Starting phenix.real_space_refine
on Fri May  9 15:11:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ymk_39396/05_2025/8ymk_39396.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ymk_39396/05_2025/8ymk_39396.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ymk_39396/05_2025/8ymk_39396.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ymk_39396/05_2025/8ymk_39396.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ymk_39396/05_2025/8ymk_39396.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ymk_39396/05_2025/8ymk_39396.cif"
  }
  resolution = 3.7
  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=  -0.007 sd=   0.029
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      24      5.16       5
     C    1752      2.51       5
     N     487      2.21       5
     O     481      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 2744
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1355
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1355
          Classifications: {'peptide': 226}
          Incomplete info: {'truncation_to_alanine': 146}
          Link IDs: {'PTRANS': 22, 'TRANS': 203}
          Unresolved chain link angles: 20
          Unresolved non-hydrogen bonds: 470
          Unresolved non-hydrogen angles: 612
          Unresolved non-hydrogen dihedrals: 395
          Unresolved non-hydrogen chiralities: 60
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 11, 'GLU:plan': 2, 'ARG:plan': 5}
          Unresolved non-hydrogen planarities: 184
    Chain: "B"
      Number of atoms: 1389
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1389
          Classifications: {'peptide': 226}
          Incomplete info: {'truncation_to_alanine': 133}
          Link IDs: {'PTRANS': 22, 'TRANS': 203}
          Unresolved chain link angles: 18
          Unresolved non-hydrogen bonds: 435
          Unresolved non-hydrogen angles: 567
          Unresolved non-hydrogen dihedrals: 371
          Unresolved non-hydrogen chiralities: 51
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 11, 'GLU:plan': 1, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 182
  Time building chain proxies: 2.67, per 1000 atoms: 0.97
  Number of scatterers: 2744
  At special positions: 0
  Unit cell: (104.94, 76.32, 98.58, 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      24     16.00
     O     481      8.00
     N     487      7.00
     C    1752      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  48 " - pdb=" SG  CYS A  65 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 107 " - pdb=" SG  CYS B 107 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 121 " - pdb=" SG  CYS A 124 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 137 " - pdb=" SG  CYS A 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 139 " - pdb=" SG  CYS A 147 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  48 " - pdb=" SG  CYS B  65 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 124 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 137 " - pdb=" SG  CYS B 149 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 139 " - pdb=" SG  CYS B 147 " distance=2.34

  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: 0.79
  Conformation dependent library (CDL) restraints added in 499.5 milliseconds
  

