.81   -7.70 1.20e+00 6.94e-01 4.12e+01
  angle pdb=" CA  GLY C 157 "
        pdb=" C   GLY C 157 "
        pdb=" N   TRP C 158 "
      ideal   model   delta    sigma   weight residual
     114.82  122.66   -7.84 1.23e+00 6.61e-01 4.06e+01
  angle pdb=" CA  GLY A 157 "
        pdb=" C   GLY A 157 "
        pdb=" N   TRP A 158 "
      ideal   model   delta    sigma   weight residual
     114.82  122.63   -7.81 1.23e+00 6.61e-01 4.03e+01
  angle pdb=" N   GLU A  69 "
        pdb=" CA  GLU A  69 "
        pdb=" C   GLU A  69 "
      ideal   model   delta    sigma   weight residual
     111.07  105.05    6.02 1.07e+00 8.73e-01 3.17e+01
  ... (remaining 6413 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.91: 2415
        9.91 -    19.82: 212
       19.82 -    29.74: 87
       29.74 -    39.65: 26
       39.65 -    49.56: 20
  Dihedral angle restraints: 2760
    sinusoidal: 1012
      harmonic: 1748
  Sorted by residual:
  dihedral pdb=" CA  PRO C 168 "
           pdb=" C   PRO C 168 "
           pdb=" N   THR C 169 "
           pdb=" CA  THR C 169 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   41.01  -41.01     0      5.00e+00 4.00e-02 6.73e+01
  dihedral pdb=" CA  PRO A 168 "
           pdb=" C   PRO A 168 "
           pdb=" N   THR A 169 "
           pdb=" CA  THR A 169 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   40.49  -40.49     0      5.00e+00 4.00e-02 6.56e+01
  dihedral pdb=" N   VAL B 111 "
           pdb=" CA  VAL B 111 "
           pdb=" CB  VAL B 111 "
           pdb=" CG1 VAL B 111 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  130.44   49.56     3      1.50e+01 4.44e-03 8.79e+00
  ... (remaining 2757 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 569
       0.052 -    0.105: 154
       0.105 -    0.157: 45
       0.157 -    0.210: 6
       0.210 -    0.262: 4
  Chirality restraints: 778
  Sorted by residual:
  chirality pdb=" CA  ASP D  71 "
            pdb=" N   ASP D  71 "
            pdb=" C   ASP D  71 "
            pdb=" CB  ASP D  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" CA  ASP B  71 "
            pdb=" N   ASP B  71 "
            pdb=" C   ASP B  71 "
            pdb=" CB  ASP B  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CA  MET C  74 "
            pdb=" N   MET C  74 "
            pdb=" C   MET C  74 "
            pdb=" CB  MET C  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 775 not shown)

  Planarity restraints: 776
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C 105 "   -0.028 2.00e-02 2.50e+03   5.50e-02 3.02e+01
        pdb=" C   PHE C 105 "    0.095 2.00e-02 2.50e+03
        pdb=" O   PHE C 105 "   -0.036 2.00e-02 2.50e+03
        pdb=" N   ASN C 106 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 105 "    0.027 2.00e-02 2.50e+03   5.46e-02 2.98e+01
        pdb=" C   PHE A 105 "   -0.094 2.00e-02 2.50e+03
        pdb=" O   PHE A 105 "    0.035 2.00e-02 2.50e+03
        pdb=" N   ASN A 106 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET C  79 "   -0.020 2.00e-02 2.50e+03   4.07e-02 1.66e+01
        pdb=" C   MET C  79 "    0.070 2.00e-02 2.50e+03
        pdb=" O   MET C  79 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   ILE C  80 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 773 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 1828
        2.86 -     3.37: 5341
        3.37 -     3.88: 7358
        3.88 -     4.39: 8054
        4.39 -     4.90: 13194
  Nonbonded interactions: 35775
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B 134 "
            pdb=" NE1 TRP C 139 "
     model   vdw
     2.348 3.200
  nonbonded pdb=" O   GLY C 166 "
            pdb=" OG1 THR C 167 "
     model   vdw
     2.366 3.040
  nonbonded pdb=" O   GLY A 166 "
            pdb=" OG1 THR A 167 "
     model   vdw
     2.385 3.040
  nonbonded pdb=" O   TRP C 151 "
            pdb=" N   ASP C 154 "
     model   vdw
     2.397 3.120
  nonbonded pdb=" O   TRP A 151 "
            pdb=" N   ASP A 154 "
     model   vdw
     2.397 3.120
  ... (remaining 35770 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: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 54 through 138 or (resid 139 through 149 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 169 through 190))
  selection = (chain 'B' and (resid 54 through 187 or (resid 188 through 190 and (name N or na \ 
me CA or name C or name O or name CB ))))
  selection = (chain 'C' and (resid 54 through 138 or (resid 139 through 149 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 169 through 190))
  selection = (chain 'D' and (resid 54 through 187 or (resid 188 through 190 and (name N or na \ 
me CA or name C or name O or name CB ))))
}
ncs_group {
  reference = chain 'E'
  selection = (chain 'F' and resid 169 through 191)
  selection = chain 'G'
  selection = (chain 'H' and resid 169 through 191)
}

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:             0.990
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     16.150
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
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      :  0.008   0.049   4728  Z= 0.644
