Starting phenix.real_space_refine
on Wed Sep 17 04:54:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ixu_60977/09_2025/9ixu_60977.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ixu_60977/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ixu_60977/09_2025/9ixu_60977.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ixu_60977/09_2025/9ixu_60977.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ixu_60977/09_2025/9ixu_60977.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ixu_60977/09_2025/9ixu_60977.map"
  }
  resolution = 3.19
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.056 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'TRP:plan': 2, 'GLN:plan1': 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: {'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU: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: {'TRP:plan': 2, 'GLN:plan1': 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: {'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU: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: 1.56, per 1000 atoms: 0.34
  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: 0.49
  Conformation dependent library (CDL) restraints added in 224.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.14
  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: 0.68

  Time building geometry restraints manager: 0.66 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: 0.00
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:             1.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.950
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.820
-------------------------------------------------------------------------------
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 : 18.81
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (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
 ARG   0.002   0.000   ARG A 134 
 TYR   0.003   0.001   TYR B 115 
 PHE   0.013   0.001   PHE B 176 
 TRP   0.010   0.001   TRP B 107 

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

*********************** 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  : 0.194 
Fit side-chains
REVERT: A   71 ASP cc_start: 0.8226 (t70) cc_final: 0.8009 (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: 0.7877 (t0)
  outliers start: 8
  outliers final: 7
  residues processed: 231
  average time/residue: 0.1121
  time to fit residues: 30.3716
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  : 0.184 
-------------------------------------------------------------------------------
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 54 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    0.1980
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   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 = 0.3066 r_free = 0.3066 target = 0.068855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.060414 restraints weight = 12518.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.2858 rms_B_bonded: 2.01
r_work: 0.2725 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.3483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4728  Z= 0.170
  Angle     :  0.557   9.998   6418  Z= 0.312
  Chirality :  0.037   0.156    778
  Planarity :  0.004   0.042    776
  Dihedral  :  6.841  58.205    646
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 15.13 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.17 (0.34), residues: 588
  helix:  2.54 (0.22), residues: 524
  sheet:  None (None), residues: 0
  loop : -1.97 (0.68), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 145 
 TYR   0.003   0.001   TYR C 164 
 PHE   0.016   0.002   PHE B 176 
 TRP   0.015   0.001   TRP A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 4728)
  covalent geometry    : angle       0.55656 ( 6418)
  hydrogen bonds       : bond        0.06229 (  407)
  hydrogen bonds       : angle       3.89504 ( 1221)

*********************** 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: 26
    poor density    : 180
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A   71 ASP cc_start: 0.8770 (t70) cc_final: 0.8519 (t0)
REVERT: E  190 LYS cc_start: 0.8653 (mmmm) cc_final: 0.8258 (mttt)
REVERT: F  190 LYS cc_start: 0.9081 (mmmm) cc_final: 0.8853 (tppp)
REVERT: F  191 MET cc_start: 0.8887 (mmm) cc_final: 0.8651 (mmt)
REVERT: C   71 ASP cc_start: 0.8909 (t70) cc_final: 0.8696 (t0)
REVERT: C  139 TRP cc_start: 0.8700 (OUTLIER) cc_final: 0.8497 (m-90)
REVERT: D   90 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7956 (mm-30)
REVERT: D   98 ASP cc_start: 0.9168 (OUTLIER) cc_final: 0.8928 (t0)
REVERT: G  190 LYS cc_start: 0.8666 (mmmm) cc_final: 0.8362 (mttt)
  outliers start: 26
  outliers final: 17
  residues processed: 196
  average time/residue: 0.1174
  time to fit residues: 26.9432
Evaluate side-chains
  187 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 168
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
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  129 VAL
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  139 TRP
Chi-restraints excluded: chain C residue  185 LEU
Chi-restraints excluded: chain D residue   69 GLU
Chi-restraints excluded: chain D residue   98 ASP
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 45 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3034 r_free = 0.3034 target = 0.067384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.059050 restraints weight = 12524.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.2852 rms_B_bonded: 1.98
r_work: 0.2720 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.3953

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= 0.160
  Angle     :  0.515   5.648   6418  Z= 0.292
  Chirality :  0.036   0.141    778
  Planarity :  0.004   0.057    776
  Dihedral  :  5.851  58.302    642
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 18.28 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.92 (0.35), residues: 588
  helix:  3.01 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.78 (0.75), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  89 
 TYR   0.003   0.001   TYR C 164 
 PHE   0.017   0.002   PHE B 176 
 TRP   0.010   0.001   TRP A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4728)
  covalent geometry    : angle       0.51520 ( 6418)
  hydrogen bonds       : bond        0.05777 (  407)
  hydrogen bonds       : angle       3.66241 ( 1221)