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  844

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 0 sheets defined
      60.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 28
      Proline residue:  A  11  - end of helix
    Processing helix  chain 'A' and resid 28 through 36
      removed outlier: 3.765A  pdb=" N   ASP A  33 " --> pdb=" O   PRO A  29 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   SER A  34 " --> pdb=" O   GLN A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 44
    Processing helix  chain 'A' and resid 73 through 101
      removed outlier: 3.772A  pdb=" N   LEU A  77 " --> pdb=" O   ARG A  73 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ARG A  79 " --> pdb=" O   MET A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 169
      removed outlier: 4.196A  pdb=" N   GLU A 164 " --> pdb=" O   LYS A 160 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   TRP A 165 " --> pdb=" O   PHE A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 184
    Processing helix  chain 'A' and resid 186 through 202
      removed outlier: 3.687A  pdb=" N   VAL A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   TRP A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   LEU A 192 " --> pdb=" O   PRO A 188 " (cutoff:3.500A)
      removed outlier: 4.811A  pdb=" N   SER A 193 " --> pdb=" O   THR A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 213
      removed outlier: 4.107A  pdb=" N   SER A 207 " --> pdb=" O   PRO A 203 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   ILE A 208 " --> pdb=" O   SER A 204 " (cutoff:3.500A)
      Proline residue:  A 211  - end of helix
    Processing helix  chain 'A' and resid 214 through 226
      removed outlier: 4.102A  pdb=" N   ILE A 218 " --> pdb=" O   PRO A 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 44
      removed outlier: 3.562A  pdb=" N   SER B   6 " --> pdb=" O   GLU B   2 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   GLY B   7 " --> pdb=" O   ASN B   3 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   GLY B  10 " --> pdb=" O   SER B   6 " (cutoff:3.500A)
      Proline residue:  B  11  - end of helix
      Proline residue:  B  29  - end of helix
      removed outlier: 3.579A  pdb=" N   THR B  37 " --> pdb=" O   ASP B  33 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   SER B  38 " --> pdb=" O   SER B  34 " (cutoff:3.500A)
      removed outlier: 4.751A  pdb=" N   LEU B  39 " --> pdb=" O   TRP B  35 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLY B  43 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   GLY B  44 " --> pdb=" O   ASN B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 102
      removed outlier: 4.444A  pdb=" N   LEU B  84 " --> pdb=" O   PHE B  80 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   PHE B  85 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 170
    Processing helix  chain 'B' and resid 171 through 185
      removed outlier: 3.911A  pdb=" N   LEU B 175 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
      Proline residue:  B 178  - end of helix
    Processing helix  chain 'B' and resid 187 through 199
      removed outlier: 4.154A  pdb=" N   SER B 193 " --> pdb=" O   THR B 189 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ILE B 195 " --> pdb=" O   TRP B 191 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TRP B 199 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 213
      removed outlier: 4.065A  pdb=" N   LEU B 205 " --> pdb=" O   TRP B 201 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ILE B 208 " --> pdb=" O   SER B 204 " (cutoff:3.500A)
      Proline residue:  B 211  - end of helix
    Processing helix  chain 'B' and resid 215 through 226
      removed outlier: 3.880A  pdb=" N   PHE B 219 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)

    163 hydrogen bonds defined for protein.
    489 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: 0.53

