Starting phenix.real_space_refine
on Wed Sep 17 12:35:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zyz_60584/09_2025/8zyz_60584.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zyz_60584/09_2025/8zyz_60584.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zyz_60584/09_2025/8zyz_60584.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zyz_60584/09_2025/8zyz_60584.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zyz_60584/09_2025/8zyz_60584.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zyz_60584/09_2025/8zyz_60584.map"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      78      5.16       5
     Na      2      4.78       5
     C    5745      2.51       5
     N    1471      2.21       5
     O    1622      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 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: 8918
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 361
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 361
          Classifications: {'peptide': 46}
          Link IDs: {'PTRANS': 1, 'TRANS': 44}
    Chain: "B"
      Number of atoms: 368
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 368
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 1, 'TRANS': 45}
    Chain: "C"
      Number of atoms: 1606
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 211, 1601
          Classifications: {'peptide': 211}
          Link IDs: {'PTRANS': 6, 'TRANS': 204}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 211, 1601
          Classifications: {'peptide': 211}
          Link IDs: {'PTRANS': 6, 'TRANS': 204}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1616
    Chain: "D"
      Number of atoms: 1621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1621
          Classifications: {'peptide': 214}
          Link IDs: {'PTRANS': 6, 'TRANS': 207}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1613
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 6, 'TRANS': 206}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1729
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1729
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 6, 'TRANS': 223}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 1613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1613
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 6, 'TRANS': 206}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NA': 1}
          Classifications: {'undetermined': 1}
    Chain: "G"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NA': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 2.60, per 1000 atoms: 0.29
  Number of scatterers: 8918
  At special positions: 0
  Unit cell: (102.6, 98.55, 106.65, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      78     16.00
     Na      2     11.00
     O    1622      8.00
     N    1471      7.00
     C    5745      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: 0.86
  Conformation dependent library (CDL) restraints added in 403.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2140

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 1 sheets defined
      91.1% alpha, 0.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 39
      removed outlier: 3.820A  pdb=" N   GLY A  20 " --> pdb=" O   PRO A  16 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   PHE A  39 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 59
    Processing helix  chain 'B' and resid 18 through 39
      removed outlier: 3.943A  pdb=" N   PHE B  39 " --> pdb=" O   LEU B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 58
    Processing helix  chain 'C' and resid 31 through 50
    Processing helix  chain 'C' and resid 51 through 68
      removed outlier: 3.548A  pdb=" N   PHE C  68 " --> pdb=" O   LYS C  64 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 87
    Processing helix  chain 'C' and resid 102 through 114
      removed outlier: 3.512A  pdb=" N   ASP C 114 " --> pdb=" O   ASP C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 168
      removed outlier: 3.500A  pdb=" N   VAL C 121 " --> pdb=" O   ASP C 117 " (cutoff:3.500A)
      Proline residue:  C 151  - end of helix
    Processing helix  chain 'C' and resid 171 through 173
      No H-bonds generated for 'chain 'C' and resid 171 through 173'
    Processing helix  chain 'C' and resid 174 through 195
      removed outlier: 3.623A  pdb=" N   ALA C 178 " --> pdb=" O   ALA C 174 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   MET C 179 " --> pdb=" O   ILE C 175 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ALA C 180 " --> pdb=" O   GLY C 176 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   THR C 185 " --> pdb=" O   VAL C 181 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   THR C 186 " --> pdb=" O   ALA C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 228
    Processing helix  chain 'C' and resid 230 through 240
    Processing helix  chain 'C' and resid 241 through 244