*********************** 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
  192 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 168
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8282 (tp30) cc_final: 0.7830 (tp30)
REVERT: B  122 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8488 (tt)
REVERT: E  190 LYS cc_start: 0.8648 (mmmm) cc_final: 0.8252 (mttt)
REVERT: D  109 ARG cc_start: 0.8738 (mtt180) cc_final: 0.8436 (mtt180)
REVERT: H  191 MET cc_start: 0.9033 (mmt) cc_final: 0.8725 (mmm)
  outliers start: 24
  outliers final: 16
  residues processed: 183
  average time/residue: 0.1139
  time to fit residues: 24.3173
Evaluate side-chains
  182 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 165
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LEU
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 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 54 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3009 r_free = 0.3009 target = 0.066209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.057854 restraints weight = 12566.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.2796 rms_B_bonded: 1.99
r_work: 0.2661 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.4267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4728  Z= 0.169
  Angle     :  0.523   5.196   6418  Z= 0.295
  Chirality :  0.037   0.183    778
  Planarity :  0.005   0.054    776
  Dihedral  :  5.716  58.102    642
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 19.12 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.99 (0.35), residues: 588
  helix:  3.04 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.61 (0.76), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 145 
 TYR   0.002   0.001   TYR C 164 
 PHE   0.017   0.002   PHE B 176 
 TRP   0.011   0.001   TRP A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 4728)
  covalent geometry    : angle       0.52331 ( 6418)
  hydrogen bonds       : bond        0.05838 (  407)
  hydrogen bonds       : angle       3.60416 ( 1221)

*********************** 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
  188 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 162
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8320 (tp30) cc_final: 0.7824 (tp30)
REVERT: A  184 SER cc_start: 0.9013 (m) cc_final: 0.8767 (p)
REVERT: B  122 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8583 (tt)
REVERT: C  172 THR cc_start: 0.8521 (m) cc_final: 0.8252 (t)
REVERT: D   98 ASP cc_start: 0.9206 (OUTLIER) cc_final: 0.8969 (t0)
  outliers start: 26
  outliers final: 18
  residues processed: 178
  average time/residue: 0.1156
  time to fit residues: 23.9316
Evaluate side-chains
  179 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 159
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
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 C residue   56 THR
Chi-restraints excluded: chain C residue   75 GLU
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   98 ASP
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  133 ILE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0170
   chunk 32 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0870
   chunk 43 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0040
   chunk 1 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.3408

-------------------------------------------------------------------------------
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 = 0.3066 r_free = 0.3066 target = 0.068693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.060210 restraints weight = 12649.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.2857 rms_B_bonded: 2.01
r_work: 0.2727 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.4543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4728  Z= 0.129
  Angle     :  0.481   5.697   6418  Z= 0.269
  Chirality :  0.034   0.139    778
  Planarity :  0.004   0.049    776
  Dihedral  :  5.461  59.369    642
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 22.48 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.47 (0.35), residues: 588
  helix:  3.38 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.49 (0.78), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 145 
 TYR   0.003   0.001   TYR C 164 
 PHE   0.011   0.001   PHE B 176 
 TRP   0.007   0.001   TRP B 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 4728)
  covalent geometry    : angle       0.48060 ( 6418)
  hydrogen bonds       : bond        0.04457 (  407)
  hydrogen bonds       : angle       3.34647 ( 1221)

*********************** 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
  186 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 168
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8277 (tp30) cc_final: 0.7786 (tp30)
REVERT: A  184 SER cc_start: 0.9001 (m) cc_final: 0.8741 (p)
REVERT: B  122 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8609 (tt)
REVERT: C  184 SER cc_start: 0.9101 (m) cc_final: 0.8886 (p)
REVERT: D   71 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8704 (t0)
REVERT: D   98 ASP cc_start: 0.9124 (OUTLIER) cc_final: 0.8910 (t0)
REVERT: H  189 LYS cc_start: 0.9021 (tttp) cc_final: 0.8515 (ttmt)
  outliers start: 18
  outliers final: 9
  residues processed: 181
  average time/residue: 0.1238
  time to fit residues: 26.0057
Evaluate side-chains
  173 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 161
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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   71 ASP
Chi-restraints excluded: chain D residue   98 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 H residue  190 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 13 optimal weight:    0.4980
   chunk 29 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   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 = 0.3022 r_free = 0.3022 target = 0.066803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.058242 restraints weight = 12878.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.2809 rms_B_bonded: 2.02
r_work: 0.2677 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.4667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4728  Z= 0.150
  Angle     :  0.514   6.514   6418  Z= 0.285
  Chirality :  0.035   0.130    778
  Planarity :  0.004   0.050    776
  Dihedral  :  4.874  57.530    636
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 20.80 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.38 (0.35), residues: 588
  helix:  3.29 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.48 (0.79), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  94 
 TYR   0.003   0.001   TYR C 164 
 PHE   0.015   0.001   PHE B 176 
 TRP   0.016   0.001   TRP C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 4728)
  covalent geometry    : angle       0.51369 ( 6418)
  hydrogen bonds       : bond        0.05263 (  407)
  hydrogen bonds       : angle       3.38478 ( 1221)