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 840
        1.34 -     1.46: 522
        1.46 -     1.58: 1421
        1.58 -     1.70: 0
        1.70 -     1.82: 24
  Bond restraints: 2807
  Sorted by residual:
  bond pdb=" CA  SER A  31 "
       pdb=" CB  SER A  31 "
    ideal  model  delta    sigma   weight residual
    1.533  1.462  0.071 1.58e-02 4.01e+03 2.02e+01
  bond pdb=" C   SER A  31 "
       pdb=" O   SER A  31 "
    ideal  model  delta    sigma   weight residual
    1.234  1.291 -0.057 1.35e-02 5.49e+03 1.76e+01
  bond pdb=" CA  CYS A 107 "
       pdb=" CB  CYS A 107 "
    ideal  model  delta    sigma   weight residual
    1.522  1.543 -0.020 7.00e-03 2.04e+04 8.57e+00
  bond pdb=" N   ILE A  28 "
       pdb=" CA  ILE A  28 "
    ideal  model  delta    sigma   weight residual
    1.463  1.497 -0.034 1.20e-02 6.94e+03 8.12e+00
  bond pdb=" N   GLN B 129 "
       pdb=" CA  GLN B 129 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.33e-02 5.65e+03 6.75e+00
  ... (remaining 2802 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 3702
        2.53 -     5.06: 146
        5.06 -     7.58: 28
        7.58 -    10.11: 9
       10.11 -    12.64: 4
  Bond angle restraints: 3889
  Sorted by residual:
  angle pdb=" C   ILE B 152 "
        pdb=" N   PRO B 153 "
        pdb=" CA  PRO B 153 "
      ideal   model   delta    sigma   weight residual
     119.85  131.60  -11.75 1.01e+00 9.80e-01 1.35e+02
  angle pdb=" C   ILE B 150 "
        pdb=" N   PRO B 151 "
        pdb=" CA  PRO B 151 "
      ideal   model   delta    sigma   weight residual
     119.85  131.02  -11.17 1.01e+00 9.80e-01 1.22e+02
  angle pdb=" N   CYS B 138 "
        pdb=" CA  CYS B 138 "
        pdb=" C   CYS B 138 "
      ideal   model   delta    sigma   weight residual
     111.14  100.67   10.47 1.08e+00 8.57e-01 9.40e+01
  angle pdb=" N   TRP A 156 "
        pdb=" CA  TRP A 156 "
        pdb=" C   TRP A 156 "
      ideal   model   delta    sigma   weight residual
     110.30   97.66   12.64 1.50e+00 4.44e-01 7.10e+01
  angle pdb=" C   ILE A 152 "
        pdb=" N   PRO A 153 "
        pdb=" CA  PRO A 153 "
      ideal   model   delta    sigma   weight residual
     119.85  126.95   -7.10 1.01e+00 9.80e-01 4.94e+01
  ... (remaining 3884 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 1477
       17.32 -    34.64: 67
       34.64 -    51.96: 24
       51.96 -    69.28: 2
       69.28 -    86.60: 2
  Dihedral angle restraints: 1572
    sinusoidal: 273
      harmonic: 1299
  Sorted by residual:
  dihedral pdb=" CB  CYS B  48 "
           pdb=" SG  CYS B  48 "
           pdb=" SG  CYS B  65 "
           pdb=" CB  CYS B  65 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  179.60  -86.60     1      1.00e+01 1.00e-02 9.03e+01
  dihedral pdb=" CB  CYS B 121 "
           pdb=" SG  CYS B 121 "
           pdb=" SG  CYS B 124 "
           pdb=" CB  CYS B 124 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -133.03   47.03     1      1.00e+01 1.00e-02 3.06e+01
  dihedral pdb=" CB  CYS B 139 "
           pdb=" SG  CYS B 139 "
           pdb=" SG  CYS B 147 "
           pdb=" CB  CYS B 147 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -130.16   44.16     1      1.00e+01 1.00e-02 2.71e+01
  ... (remaining 1569 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 381
       0.072 -    0.143: 70
       0.143 -    0.215: 9
       0.215 -    0.286: 6
       0.286 -    0.358: 1
  Chirality restraints: 467
  Sorted by residual:
  chirality pdb=" CA  CYS B 137 "
            pdb=" N   CYS B 137 "
            pdb=" C   CYS B 137 "
            pdb=" CB  CYS B 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.20e+00
  chirality pdb=" CA  CYS B 138 "
            pdb=" N   CYS B 138 "
            pdb=" C   CYS B 138 "
            pdb=" CB  CYS B 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  PRO B 135 "
            pdb=" N   PRO B 135 "
            pdb=" C   PRO B 135 "
            pdb=" CB  PRO B 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.96   -0.24 2.00e-01 2.50e+01 1.48e+00
  ... (remaining 464 not shown)