      removed outlier: 3.609A  pdb=" N   GLU C 244 " --> pdb=" O   TYR C 241 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 241 through 244'
    Processing helix  chain 'D' and resid 31 through 48
    Processing helix  chain 'D' and resid 51 through 68
    Processing helix  chain 'D' and resid 72 through 85
      removed outlier: 3.989A  pdb=" N   ASP D  85 " --> pdb=" O   VAL D  81 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 115
    Processing helix  chain 'D' and resid 117 through 167
      Proline residue:  D 151  - end of helix
    Processing helix  chain 'D' and resid 175 through 196
      removed outlier: 3.771A  pdb=" N   VAL D 181 " --> pdb=" O   PRO D 177 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   ALA D 182 " --> pdb=" O   ALA D 178 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 196 through 228
    Processing helix  chain 'D' and resid 230 through 239
      removed outlier: 4.067A  pdb=" N   ILE D 234 " --> pdb=" O   ASN D 230 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ASP D 235 " --> pdb=" O   PRO D 231 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER D 236 " --> pdb=" O   ARG D 232 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   TYR D 237 " --> pdb=" O   VAL D 233 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   LYS D 239 " --> pdb=" O   ASP D 235 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 244 through 250
      removed outlier: 3.523A  pdb=" N   ARG D 247 " --> pdb=" O   GLU D 244 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU D 249 " --> pdb=" O   LYS D 246 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 27 through 50
      removed outlier: 3.795A  pdb=" N   ASP E  31 " --> pdb=" O   GLY E  27 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   MET E  48 " --> pdb=" O   PHE E  44 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LYS E  49 " --> pdb=" O   VAL E  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 68
    Processing helix  chain 'E' and resid 72 through 87
    Processing helix  chain 'E' and resid 102 through 114
    Processing helix  chain 'E' and resid 117 through 168
      Proline residue:  E 151  - end of helix
    Processing helix  chain 'E' and resid 171 through 196
      removed outlier: 3.552A  pdb=" N   ILE E 175 " --> pdb=" O   ASP E 171 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   GLY E 176 " --> pdb=" O   PRO E 172 " (cutoff:3.500A)
      Proline residue:  E 177  - end of helix
    Processing helix  chain 'E' and resid 196 through 228
    Processing helix  chain 'E' and resid 230 through 240
    Processing helix  chain 'E' and resid 241 through 244
    Processing helix  chain 'F' and resid 4 through 23
    Processing helix  chain 'F' and resid 32 through 47
      removed outlier: 3.536A  pdb=" N   VAL F  38 " --> pdb=" O   SER F  34 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 51 through 68
    Processing helix  chain 'F' and resid 72 through 87
    Processing helix  chain 'F' and resid 102 through 115
    Processing helix  chain 'F' and resid 117 through 167
      Proline residue:  F 151  - end of helix
    Processing helix  chain 'F' and resid 171 through 173
      No H-bonds generated for 'chain 'F' and resid 171 through 173'
    Processing helix  chain 'F' and resid 174 through 195
      removed outlier: 3.734A  pdb=" N   THR F 185 " --> pdb=" O   VAL F 181 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   THR F 186 " --> pdb=" O   ALA F 182 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 196 through 227
    Processing helix  chain 'F' and resid 230 through 243
    Processing helix  chain 'F' and resid 244 through 251
      removed outlier: 3.700A  pdb=" N   ARG F 247 " --> pdb=" O   GLU F 244 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ILE F 251 " --> pdb=" O   ALA F 248 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 50
    Processing helix  chain 'G' and resid 51 through 67
    Processing helix  chain 'G' and resid 72 through 87
    Processing helix  chain 'G' and resid 102 through 115
      removed outlier: 3.610A  pdb=" N   ASP G 114 " --> pdb=" O   ASP G 110 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 118 through 169
      Proline residue:  G 151  - end of helix
    Processing helix  chain 'G' and resid 171 through 196
      removed outlier: 3.565A  pdb=" N   GLY G 176 " --> pdb=" O   PRO G 172 " (cutoff:3.500A)
      Proline residue:  G 177  - end of helix
    Processing helix  chain 'G' and resid 196 through 228
    Processing helix  chain 'G' and resid 230 through 243
      removed outlier: 3.937A  pdb=" N   ASN G 240 " --> pdb=" O   SER G 236 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   TYR G 241 " --> pdb=" O   TYR G 237 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ASN G 243 " --> pdb=" O   LYS G 239 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 244 through 249
      removed outlier: 3.791A  pdb=" N   ARG G 247 " --> pdb=" O   GLU G 244 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42

    812 hydrogen bonds defined for protein.