  Angle     :  1.097   7.837   6418  Z= 0.824
  Chirality :  0.055   0.262    778
  Planarity :  0.006   0.055    776
  Dihedral  : 10.625  49.558   1616
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 19.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  5.46 %
    Favored  : 92.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

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: -0.47 (0.29), residues: 588
  helix: -0.00 (0.19), residues: 512
  sheet:  None (None), residues: 0
  loop : -1.50 (0.62), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 107 
 PHE   0.013   0.001   PHE B 176 
 TYR   0.003   0.001   TYR B 115 
 ARG   0.002   0.000   ARG A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16367 (  407)
  hydrogen bonds       : angle       6.44326 ( 1221)
  covalent geometry    : bond        0.00836 ( 4728)
  covalent geometry    : angle       1.09677 ( 6418)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 227
  time to evaluate  : 0.554 
Fit side-chains
REVERT: A   71 ASP cc_start: 0.8226 (t70) cc_final: 0.7970 (t0)
REVERT: F  191 MET cc_start: 0.8570 (mmm) cc_final: 0.8325 (mmt)
REVERT: C   71 ASP cc_start: 0.8129 (t70) cc_final: 0.7872 (t0)
  outliers start: 8
  outliers final: 7
  residues processed: 231
  average time/residue: 0.2397
  time to fit residues: 64.8285
Evaluate side-chains
  184 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 177
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain C residue  133 ILE
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue   83 VAL
Chi-restraints excluded: chain D residue  111 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 16 optimal weight:    0.1980
   chunk 26 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   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 = 0.3076 r_free = 0.3076 target = 0.069244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.060918 restraints weight = 12298.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 1.97
r_work: 0.2766 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.3453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4728  Z= 0.172
  Angle     :  0.561   9.821   6418  Z= 0.313
  Chirality :  0.037   0.147    778
  Planarity :  0.004   0.041    776
  Dihedral  :  6.789  57.486    646
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 15.34 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    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:  3.17 (0.34), residues: 588
  helix:  2.54 (0.22), residues: 524
  sheet:  None (None), residues: 0
  loop : -2.00 (0.68), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 170 
 PHE   0.014   0.002   PHE B 176 
 TYR   0.003   0.001   TYR A 164 
 ARG   0.006   0.001   ARG A 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06234 (  407)
  hydrogen bonds       : angle       3.88956 ( 1221)
  covalent geometry    : bond        0.00354 ( 4728)
  covalent geometry    : angle       0.56113 ( 6418)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 182
  time to evaluate  : 0.519 
Fit side-chains
REVERT: A   71 ASP cc_start: 0.8771 (t70) cc_final: 0.8515 (t0)
REVERT: A   75 GLU cc_start: 0.8193 (tp30) cc_final: 0.7737 (tp30)
REVERT: E  190 LYS cc_start: 0.8636 (mmmm) cc_final: 0.8257 (mttt)
REVERT: F  190 LYS cc_start: 0.9080 (mmmm) cc_final: 0.8857 (tppp)
REVERT: F  191 MET cc_start: 0.8897 (mmm) cc_final: 0.8653 (mmt)
REVERT: C   71 ASP cc_start: 0.8904 (t70) cc_final: 0.8687 (t0)
REVERT: D   90 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7918 (mm-30)
REVERT: G  190 LYS cc_start: 0.8655 (mmmm) cc_final: 0.8361 (mttt)
  outliers start: 24
  outliers final: 16
  residues processed: 196
  average time/residue: 0.2413
  time to fit residues: 55.5528
Evaluate side-chains
  185 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 169
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  125 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain E residue  169 THR
Chi-restraints excluded: chain E residue  191 MET
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain G residue  169 THR
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  190 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 10 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 17 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   chunk 3 optimal weight:    0.3980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
C 104 ASN
D 104 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.068002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.059690 restraints weight = 12641.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 2.00
r_work: 0.2707 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.3985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4728  Z= 0.155
  Angle     :  0.506   5.423   6418  Z= 0.286
  Chirality :  0.035   0.143    778
  Planarity :  0.004   0.062    776
  Dihedral  :  5.820  58.812    642
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 17.86 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    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:  4.05 (0.35), residues: 588