  Planarity restraints: 503
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A  33 "    0.015 2.00e-02 2.50e+03   3.22e-02 1.03e+01
        pdb=" C   ASP A  33 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   ASP A  33 "    0.021 2.00e-02 2.50e+03
        pdb=" N   SER A  34 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  83 "   -0.022 2.00e-02 2.50e+03   2.37e-02 9.87e+00
        pdb=" CG  PHE B  83 "    0.055 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  83 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  83 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  83 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  83 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  83 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 177 "    0.029 5.00e-02 4.00e+02   4.47e-02 3.20e+00
        pdb=" N   PRO B 178 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 178 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 178 "    0.025 5.00e-02 4.00e+02
  ... (remaining 500 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 886
        2.82 -     3.34: 2859
        3.34 -     3.86: 4083
        3.86 -     4.38: 4076
        4.38 -     4.90: 6427
  Nonbonded interactions: 18331
  Sorted by model distance:
  nonbonded pdb=" O   SER A  34 "
            pdb=" N   THR A  37 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" O   ALA A 166 "
            pdb=" CB  PHE A 170 "
     model   vdw
     2.348 3.440
  nonbonded pdb=" O   LEU B 209 "
            pdb=" N   LEU B 213 "
     model   vdw
     2.357 3.120
  nonbonded pdb=" O   GLY A  43 "
            pdb=" N   LEU B  49 "
     model   vdw
     2.366 3.120
  nonbonded pdb=" O   SER A  34 "
            pdb=" C   TRP A  35 "
     model   vdw
     2.378 3.270
  ... (remaining 18326 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 40 or (resid 41 through 42 and (name N or name C \ 
A or name C or name O or name CB )) or resid 43 through 79 or (resid 80 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 81 through 205 or (res \ 
id 206 through 220 and (name N or name CA or name C or name O or name CB )) or r \ 
esid 221 through 226))
  selection = (chain 'B' and ((resid 1 through 27 and (name N or name CA or name C or name O o \ 
r name CB )) or resid 28 through 76 or (resid 77 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 78 through 92 or (resid 93 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 94 through 157 or (resid 158 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 159 through 163 o \ 
r (resid 164 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 
65 through 173 or (resid 174 through 181 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 182 through 214 or (resid 215 through 220 and (name N \ 
 or name CA or name C or name O or name CB )) or resid 221 through 226))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.030
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.030
  Find NCS groups from input model:        0.080
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6341
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   0.313   2816  Z= 0.446
  Angle     :  1.579  56.517   3907  Z= 0.969
  Chirality :  0.061   0.358    467
  Planarity :  0.005   0.055    503
  Dihedral  : 11.932  72.533    701
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 16.34
  Ramachandran Plot:
    Outliers :  1.56 %
    Allowed  : 14.06 %
    Favored  : 84.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.43), residues: 448
  helix:  0.90 (0.35), residues: 243
  sheet:  None (None), residues: 0
  loop : -3.98 (0.43), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  36 
 PHE   0.055   0.002   PHE B  83 
 TYR   0.004   0.001   TYR B 100 
 ARG   0.019   0.004   ARG B  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17312 (  163)
  hydrogen bonds       : angle       7.05489 (  489)
  SS BOND              : bond        0.10446 (    9)
  SS BOND              : angle      14.86909 (   18)
  covalent geometry    : bond        0.00486 ( 2807)
  covalent geometry    : angle       1.21728 ( 3889)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 CYS cc_start: 0.9015 (t) cc_final: 0.8644 (m)
REVERT: B   33 ASP cc_start: 0.8820 (m-30) cc_final: 0.8605 (m-30)
REVERT: B   36 TRP cc_start: 0.9553 (m100) cc_final: 0.8961 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1039
  time to fit residues: 10.3138
Evaluate side-chains
  55 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 37 optimal weight:    0.0770
   chunk 33 optimal weight:    0.6980
   chunk 18 optimal weight:    0.3980
   chunk 11 optimal weight:    9.9990
   chunk 22 optimal weight:    8.9990
   chunk 17 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0040
   chunk 13 optimal weight:    0.4980
   chunk 20 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 39 optimal weight:    7.9990
   overall best weight:    0.3350

-------------------------------------------------------------------------------
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 = 0.4499 r_free = 0.4499 target = 0.123145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.109554 restraints weight = 23058.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.109094 restraints weight = 23454.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.109962 restraints weight = 23352.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.4203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6276
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   2816  Z= 0.166
  Angle     :  0.851   9.479   3907  Z= 0.426
  Chirality :  0.053   0.414    467
  Planarity :  0.006   0.066    503
  Dihedral  :  5.906  29.907    458
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  1.56 %
    Allowed  : 10.49 %
    Favored  : 87.95 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 24.81 %
    Favored  : 69.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.82 (0.41), residues: 448
  helix:  0.96 (0.33), residues: 247
  sheet:  None (None), residues: 0
  loop : -4.32 (0.39), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A  36 
 PHE   0.052   0.003   PHE B  83 
 TYR   0.010   0.002   TYR A 206 
 ARG   0.008   0.002   ARG B  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04913 (  163)
  hydrogen bonds       : angle       5.72617 (  489)
  SS BOND              : bond        0.00359 (    9)
  SS BOND              : angle       1.35146 (   18)
  covalent geometry    : bond        0.00349 ( 2807)
  covalent geometry    : angle       0.84778 ( 3889)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
  outliers start: 8
  outliers final: 2
  residues processed: 60
  average time/residue: 0.0798
  time to fit residues: 6.4381
Evaluate side-chains
  56 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain B residue   84 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 1 optimal weight:    0.0070
   chunk 28 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 18 optimal weight:    9.9990
   chunk 12 optimal weight:    9.9990
   chunk 42 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 39 optimal weight:    0.4980
   overall best weight:    0.6798