    2411 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.46

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2896
        1.34 -     1.46: 1892
        1.46 -     1.59: 4093
        1.59 -     1.71: 0
        1.71 -     1.83: 154
  Bond restraints: 9035
  Sorted by residual:
  bond pdb=" CB  MET C 179 "
       pdb=" CG  MET C 179 "
    ideal  model  delta    sigma   weight residual
    1.520  1.483  0.037 3.00e-02 1.11e+03 1.51e+00
  bond pdb=" CB  ASN G 243 "
       pdb=" CG  ASN G 243 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 2.50e-02 1.60e+03 1.24e+00
  bond pdb=" CB  MET D 179 "
       pdb=" CG  MET D 179 "
    ideal  model  delta    sigma   weight residual
    1.520  1.490  0.030 3.00e-02 1.11e+03 1.02e+00
  bond pdb=" CB  THR C 158 "
       pdb=" CG2 THR C 158 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.30e-01
  bond pdb=" CB  ILE C  61 "
       pdb=" CG2 ILE C  61 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.86e-01
  ... (remaining 9030 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 12099
        2.58 -     5.17: 62
        5.17 -     7.75: 6
        7.75 -    10.34: 1
       10.34 -    12.92: 1
  Bond angle restraints: 12169
  Sorted by residual:
  angle pdb=" CB  MET G  83 "
        pdb=" CG  MET G  83 "
        pdb=" SD  MET G  83 "
      ideal   model   delta    sigma   weight residual
     112.70  125.62  -12.92 3.00e+00 1.11e-01 1.86e+01
  angle pdb=" CG  MET G  83 "
        pdb=" SD  MET G  83 "
        pdb=" CE  MET G  83 "
      ideal   model   delta    sigma   weight residual
     100.90  106.34   -5.44 2.20e+00 2.07e-01 6.12e+00
  angle pdb=" CB  MET F  52 "
        pdb=" CG  MET F  52 "
        pdb=" SD  MET F  52 "
      ideal   model   delta    sigma   weight residual
     112.70  120.06   -7.36 3.00e+00 1.11e-01 6.02e+00
  angle pdb=" C   ASP E 148 "
        pdb=" N   VAL E 149 "
        pdb=" CA  VAL E 149 "
      ideal   model   delta    sigma   weight residual
     121.55  118.18    3.37 1.42e+00 4.96e-01 5.63e+00
  angle pdb=" CB  MET B  30 "
        pdb=" CG  MET B  30 "
        pdb=" SD  MET B  30 "
      ideal   model   delta    sigma   weight residual
     112.70  105.71    6.99 3.00e+00 1.11e-01 5.43e+00
  ... (remaining 12164 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 4577
       17.90 -    35.79: 655
       35.79 -    53.69: 175
       53.69 -    71.59: 32
       71.59 -    89.48: 11
  Dihedral angle restraints: 5450
    sinusoidal: 2132
      harmonic: 3318
  Sorted by residual:
  dihedral pdb=" CA  ASP D 133 "
           pdb=" CB  ASP D 133 "
           pdb=" CG  ASP D 133 "
           pdb=" OD1 ASP D 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.40   59.40     1      2.00e+01 2.50e-03 1.18e+01
  dihedral pdb=" CB  GLU C 211 "
           pdb=" CG  GLU C 211 "
           pdb=" CD  GLU C 211 "
           pdb=" OE1 GLU C 211 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.48   89.48     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CA  ASP F  31 "
           pdb=" CB  ASP F  31 "
           pdb=" CG  ASP F  31 "
           pdb=" OD1 ASP F  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.55   55.55     1      2.00e+01 2.50e-03 1.04e+01
  ... (remaining 5447 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 909
       0.029 -    0.059: 370
       0.059 -    0.088: 119
       0.088 -    0.118: 44
       0.118 -    0.147: 5
  Chirality restraints: 1447
  Sorted by residual:
  chirality pdb=" CA  ASP E 148 "
            pdb=" N   ASP E 148 "
            pdb=" C   ASP E 148 "
            pdb=" CB  ASP E 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.40e-01
  chirality pdb=" CA  ASN G 243 "
            pdb=" N   ASN G 243 "
            pdb=" C   ASN G 243 "
            pdb=" CB  ASN G 243 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.25e-01
  chirality pdb=" CA  PRO D 151 "
            pdb=" N   PRO D 151 "
            pdb=" C   PRO D 151 "
            pdb=" CB  PRO D 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.21e-01
  ... (remaining 1444 not shown)

  Planarity restraints: 1544
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN G 243 "    0.014 2.00e-02 2.50e+03   2.77e-02 7.67e+00