*********************** 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
  191 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 SER cc_start: 0.9020 (m) cc_final: 0.8786 (p)
REVERT: B  122 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8647 (tt)
REVERT: D   98 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8888 (t0)
REVERT: D  125 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8034 (mp)
REVERT: H  189 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8538 (ttmt)
  outliers start: 25
  outliers final: 19
  residues processed: 182
  average time/residue: 0.1225
  time to fit residues: 25.9752
Evaluate side-chains
  186 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 163
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
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  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  172 THR
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain D residue   71 ASP
Chi-restraints excluded: chain D residue   98 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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0270
   chunk 29 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.6238

-------------------------------------------------------------------------------
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 = 0.3038 r_free = 0.3038 target = 0.067332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.058701 restraints weight = 12641.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.2819 rms_B_bonded: 2.01
r_work: 0.2686 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.4762

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= 0.146
  Angle     :  0.526   6.740   6418  Z= 0.288
  Chirality :  0.035   0.173    778
  Planarity :  0.004   0.051    776
  Dihedral  :  4.850  58.579    636
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.23 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 22.27 %
    Favored  : 72.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.39 (0.35), residues: 588
  helix:  3.30 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.48 (0.80), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 145 
 TYR   0.003   0.001   TYR C 164 
 PHE   0.014   0.001   PHE B 176 
 TRP   0.013   0.001   TRP C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 4728)
  covalent geometry    : angle       0.52621 ( 6418)
  hydrogen bonds       : bond        0.05034 (  407)
  hydrogen bonds       : angle       3.35898 ( 1221)

*********************** 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: 27
    poor density    : 164
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 TRP cc_start: 0.8593 (OUTLIER) cc_final: 0.8298 (t-100)
REVERT: A  184 SER cc_start: 0.9026 (m) cc_final: 0.8789 (p)
REVERT: B  122 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8619 (tt)
REVERT: C  147 ARG cc_start: 0.8106 (mtp85) cc_final: 0.7876 (mmp80)
REVERT: G  188 TRP cc_start: 0.8702 (t60) cc_final: 0.8480 (t60)
REVERT: H  189 LYS cc_start: 0.9024 (tttp) cc_final: 0.8536 (ttmt)
  outliers start: 27
  outliers final: 24
  residues processed: 181
  average time/residue: 0.1186
  time to fit residues: 25.0478
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  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 TRP
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 E residue  191 MET
Chi-restraints excluded: chain C residue   56 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  185 LEU
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  129 VAL
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain G residue  169 THR
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:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 47 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 11 optimal weight:    0.1980
   chunk 3 optimal weight:    0.9980
   chunk 18 optimal weight:    0.3980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.067536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.058939 restraints weight = 12810.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.2818 rms_B_bonded: 2.03
r_work: 0.2686 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.4867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4728  Z= 0.143
  Angle     :  0.528   6.731   6418  Z= 0.288
  Chirality :  0.035   0.162    778
  Planarity :  0.004   0.052    776
  Dihedral  :  4.836  58.441    636
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.57 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 22.48 %
    Favored  : 71.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.39 (0.35), residues: 588
  helix:  3.30 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.45 (0.81), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 134 
 TYR   0.003   0.001   TYR C 164 
 PHE   0.013   0.001   PHE B 176 
 TRP   0.014   0.001   TRP C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 4728)
  covalent geometry    : angle       0.52810 ( 6418)
  hydrogen bonds       : bond        0.04948 (  407)
  hydrogen bonds       : angle       3.32817 ( 1221)