-------------------------------------------------------------------------------
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 = 0.4492 r_free = 0.4492 target = 0.121395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.107953 restraints weight = 23041.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.107676 restraints weight = 23107.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.107919 restraints weight = 23471.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6298
moved from start:          0.3558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2816  Z= 0.142
  Angle     :  0.810  11.732   3907  Z= 0.396
  Chirality :  0.049   0.235    467
  Planarity :  0.006   0.088    503
  Dihedral  :  5.600  26.872    458
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  1.56 %
    Allowed  : 10.94 %
    Favored  : 87.50 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 27.07 %
    Favored  : 69.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.42), residues: 448
  helix:  1.15 (0.34), residues: 247
  sheet:  None (None), residues: 0
  loop : -4.33 (0.38), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A  36 
 PHE   0.039   0.003   PHE B  83 
 TYR   0.003   0.001   TYR A 206 
 ARG   0.009   0.002   ARG B  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04427 (  163)
  hydrogen bonds       : angle       5.57589 (  489)
  SS BOND              : bond        0.00246 (    9)
  SS BOND              : angle       1.28495 (   18)
  covalent geometry    : bond        0.00287 ( 2807)
  covalent geometry    : angle       0.80693 ( 3889)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 3
  residues processed: 57
  average time/residue: 0.0955
  time to fit residues: 7.1219
Evaluate side-chains
  56 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  107 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 39 optimal weight:    0.6980
   chunk 22 optimal weight:    8.9990
   chunk 33 optimal weight:    6.9990
   chunk 17 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   chunk 15 optimal weight:   20.0000
   chunk 13 optimal weight:    0.0470
   chunk 29 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    1.1282

-------------------------------------------------------------------------------
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 = 0.4467 r_free = 0.4467 target = 0.119728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.106717 restraints weight = 23240.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.107007 restraints weight = 22654.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.107203 restraints weight = 22981.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6270
moved from start:          0.3938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2816  Z= 0.140
  Angle     :  0.852  13.459   3907  Z= 0.402
  Chirality :  0.049   0.286    467
  Planarity :  0.005   0.063    503
  Dihedral  :  5.472  26.036    458
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  1.56 %
    Allowed  : 11.38 %
    Favored  : 87.05 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 27.07 %
    Favored  : 66.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.42), residues: 448
  helix:  1.27 (0.34), residues: 247
  sheet:  None (None), residues: 0
  loop : -4.24 (0.39), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  74 
 PHE   0.039   0.003   PHE A  85 
 TYR   0.006   0.001   TYR A 206 
 ARG   0.009   0.002   ARG B  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04158 (  163)
  hydrogen bonds       : angle       5.47359 (  489)
  SS BOND              : bond        0.00198 (    9)
  SS BOND              : angle       1.01979 (   18)
  covalent geometry    : bond        0.00289 ( 2807)
  covalent geometry    : angle       0.85102 ( 3889)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: B   37 THR cc_start: 0.8917 (m) cc_final: 0.8700 (p)
  outliers start: 8
  outliers final: 6
  residues processed: 59
  average time/residue: 0.0815
  time to fit residues: 6.5150
Evaluate side-chains
  59 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  218 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0980
   chunk 18 optimal weight:    0.0050
   chunk 2 optimal weight:    0.0020
   chunk 30 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 36 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.3802