        pdb=" C   ASN G 243 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   ASN G 243 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLU G 244 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP C 148 "   -0.009 2.00e-02 2.50e+03   1.79e-02 3.20e+00
        pdb=" CG  ASP C 148 "    0.031 2.00e-02 2.50e+03
        pdb=" OD1 ASP C 148 "   -0.011 2.00e-02 2.50e+03
        pdb=" OD2 ASP C 148 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  15 "   -0.028 5.00e-02 4.00e+02   4.21e-02 2.84e+00
        pdb=" N   PRO B  16 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B  16 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B  16 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1541 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 50
        2.65 -     3.21: 8360
        3.21 -     3.77: 14464
        3.77 -     4.34: 18178
        4.34 -     4.90: 31349
  Nonbonded interactions: 72401
  Sorted by model distance:
  nonbonded pdb=" OG1 THR E 158 "
            pdb=" OG1 THR E 186 "
     model   vdw
     2.087 3.040
  nonbonded pdb=" O   PHE D  29 "
            pdb=" OH  TYR D 188 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" O   ASN G 243 "
            pdb=" ND2 ASN G 243 "
     model   vdw
     2.157 3.120
  nonbonded pdb=" OD1 ASP E  31 "
            pdb=" OH  TYR E 188 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" O   LEU A  35 "
            pdb=" OG  SER A  38 "
     model   vdw
     2.201 3.040
  ... (remaining 72396 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'
  selection = (chain 'B' and resid 14 through 59)
}
ncs_group {
  reference = (chain 'C' and (resid 29 through 154 or resid 156 through 250))
  selection = (chain 'D' and (resid 29 through 154 or resid 156 through 250))
  selection = (chain 'E' and (resid 29 through 154 or resid 156 through 250))
  selection = (chain 'F' and (resid 15 through 16 or resid 31 through 154 or resid 156 through \ 
 250))
  selection = (chain 'G' and (resid 29 through 154 or resid 156 through 250))
}

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=0.39 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.710
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9035  Z= 0.152
  Angle     :  0.530  12.923  12169  Z= 0.271
  Chirality :  0.037   0.147   1447
  Planarity :  0.004   0.042   1544
  Dihedral  : 18.051  89.484   3310
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  : 29.12 %
    Favored  : 70.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.30 (0.25), residues: 1149
  helix:  2.52 (0.16), residues: 996
  sheet:  None (None), residues: 0
  loop : -0.18 (0.54), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G 216 
 TYR   0.008   0.001   TYR D 241 
 PHE   0.014   0.002   PHE E 143 
 TRP   0.004   0.002   TRP A  18 
 HIS   0.004   0.001   HIS E 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 9035)
  covalent geometry    : angle       0.53008 (12169)
  hydrogen bonds       : bond        0.10331 (  812)
  hydrogen bonds       : angle       4.90308 ( 2411)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.332 
Fit side-chains
REVERT: B   30 MET cc_start: 0.8053 (ttt) cc_final: 0.7768 (ttm)
REVERT: E   75 ASP cc_start: 0.8422 (m-30) cc_final: 0.7674 (t70)
  outliers start: 1
  outliers final: 1
  residues processed: 125
  average time/residue: 0.0891
  time to fit residues: 16.1151
Evaluate side-chains
  127 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  243 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0070
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.0040
   overall best weight:    0.4812

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.186506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.139824 restraints weight = 18425.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 6.65
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3484
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3484 r_free = 0.3484    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3484 r_free = 0.3484    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3484
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.0769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9035  Z= 0.109
  Angle     :  0.445   7.149  12169  Z= 0.231