  helix:  3.08 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.69 (0.75), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 170 
 PHE   0.016   0.001   PHE B 176 
 TYR   0.003   0.001   TYR C 164 
 ARG   0.003   0.000   ARG D  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05526 (  407)
  hydrogen bonds       : angle       3.61179 ( 1221)
  covalent geometry    : bond        0.00327 ( 4728)
  covalent geometry    : angle       0.50626 ( 6418)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 170
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8283 (tp30) cc_final: 0.7818 (tp30)
REVERT: B  122 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8505 (tt)
REVERT: D  109 ARG cc_start: 0.8714 (mtt180) cc_final: 0.8430 (mtt180)
  outliers start: 26
  outliers final: 17
  residues processed: 187
  average time/residue: 0.2423
  time to fit residues: 52.9429
Evaluate side-chains
  183 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 165
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 THR
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain E residue  169 THR
Chi-restraints excluded: chain E residue  191 MET
Chi-restraints excluded: chain C residue   56 THR
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  135 THR
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain G residue  169 THR
Chi-restraints excluded: chain H residue  190 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   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 = 0.3022 r_free = 0.3022 target = 0.066790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.058462 restraints weight = 12665.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.2811 rms_B_bonded: 1.98
r_work: 0.2677 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.4317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4728  Z= 0.158
  Angle     :  0.510   5.056   6418  Z= 0.286
  Chirality :  0.036   0.161    778
  Planarity :  0.005   0.054    776
  Dihedral  :  5.663  58.922    642
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 20.80 %
    Favored  : 74.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    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:  4.14 (0.35), residues: 588
  helix:  3.14 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.55 (0.76), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 107 
 PHE   0.017   0.002   PHE B 176 
 TYR   0.003   0.001   TYR C 164 
 ARG   0.007   0.001   ARG A 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05558 (  407)
  hydrogen bonds       : angle       3.52924 ( 1221)
  covalent geometry    : bond        0.00343 ( 4728)
  covalent geometry    : angle       0.51024 ( 6418)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 160
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 SER cc_start: 0.9009 (m) cc_final: 0.8755 (p)
REVERT: B  122 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8574 (tt)
REVERT: F  191 MET cc_start: 0.8914 (mmm) cc_final: 0.8627 (mmp)
REVERT: C  172 THR cc_start: 0.8513 (m) cc_final: 0.8261 (t)
  outliers start: 22
  outliers final: 13
  residues processed: 175
  average time/residue: 0.2513
  time to fit residues: 51.3300
Evaluate side-chains
  174 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 160
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  171 GLN
Chi-restraints excluded: chain E residue  169 THR
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain D residue   71 ASP
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain G residue  169 THR
Chi-restraints excluded: chain H residue  190 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   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 = 0.3024 r_free = 0.3024 target = 0.066940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.058510 restraints weight = 12740.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.2809 rms_B_bonded: 2.00
r_work: 0.2676 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.4464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4728  Z= 0.147
  Angle     :  0.489   5.127   6418  Z= 0.277
  Chirality :  0.035   0.139    778
  Planarity :  0.004   0.047    776
  Dihedral  :  5.288  59.855    639
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 20.17 %
    Favored  : 75.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    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:  4.28 (0.35), residues: 588
  helix:  3.23 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.55 (0.78), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 107 
 PHE   0.015   0.001   PHE B 176 
 TYR   0.003   0.001   TYR C 164 
 ARG   0.007   0.000   ARG A 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05266 (  407)
  hydrogen bonds       : angle       3.44606 ( 1221)
  covalent geometry    : bond        0.00314 ( 4728)
  covalent geometry    : angle       0.48937 ( 6418)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 163
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 SER cc_start: 0.9007 (m) cc_final: 0.8761 (p)
REVERT: B  122 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8578 (tt)
  outliers start: 22
  outliers final: 19
  residues processed: 178