-------------------------------------------------------------------------------
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 = 0.4477 r_free = 0.4477 target = 0.120536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.107298 restraints weight = 23462.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.107312 restraints weight = 23322.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.107435 restraints weight = 23709.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6226
moved from start:          0.4209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2816  Z= 0.137
  Angle     :  0.871  11.645   3907  Z= 0.411
  Chirality :  0.054   0.364    467
  Planarity :  0.005   0.050    503
  Dihedral  :  5.288  25.134    458
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  1.56 %
    Allowed  : 10.94 %
    Favored  : 87.50 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 30.83 %
    Favored  : 63.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.42), residues: 448
  helix:  1.33 (0.34), residues: 248
  sheet:  None (None), residues: 0
  loop : -4.19 (0.40), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  36 
 PHE   0.058   0.004   PHE A  85 
 TYR   0.019   0.001   TYR A 206 
 ARG   0.007   0.002   ARG B  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04027 (  163)
  hydrogen bonds       : angle       5.38050 (  489)
  SS BOND              : bond        0.00361 (    9)
  SS BOND              : angle       1.20286 (   18)
  covalent geometry    : bond        0.00281 ( 2807)
  covalent geometry    : angle       0.86913 ( 3889)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: B   37 THR cc_start: 0.8964 (m) cc_final: 0.8732 (p)
  outliers start: 7
  outliers final: 6
  residues processed: 58
  average time/residue: 0.0797
  time to fit residues: 6.2310
Evaluate side-chains
  59 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  218 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 22 optimal weight:    9.9990
   chunk 18 optimal weight:    0.0050
   chunk 33 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0980
   chunk 6 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0470
   chunk 12 optimal weight:    7.9990
   overall best weight:    0.3692

-------------------------------------------------------------------------------
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 = 0.4487 r_free = 0.4487 target = 0.121172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.107960 restraints weight = 23438.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.107796 restraints weight = 22916.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.108141 restraints weight = 23351.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.4022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6218
moved from start:          0.4382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2816  Z= 0.135
  Angle     :  0.862  14.238   3907  Z= 0.406
  Chirality :  0.051   0.311    467
  Planarity :  0.004   0.046    503
  Dihedral  :  5.111  24.942    458
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  1.56 %
    Allowed  : 10.49 %
    Favored  : 87.95 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 34.59 %
    Favored  : 63.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.42), residues: 448
  helix:  1.40 (0.34), residues: 241
  sheet:  None (None), residues: 0
  loop : -3.93 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  74 
 PHE   0.058   0.004   PHE B  83 
 TYR   0.011   0.001   TYR A 206 
 ARG   0.006   0.002   ARG B  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03823 (  163)
  hydrogen bonds       : angle       5.32392 (  489)
  SS BOND              : bond        0.00168 (    9)
  SS BOND              : angle       1.10641 (   18)
  covalent geometry    : bond        0.00274 ( 2807)
  covalent geometry    : angle       0.86034 ( 3889)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: B   37 THR cc_start: 0.9043 (m) cc_final: 0.8823 (p)
  outliers start: 3
  outliers final: 3
  residues processed: 58
  average time/residue: 0.0829
  time to fit residues: 6.5241
Evaluate side-chains
  54 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain B residue  139 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 20 optimal weight:    9.9990
   chunk 13 optimal weight:    0.0980
   chunk 1 optimal weight:    0.0870
   chunk 16 optimal weight:    1.9990
   chunk 15 optimal weight:    0.4980
   chunk 10 optimal weight:    0.0770
   chunk 26 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.3516

-------------------------------------------------------------------------------
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 = 0.4121 r_free = 0.4121 target = 0.102874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.085499 restraints weight = 16512.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.084469 restraints weight = 17285.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.083699 restraints weight = 20115.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6105
moved from start:          0.4596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2816  Z= 0.137
  Angle     :  0.929  17.683   3907  Z= 0.427
  Chirality :  0.054   0.333    467
  Planarity :  0.004   0.046    503
  Dihedral  :  4.953  24.401    458
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  1.56 %
    Allowed  : 10.49 %
    Favored  : 87.95 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 39.10 %
    Favored  : 57.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.42), residues: 448
  helix:  1.55 (0.35), residues: 241
  sheet:  None (None), residues: 0
  loop : -3.89 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  74 
 PHE   0.057   0.003   PHE A  85 
 TYR   0.025   0.001   TYR A 206 
 ARG   0.004   0.001   ARG A  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03824 (  163)
  hydrogen bonds       : angle       5.28576 (  489)
  SS BOND              : bond        0.00175 (    9)
  SS BOND              : angle       1.04475 (   18)
  covalent geometry    : bond        0.00279 ( 2807)
  covalent geometry    : angle       0.92800 ( 3889)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 56
  average time/residue: 0.0834
  time to fit residues: 6.3484
Evaluate side-chains
  56 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain B residue  139 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    0.6980
   chunk 38 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 25 optimal weight:    6.9990
   chunk 15 optimal weight:    9.9990
   chunk 26 optimal weight:   30.0000
   chunk 22 optimal weight:    9.9990
   overall best weight:    4.3388