  Chirality :  0.035   0.110   1447
  Planarity :  0.003   0.041   1544
  Dihedral  :  3.317  13.772   1225
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  : 27.42 %
    Favored  : 71.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.96 (0.25), residues: 1149
  helix:  2.96 (0.16), residues: 1007
  sheet:  None (None), residues: 0
  loop : -0.17 (0.55), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 216 
 TYR   0.004   0.001   TYR G 241 
 PHE   0.016   0.001   PHE A  39 
 TRP   0.003   0.001   TRP A  18 
 HIS   0.002   0.001   HIS C 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 9035)
  covalent geometry    : angle       0.44482 (12169)
  hydrogen bonds       : bond        0.03883 (  812)
  hydrogen bonds       : angle       3.57126 ( 2411)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 130
  time to evaluate  : 0.347 
Fit side-chains
REVERT: C   67 MET cc_start: 0.7223 (ptt) cc_final: 0.6785 (ptp)
REVERT: C  239 LYS cc_start: 0.7415 (mtpp) cc_final: 0.7078 (mtpp)
REVERT: E   75 ASP cc_start: 0.8530 (m-30) cc_final: 0.7635 (t70)
REVERT: E  179 MET cc_start: 0.8403 (tpt) cc_final: 0.6969 (tpt)
REVERT: F  148 ASP cc_start: 0.7725 (m-30) cc_final: 0.7477 (m-30)
REVERT: F  207 ARG cc_start: 0.8354 (tpt-90) cc_final: 0.8102 (tpp80)
  outliers start: 6
  outliers final: 2
  residues processed: 134
  average time/residue: 0.0846
  time to fit residues: 16.9198
Evaluate side-chains
  128 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 126
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain E residue  205 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0470
   chunk 11 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0040
   chunk 62 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 101 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9980
   overall best weight:    0.6092

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.186522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.135172 restraints weight = 15382.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 1.80
r_work: 0.3157 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3135
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3135
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.0971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9035  Z= 0.106
  Angle     :  0.427   5.832  12169  Z= 0.223
  Chirality :  0.035   0.114   1447
  Planarity :  0.003   0.042   1544
  Dihedral  :  3.242  13.107   1223
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 27.42 %
    Favored  : 71.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.18 (0.25), residues: 1149
  helix:  3.10 (0.16), residues: 1009
  sheet:  None (None), residues: 0
  loop : -0.13 (0.55), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G 216 
 TYR   0.004   0.001   TYR F 188 
 PHE   0.014   0.001   PHE A  39 
 TRP   0.003   0.001   TRP B  18 
 HIS   0.002   0.001   HIS E 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 9035)
  covalent geometry    : angle       0.42673 (12169)
  hydrogen bonds       : bond        0.03773 (  812)
  hydrogen bonds       : angle       3.44704 ( 2411)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 133
  time to evaluate  : 0.338 
Fit side-chains
REVERT: C   67 MET cc_start: 0.7663 (ptt) cc_final: 0.7129 (ptp)
REVERT: C  239 LYS cc_start: 0.7337 (mtpp) cc_final: 0.7084 (mtpp)
REVERT: E   75 ASP cc_start: 0.8521 (m-30) cc_final: 0.7535 (t70)
REVERT: F  148 ASP cc_start: 0.8344 (m-30) cc_final: 0.8025 (m-30)
REVERT: F  207 ARG cc_start: 0.8856 (tpt-90) cc_final: 0.8532 (tpp80)
REVERT: G   83 MET cc_start: 0.4914 (mmp) cc_final: 0.4629 (mmm)
  outliers start: 8
  outliers final: 6
  residues processed: 137
  average time/residue: 0.0851
  time to fit residues: 17.1994
Evaluate side-chains
  134 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 128
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain C residue  165 MET
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain E residue  105 MET
Chi-restraints excluded: chain G residue  183 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 114 optimal weight:    0.9990
   chunk 69 optimal weight:    7.9990
   chunk 27 optimal weight:    9.9990