  average time/residue: 0.2584
  time to fit residues: 53.4766
Evaluate side-chains
  180 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 160
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain E residue  169 THR
Chi-restraints excluded: chain C residue   56 THR
Chi-restraints excluded: chain C residue  128 LYS
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue   71 ASP
Chi-restraints excluded: chain D residue  104 ASN
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  133 ILE
Chi-restraints excluded: chain G residue  169 THR
Chi-restraints excluded: chain H residue  190 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 25 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0170
   chunk 14 optimal weight:    0.6980
   chunk 11 optimal weight:    0.2980
   overall best weight:    0.4618

-------------------------------------------------------------------------------
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 = 0.3043 r_free = 0.3043 target = 0.067776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.059331 restraints weight = 12628.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.2836 rms_B_bonded: 2.00
r_work: 0.2704 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.4698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4728  Z= 0.134
  Angle     :  0.488   5.980   6418  Z= 0.271
  Chirality :  0.034   0.142    778
  Planarity :  0.004   0.049    776
  Dihedral  :  4.828  57.952    636
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 21.01 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    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:  4.44 (0.35), residues: 588
  helix:  3.36 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.51 (0.79), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 170 
 PHE   0.012   0.001   PHE B 176 
 TYR   0.003   0.001   TYR C 164 
 ARG   0.004   0.000   ARG A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04713 (  407)
  hydrogen bonds       : angle       3.32668 ( 1221)
  covalent geometry    : bond        0.00283 ( 4728)
  covalent geometry    : angle       0.48839 ( 6418)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 168
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 SER cc_start: 0.9026 (m) cc_final: 0.8781 (p)
REVERT: B  122 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8610 (tt)
REVERT: H  189 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8539 (ttmt)
  outliers start: 24
  outliers final: 16
  residues processed: 183
  average time/residue: 0.2457
  time to fit residues: 52.4332
Evaluate side-chains
  180 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 162
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain E residue  169 THR
Chi-restraints excluded: chain E residue  191 MET
Chi-restraints excluded: chain C residue   56 THR
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue   71 ASP
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain G residue  169 THR
Chi-restraints excluded: chain H residue  189 LYS
Chi-restraints excluded: chain H residue  190 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0040
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.7194

-------------------------------------------------------------------------------
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 = 0.3018 r_free = 0.3018 target = 0.066527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.057994 restraints weight = 12560.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.2798 rms_B_bonded: 2.00
r_work: 0.2665 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.4722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4728  Z= 0.153
  Angle     :  0.523   6.255   6418  Z= 0.290
  Chirality :  0.036   0.170    778
  Planarity :  0.004   0.050    776
  Dihedral  :  4.834  57.296    636
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.23 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 21.64 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    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:  4.34 (0.35), residues: 588
  helix:  3.29 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.52 (0.78), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 170 
 PHE   0.014   0.001   PHE D 176 
 TYR   0.003   0.001   TYR C 164 
 ARG   0.007   0.000   ARG A 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05275 (  407)
  hydrogen bonds       : angle       3.37715 ( 1221)
  covalent geometry    : bond        0.00332 ( 4728)
  covalent geometry    : angle       0.52291 ( 6418)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 162
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 TRP cc_start: 0.8609 (OUTLIER) cc_final: 0.8319 (t-100)
REVERT: A  184 SER cc_start: 0.9038 (m) cc_final: 0.8817 (p)
REVERT: B  122 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8611 (tt)
REVERT: E  190 LYS cc_start: 0.8466 (mmmm) cc_final: 0.8248 (mttt)
REVERT: G  188 TRP cc_start: 0.8699 (t60) cc_final: 0.8469 (t60)
REVERT: H  189 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8557 (ttmt)
  outliers start: 29
  outliers final: 21
  residues processed: 178
  average time/residue: 0.2473