-------------------------------------------------------------------------------
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 = 0.4330 r_free = 0.4330 target = 0.108048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.095851 restraints weight = 24259.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.095640 restraints weight = 24299.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.096024 restraints weight = 22452.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6619
moved from start:          0.5859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.083   2816  Z= 0.312
  Angle     :  1.066  13.067   3907  Z= 0.561
  Chirality :  0.059   0.298    467
  Planarity :  0.007   0.076    503
  Dihedral  :  6.804  27.220    458
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 21.65
  Ramachandran Plot:
    Outliers :  1.56 %
    Allowed  : 16.52 %
    Favored  : 81.92 %
  Rotamer:
    Outliers :  7.52 %
    Allowed  : 36.84 %
    Favored  : 55.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.12 (0.41), residues: 448
  helix:  0.53 (0.33), residues: 245
  sheet:  None (None), residues: 0
  loop : -4.14 (0.41), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP B  35 
 PHE   0.042   0.004   PHE A  85 
 TYR   0.019   0.002   TYR A 206 
 ARG   0.010   0.003   ARG A  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05595 (  163)
  hydrogen bonds       : angle       6.35193 (  489)
  SS BOND              : bond        0.00502 (    9)
  SS BOND              : angle       1.52234 (   18)
  covalent geometry    : bond        0.00594 ( 2807)
  covalent geometry    : angle       1.06345 ( 3889)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
  outliers start: 10
  outliers final: 6
  residues processed: 52
  average time/residue: 0.0812
  time to fit residues: 5.7453
Evaluate side-chains
  53 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 PHE
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  163 TRP
Chi-restraints excluded: chain B residue  218 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0170
   chunk 34 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    0.4980
   chunk 15 optimal weight:   10.0000
   chunk 9 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.6220

-------------------------------------------------------------------------------
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 = 0.4398 r_free = 0.4398 target = 0.114275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.102400 restraints weight = 23236.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.101978 restraints weight = 21985.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.102426 restraints weight = 22008.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.4120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6478
moved from start:          0.5825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   2816  Z= 0.158
  Angle     :  1.011  15.481   3907  Z= 0.479
  Chirality :  0.059   0.415    467
  Planarity :  0.004   0.045    503
  Dihedral  :  5.930  26.730    458
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  1.56 %
    Allowed  : 12.05 %
    Favored  : 86.38 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 42.11 %
    Favored  : 54.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.42), residues: 448
  helix:  1.19 (0.34), residues: 244
  sheet:  None (None), residues: 0
  loop : -4.10 (0.39), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 223 
 PHE   0.060   0.004   PHE A  85 
 TYR   0.007   0.001   TYR A 206 
 ARG   0.004   0.001   ARG A  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04152 (  163)
  hydrogen bonds       : angle       5.61144 (  489)
  SS BOND              : bond        0.00274 (    9)
  SS BOND              : angle       1.31113 (   18)
  covalent geometry    : bond        0.00327 ( 2807)
  covalent geometry    : angle       1.00987 ( 3889)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 53
  average time/residue: 0.0820
  time to fit residues: 5.9982
Evaluate side-chains
  54 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  107 CYS
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  163 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 26 optimal weight:   20.0000
   chunk 30 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 24 optimal weight:    0.2980
   chunk 21 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:    6.9990
   chunk 43 optimal weight:    0.4980
   chunk 42 optimal weight:    8.9990
   chunk 35 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   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 = 0.4403 r_free = 0.4403 target = 0.113917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.101657 restraints weight = 23831.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.101440 restraints weight = 24606.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.102219 restraints weight = 21349.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.4134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6462
moved from start:          0.5979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   2816  Z= 0.156
  Angle     :  1.101  22.646   3907  Z= 0.499
  Chirality :  0.058   0.370    467
  Planarity :  0.004   0.045    503
  Dihedral  :  5.448  25.444    458
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  1.34 %
    Allowed  : 13.17 %
    Favored  : 85.49 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 42.86 %
    Favored  : 54.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.43), residues: 448
  helix:  1.39 (0.35), residues: 242
  sheet:  None (None), residues: 0
  loop : -3.71 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  36 
 PHE   0.064   0.004   PHE A  85 
 TYR   0.003   0.000   TYR A 206 
 ARG   0.004   0.001   ARG A  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03972 (  163)
  hydrogen bonds       : angle       5.59716 (  489)
  SS BOND              : bond        0.00213 (    9)
  SS BOND              : angle       1.25443 (   18)
  covalent geometry    : bond        0.00361 ( 2807)
  covalent geometry    : angle       1.10008 ( 3889)