   chunk 39 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.185708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.132131 restraints weight = 15647.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 1.76
r_work: 0.3137 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3110
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3110 r_free = 0.3110    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3110
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.1018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9035  Z= 0.115
  Angle     :  0.435   6.605  12169  Z= 0.227
  Chirality :  0.035   0.145   1447
  Planarity :  0.003   0.043   1544
  Dihedral  :  3.256  13.147   1223
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 26.25 %
    Favored  : 71.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.17 (0.25), residues: 1149
  helix:  3.09 (0.16), residues: 1012
  sheet:  None (None), residues: 0
  loop : -0.11 (0.55), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G 216 
 TYR   0.004   0.001   TYR D 241 
 PHE   0.014   0.001   PHE A  39 
 TRP   0.003   0.001   TRP B  18 
 HIS   0.002   0.001   HIS E 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9035)
  covalent geometry    : angle       0.43497 (12169)
  hydrogen bonds       : bond        0.03832 (  812)
  hydrogen bonds       : angle       3.42623 ( 2411)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.344 
Fit side-chains
REVERT: B   56 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.6650 (m-10)
REVERT: C   56 PHE cc_start: 0.7170 (m-10) cc_final: 0.6916 (m-80)
REVERT: C   67 MET cc_start: 0.7486 (ptt) cc_final: 0.6931 (ptp)
REVERT: C   69 LYS cc_start: 0.8204 (mttp) cc_final: 0.7460 (ptmm)
REVERT: C  239 LYS cc_start: 0.7276 (mtpp) cc_final: 0.7066 (mtpp)
REVERT: D  179 MET cc_start: 0.7705 (tpp) cc_final: 0.7333 (ttt)
REVERT: E   75 ASP cc_start: 0.8517 (m-30) cc_final: 0.7557 (t70)
REVERT: F   83 MET cc_start: 0.4847 (mmt) cc_final: 0.4547 (mmt)
REVERT: F  148 ASP cc_start: 0.8391 (m-30) cc_final: 0.7990 (m-30)
REVERT: F  207 ARG cc_start: 0.8843 (tpt-90) cc_final: 0.8496 (tpp80)
REVERT: G   83 MET cc_start: 0.4930 (mmp) cc_final: 0.4689 (mmm)
REVERT: G  135 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7230 (mtp180)
  outliers start: 19
  outliers final: 9
  residues processed: 147
  average time/residue: 0.0877
  time to fit residues: 18.9061
Evaluate side-chains
  141 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 130
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain E residue  105 MET
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain G residue  135 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 78 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 95 optimal weight:    0.7980
   chunk 109 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 91 optimal weight:    6.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.180879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.128950 restraints weight = 14413.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.69
r_work: 0.3073 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2913 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.1081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   9035  Z= 0.186
  Angle     :  0.524   8.078  12169  Z= 0.271
  Chirality :  0.039   0.136   1447
  Planarity :  0.004   0.045   1544
  Dihedral  :  3.519  12.946   1223
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 26.57 %
    Favored  : 71.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.65 (0.25), residues: 1149
  helix:  2.73 (0.16), residues: 1010
  sheet:  None (None), residues: 0
  loop : -0.12 (0.55), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG G 216 
 TYR   0.011   0.001   TYR D 237 
 PHE   0.027   0.002   PHE A  32 
 TRP   0.004   0.002   TRP A  18 
 HIS   0.005   0.001   HIS D 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 9035)
  covalent geometry    : angle       0.52424 (12169)
  hydrogen bonds       : bond        0.04705 (  812)
  hydrogen bonds       : angle       3.63768 ( 2411)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.345 
Fit side-chains
REVERT: B   56 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.6642 (m-10)