  time to fit residues: 51.4727
Evaluate side-chains
  186 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 TRP
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain E residue  169 THR
Chi-restraints excluded: chain C residue   56 THR
Chi-restraints excluded: chain C residue  128 LYS
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue   71 ASP
Chi-restraints excluded: chain D residue  104 ASN
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  133 ILE
Chi-restraints excluded: chain G residue  169 THR
Chi-restraints excluded: chain H residue  189 LYS
Chi-restraints excluded: chain H residue  190 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 15 optimal weight:    0.3980
   chunk 41 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3014 r_free = 0.3014 target = 0.066251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.057727 restraints weight = 12720.158|
|-----------------------------------------------------------------------------|
r_work (start): 0.2794 rms_B_bonded: 2.03
r_work: 0.2660 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.4809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4728  Z= 0.155
  Angle     :  0.542   6.987   6418  Z= 0.298
  Chirality :  0.036   0.157    778
  Planarity :  0.004   0.051    776
  Dihedral  :  4.883  58.871    636
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.57 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  6.72 %
    Allowed  : 21.01 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    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:  4.30 (0.35), residues: 588
  helix:  3.24 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.53 (0.82), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 170 
 PHE   0.015   0.001   PHE D 176 
 TYR   0.003   0.001   TYR C 164 
 ARG   0.004   0.000   ARG A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05336 (  407)
  hydrogen bonds       : angle       3.39343 ( 1221)
  covalent geometry    : bond        0.00342 ( 4728)
  covalent geometry    : angle       0.54228 ( 6418)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 162
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8419 (tp30) cc_final: 0.7940 (tp30)
REVERT: A  184 SER cc_start: 0.9057 (m) cc_final: 0.8826 (p)
REVERT: B  122 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8615 (tt)
REVERT: C  147 ARG cc_start: 0.8116 (mtp85) cc_final: 0.7886 (mmp80)
REVERT: D  125 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.7999 (mp)
REVERT: G  188 TRP cc_start: 0.8718 (t60) cc_final: 0.8492 (t60)
REVERT: H  189 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8557 (ttmt)
  outliers start: 32
  outliers final: 25
  residues processed: 182
  average time/residue: 0.2488
  time to fit residues: 53.3882
Evaluate side-chains
  189 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 161
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain E residue  169 THR
Chi-restraints excluded: chain C residue   75 GLU
Chi-restraints excluded: chain C residue  128 LYS
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   57 LYS
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue   71 ASP
Chi-restraints excluded: chain D residue  104 ASN
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  133 ILE
Chi-restraints excluded: chain G residue  169 THR
Chi-restraints excluded: chain H residue  189 LYS
Chi-restraints excluded: chain H residue  190 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 5 optimal weight:    0.3980
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3020 r_free = 0.3020 target = 0.066564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.057964 restraints weight = 12756.386|
|-----------------------------------------------------------------------------|
r_work (start): 0.2804 rms_B_bonded: 2.03
r_work: 0.2671 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.4862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4728  Z= 0.154
  Angle     :  0.545   6.749   6418  Z= 0.300
  Chirality :  0.036   0.162    778
  Planarity :  0.005   0.053    776
  Dihedral  :  4.912  59.424    636
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.40 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 23.11 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    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:  4.29 (0.35), residues: 588
  helix:  3.25 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.54 (0.80), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 170 
 PHE   0.014   0.001   PHE D 176 
 TYR   0.003   0.001   TYR C 164 
 ARG   0.007   0.000   ARG A 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05267 (  407)
  hydrogen bonds       : angle       3.38969 ( 1221)
  covalent geometry    : bond        0.00339 ( 4728)
  covalent geometry    : angle       0.54500 ( 6418)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 164
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8400 (tp30) cc_final: 0.7925 (tp30)
REVERT: A  184 SER cc_start: 0.9058 (m) cc_final: 0.8847 (p)
REVERT: B  122 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8618 (tt)
REVERT: D  125 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.7990 (mp)