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

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

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  896 Ramachandran restraints generated.
    448 Oldfield, 0 Emsley, 448 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 54
  average time/residue: 0.0813
  time to fit residues: 5.9596
Evaluate side-chains
  55 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  163 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 66.3783 > 50:
  distance: 3 - 17:  20.861
  distance: 14 - 17:  22.867
  distance: 17 - 18:  21.751
  distance: 18 - 19:  28.861
  distance: 18 - 21:   3.890
  distance: 19 - 20:  35.096
  distance: 19 - 22:  16.878
  distance: 22 - 23:  15.223
  distance: 23 - 24:  34.328
  distance: 23 - 26:  31.684
  distance: 24 - 25:  31.509
  distance: 24 - 27:  43.584
  distance: 27 - 28:  13.827
  distance: 28 - 29:  28.991
  distance: 28 - 31:  36.740
  distance: 29 - 30:  56.455
  distance: 29 - 32:  40.641
  distance: 32 - 33:  45.802
  distance: 33 - 34:  40.726
  distance: 33 - 36:   9.879
  distance: 34 - 35:  46.281
  distance: 34 - 37:  18.519
  distance: 37 - 38:  52.615
  distance: 38 - 39:  37.664
  distance: 38 - 41:  21.221
  distance: 39 - 40:  39.897
  distance: 39 - 42:  64.814
  distance: 42 - 43:  28.865
  distance: 43 - 44:  12.220
  distance: 43 - 46:  49.317
  distance: 44 - 45:  56.143
  distance: 44 - 50:  62.268
  distance: 46 - 47:  39.496
  distance: 47 - 48:  25.925
  distance: 47 - 49:  40.458
  distance: 50 - 51:  56.206
  distance: 51 - 52:  38.734
  distance: 51 - 54:  19.151
  distance: 52 - 53:   7.027
  distance: 52 - 58:  12.559
  distance: 53 - 78:  13.805
  distance: 54 - 55:  53.040
  distance: 55 - 56:  54.713
  distance: 55 - 57:  46.785
  distance: 58 - 59:  26.868
  distance: 58 - 64:  31.721
  distance: 59 - 60:  35.018
  distance: 59 - 62:  34.947
  distance: 60 - 61:  26.568
  distance: 60 - 65:  18.172
  distance: 61 - 83:  25.825
  distance: 62 - 63:  13.532
  distance: 63 - 64:  32.142
  distance: 65 - 66:  36.205
  distance: 66 - 67:  49.682
  distance: 66 - 69:   5.752
  distance: 67 - 68:  18.055
  distance: 67 - 73:   5.028
  distance: 68 - 89:  25.391
  distance: 69 - 70:  56.088
  distance: 69 - 71:  36.565
  distance: 70 - 72:  53.833
  distance: 73 - 74:  17.912
  distance: 74 - 75:  29.067
  distance: 74 - 77:  32.537
  distance: 75 - 76:  32.223
  distance: 75 - 78:  16.841
  distance: 76 - 94:  19.142