REVERT: C   56 PHE cc_start: 0.7482 (m-10) cc_final: 0.7046 (m-80)
REVERT: C  239 LYS cc_start: 0.7255 (mtpp) cc_final: 0.6985 (mtpp)
REVERT: D  179 MET cc_start: 0.8159 (tpp) cc_final: 0.7688 (ttt)
REVERT: G   83 MET cc_start: 0.4991 (mmp) cc_final: 0.4686 (mmm)
REVERT: G  135 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7299 (mtp180)
  outliers start: 21
  outliers final: 13
  residues processed: 141
  average time/residue: 0.0934
  time to fit residues: 19.0702
Evaluate side-chains
  137 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  237 TYR
Chi-restraints excluded: chain E residue  105 MET
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain G residue  135 ARG
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  183 LEU
Chi-restraints excluded: chain G residue  212 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 33 optimal weight:    0.0000
   chunk 47 optimal weight:    0.1980
   chunk 6 optimal weight:    0.0970
   chunk 71 optimal weight:    6.9990
   chunk 98 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 68 optimal weight:    6.9990
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.5784

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.185232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.133057 restraints weight = 11690.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.55
r_work: 0.3155 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2929
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2929
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9035  Z= 0.110
  Angle     :  0.437   8.231  12169  Z= 0.230
  Chirality :  0.035   0.124   1447
  Planarity :  0.003   0.042   1544
  Dihedral  :  3.342  12.792   1223
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 27.31 %
    Favored  : 71.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.08 (0.25), residues: 1149
  helix:  3.02 (0.16), residues: 1012
  sheet:  None (None), residues: 0
  loop : -0.12 (0.54), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 216 
 TYR   0.011   0.001   TYR D 237 
 PHE   0.017   0.001   PHE A  32 
 TRP   0.004   0.001   TRP A  18 
 HIS   0.002   0.001   HIS C 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 9035)
  covalent geometry    : angle       0.43697 (12169)
  hydrogen bonds       : bond        0.03795 (  812)
  hydrogen bonds       : angle       3.46095 ( 2411)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.365 
Fit side-chains
REVERT: B   56 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.6710 (m-10)
REVERT: C   56 PHE cc_start: 0.7388 (m-10) cc_final: 0.7070 (m-80)
REVERT: C   67 MET cc_start: 0.7347 (ptt) cc_final: 0.6851 (ptp)
REVERT: C   69 LYS cc_start: 0.8150 (mttp) cc_final: 0.7324 (ptmm)
REVERT: C  239 LYS cc_start: 0.7246 (mtpp) cc_final: 0.7034 (mtpp)
REVERT: E   75 ASP cc_start: 0.8576 (m-30) cc_final: 0.7564 (t70)
REVERT: E  243 ASN cc_start: 0.7639 (m-40) cc_final: 0.7100 (m-40)
REVERT: F  148 ASP cc_start: 0.8515 (m-30) cc_final: 0.8101 (m-30)
REVERT: G   83 MET cc_start: 0.4867 (mmp) cc_final: 0.4557 (mmm)
REVERT: G  135 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7337 (mtp180)
  outliers start: 15
  outliers final: 11
  residues processed: 143
  average time/residue: 0.0877
  time to fit residues: 18.4534
Evaluate side-chains
  140 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  237 TYR
Chi-restraints excluded: chain E residue  105 MET
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain G residue  135 ARG
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  183 LEU
Chi-restraints excluded: chain G residue  212 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 15 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 106 optimal weight:    4.9990
   chunk 111 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.184898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 109)---------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.122950 restraints weight = 10690.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 1.87
r_work: 0.3070 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3039