*********************** 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
  195 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 167
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 SER cc_start: 0.9045 (m) cc_final: 0.8806 (p)
REVERT: B  122 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8624 (tt)
REVERT: C  147 ARG cc_start: 0.8114 (mtp85) cc_final: 0.7895 (mmp80)
REVERT: G  188 TRP cc_start: 0.8732 (t60) cc_final: 0.8475 (t60)
REVERT: H  189 LYS cc_start: 0.9023 (tttp) cc_final: 0.8540 (ttmt)
  outliers start: 28
  outliers final: 23
  residues processed: 183
  average time/residue: 0.1177
  time to fit residues: 25.1048
Evaluate side-chains
  191 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 167
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   56 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 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  129 VAL
Chi-restraints excluded: chain D residue  132 LEU
Chi-restraints excluded: chain G residue  169 THR
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 32 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.066494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.058020 restraints weight = 12526.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.2801 rms_B_bonded: 1.98
r_work: 0.2669 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.4870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4728  Z= 0.165
  Angle     :  0.569   6.877   6418  Z= 0.309
  Chirality :  0.037   0.177    778
  Planarity :  0.004   0.051    776
  Dihedral  :  4.922  59.965    636
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.57 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 24.16 %
    Favored  : 70.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.22 (0.35), residues: 588
  helix:  3.19 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.48 (0.81), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 145 
 TYR   0.003   0.001   TYR C 164 
 PHE   0.015   0.001   PHE D 176 
 TRP   0.013   0.001   TRP C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 4728)
  covalent geometry    : angle       0.56862 ( 6418)
  hydrogen bonds       : bond        0.05524 (  407)
  hydrogen bonds       : angle       3.42061 ( 1221)

*********************** 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
  192 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 167
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8319 (tp30) cc_final: 0.7914 (tp30)
REVERT: A  184 SER cc_start: 0.9066 (m) cc_final: 0.8853 (p)
REVERT: B  122 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8648 (tt)
REVERT: C  147 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7868 (mmp80)
REVERT: G  188 TRP cc_start: 0.8742 (t60) cc_final: 0.8515 (t60)
REVERT: H  189 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8554 (ttmt)
  outliers start: 25
  outliers final: 20
  residues processed: 184
  average time/residue: 0.1146
  time to fit residues: 24.6147
Evaluate side-chains
  189 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 167
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  111 VAL
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain E residue  169 THR
Chi-restraints excluded: chain C residue  172 THR
Chi-restraints excluded: chain C residue  185 LEU
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  111 VAL
Chi-restraints excluded: chain D residue  121 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  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 43 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0970
   chunk 29 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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 = 0.3033 r_free = 0.3033 target = 0.067185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.058649 restraints weight = 12804.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 2.00
r_work: 0.2683 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.5010

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= 0.147
  Angle     :  0.538   6.822   6418  Z= 0.296
  Chirality :  0.036   0.180    778
  Planarity :  0.004   0.053    776
  Dihedral  :  4.858  58.735    636
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.57 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 24.37 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.41 (0.35), residues: 588
  helix:  3.30 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.31 (0.84), residues: 60

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 4728)
  covalent geometry    : angle       0.53842 ( 6418)
  hydrogen bonds       : bond        0.04981 (  407)
  hydrogen bonds       : angle       3.35183 ( 1221)

********************** 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: 22
    poor density    : 167
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8296 (tp30) cc_final: 0.7892 (tp30)
REVERT: A  184 SER cc_start: 0.9077 (m) cc_final: 0.8850 (p)
REVERT: B  122 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8653 (tt)
REVERT: C  147 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7872 (mmp80)
REVERT: H  189 LYS cc_start: 0.9032 (tttp) cc_final: 0.8547 (ttmt)
REVERT: H  190 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8681 (tttm)
  outliers start: 22
  outliers final: 19
  residues processed: 181
  average time/residue: 0.1121
  time to fit residues: 23.7726
Evaluate side-chains
  187 residues out of total 524 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 VAL
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   75 GLU
Chi-restraints excluded: chain C residue  126 CYS
Chi-restraints excluded: chain C residue  172 THR
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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 16 optimal weight:    0.0170
   chunk 47 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 8 optimal weight:    0.1980
   chunk 15 optimal weight:    0.9990
   chunk 35 optimal weight:    0.3980
   chunk 21 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.4018

-------------------------------------------------------------------------------
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 = 0.3060 r_free = 0.3060 target = 0.068476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.059902 restraints weight = 12782.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 2.00
r_work: 0.2715 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
moved from start:          0.5092

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= 0.140
  Angle     :  0.550   6.822   6418  Z= 0.297
  Chirality :  0.036   0.183    778
  Planarity :  0.004   0.053    776
  Dihedral  :  4.903  59.898    636
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.23 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 24.79 %
    Favored  : 71.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.46 (0.35), residues: 588
  helix:  3.34 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.18 (0.82), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 145 
 TYR   0.003   0.001   TYR C 164 
 PHE   0.011   0.001   PHE B 176 
 TRP   0.014   0.001   TRP C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 4728)
  covalent geometry    : angle       0.55016 ( 6418)
  hydrogen bonds       : bond        0.04571 (  407)
  hydrogen bonds       : angle       3.31131 ( 1221)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1230.00 seconds
wall clock time: 21 minutes 48.85 seconds (1308.85 seconds total)