REVERT: H  189 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8559 (ttmt)
  outliers start: 26
  outliers final: 22
  residues processed: 181
  average time/residue: 0.2404
  time to fit residues: 50.8252
Evaluate side-chains
  188 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 163
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  169 THR
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain E residue  169 THR
Chi-restraints excluded: chain C residue   75 GLU
Chi-restraints excluded: chain C residue  128 LYS
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue   71 ASP
Chi-restraints excluded: chain D residue  104 ASN
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain D residue  133 ILE
Chi-restraints excluded: chain G residue  169 THR
Chi-restraints excluded: chain H residue  189 LYS
Chi-restraints excluded: chain H residue  190 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0020
   chunk 27 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.5788

-------------------------------------------------------------------------------
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 = 0.3032 r_free = 0.3032 target = 0.067178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.058656 restraints weight = 12696.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.2815 rms_B_bonded: 2.00
r_work: 0.2681 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.4982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4728  Z= 0.149
  Angle     :  0.551   6.953   6418  Z= 0.301
  Chirality :  0.035   0.173    778
  Planarity :  0.004   0.052    776
  Dihedral  :  4.867  59.169    636
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.23 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 23.32 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    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:  4.36 (0.35), residues: 588
  helix:  3.29 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.43 (0.82), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 170 
 PHE   0.013   0.001   PHE B 176 
 TYR   0.003   0.001   TYR C 164 
 ARG   0.004   0.000   ARG A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04923 (  407)
  hydrogen bonds       : angle       3.34377 ( 1221)
  covalent geometry    : bond        0.00322 ( 4728)
  covalent geometry    : angle       0.55068 ( 6418)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 164
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8376 (tp30) cc_final: 0.7942 (tp30)
REVERT: A  184 SER cc_start: 0.9063 (m) cc_final: 0.8859 (p)
REVERT: B  122 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8644 (tt)
REVERT: C  147 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7852 (mmp80)
REVERT: D  125 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.7995 (mp)
REVERT: H  189 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8568 (ttmt)
  outliers start: 25
  outliers final: 19
  residues processed: 181
  average time/residue: 0.2450
  time to fit residues: 51.7982
Evaluate side-chains
  185 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 163
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue   71 ASP
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain E residue  169 THR
Chi-restraints excluded: chain C residue   75 GLU
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue   71 ASP
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  121 VAL
Chi-restraints excluded: chain D residue  125 LEU
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain G residue  169 THR
Chi-restraints excluded: chain H residue  189 LYS
Chi-restraints excluded: chain H residue  190 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 50 optimal weight:    5.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.2995 r_free = 0.2995 target = 0.065531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.056984 restraints weight = 12728.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.2776 rms_B_bonded: 2.00
r_work: 0.2639 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.4914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4728  Z= 0.177
  Angle     :  0.581   6.815   6418  Z= 0.317
  Chirality :  0.037   0.163    778
  Planarity :  0.005   0.052    776
  Dihedral  :  4.950  59.984    636
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.57 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 23.32 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    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:  4.22 (0.35), residues: 588
  helix:  3.17 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.38 (0.84), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 170 
 PHE   0.015   0.001   PHE D 176 
 TYR   0.003   0.001   TYR C 164 
 ARG   0.006   0.000   ARG A 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05594 (  407)
  hydrogen bonds       : angle       3.40933 ( 1221)
  covalent geometry    : bond        0.00403 ( 4728)
  covalent geometry    : angle       0.58057 ( 6418)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2523.96 seconds
wall clock time: 44 minutes 0.92 seconds (2640.92 seconds total)