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3039 r_free = 0.3039    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3039 r_free = 0.3039    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3039
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9035  Z= 0.113
  Angle     :  0.434   5.836  12169  Z= 0.229
  Chirality :  0.035   0.127   1447
  Planarity :  0.003   0.042   1544
  Dihedral  :  3.295  12.432   1223
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 27.10 %
    Favored  : 70.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.18 (0.24), residues: 1149
  helix:  3.11 (0.16), residues: 1006
  sheet:  None (None), residues: 0
  loop : -0.15 (0.53), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G 216 
 TYR   0.011   0.001   TYR D 237 
 PHE   0.022   0.001   PHE F  44 
 TRP   0.002   0.001   TRP B  18 
 HIS   0.002   0.001   HIS D 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 9035)
  covalent geometry    : angle       0.43405 (12169)
  hydrogen bonds       : bond        0.03862 (  812)
  hydrogen bonds       : angle       3.43715 ( 2411)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.387 
Fit side-chains
REVERT: B   56 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.6503 (m-10)
REVERT: C   56 PHE cc_start: 0.7118 (m-10) cc_final: 0.6787 (m-80)
REVERT: C   67 MET cc_start: 0.7265 (ptt) cc_final: 0.6758 (ptp)
REVERT: C   69 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7229 (ptmm)
REVERT: D  179 MET cc_start: 0.7791 (tpp) cc_final: 0.7377 (ttt)
REVERT: E   75 ASP cc_start: 0.8487 (m-30) cc_final: 0.7433 (t70)
REVERT: F  148 ASP cc_start: 0.8361 (m-30) cc_final: 0.7942 (m-30)
REVERT: G   83 MET cc_start: 0.4831 (mmp) cc_final: 0.4570 (mmm)
REVERT: G  135 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7123 (mtp180)
  outliers start: 19
  outliers final: 13
  residues processed: 143
  average time/residue: 0.0837
  time to fit residues: 17.7154
Evaluate side-chains
  144 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain C residue  165 MET
Chi-restraints excluded: chain C residue  205 SER
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  237 TYR
Chi-restraints excluded: chain E residue  105 MET
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain G residue  135 ARG
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  183 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 27 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.185059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.131852 restraints weight = 14459.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.73
r_work: 0.3124 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2926
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2926 r_free = 0.2926    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2926 r_free = 0.2926    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2926
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9035  Z= 0.116
  Angle     :  0.449   7.264  12169  Z= 0.233
  Chirality :  0.036   0.128   1447
  Planarity :  0.003   0.043   1544
  Dihedral  :  3.321  12.694   1223
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 27.31 %
    Favored  : 70.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.18 (0.24), residues: 1149
  helix:  3.12 (0.16), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.18 (0.52), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G 216 
 TYR   0.011   0.001   TYR D 237 
 PHE   0.020   0.001   PHE A  32 
 TRP   0.002   0.001   TRP B  18 
 HIS   0.002   0.001   HIS D 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 9035)
  covalent geometry    : angle       0.44862 (12169)
  hydrogen bonds       : bond        0.03865 (  812)
  hydrogen bonds       : angle       3.45034 ( 2411)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.346 
Fit side-chains
REVERT: B   56 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.6624 (m-10)
REVERT: C   56 PHE cc_start: 0.7315 (m-10) cc_final: 0.6978 (m-80)
REVERT: C   67 MET cc_start: 0.7358 (ptt) cc_final: 0.6846 (ptp)
REVERT: C   69 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7272 (ptmm)
REVERT: D  179 MET cc_start: 0.7976 (tpp) cc_final: 0.7576 (ttt)
REVERT: E   75 ASP cc_start: 0.8517 (m-30) cc_final: 0.7580 (t70)
REVERT: F  148 ASP cc_start: 0.8546 (m-30) cc_final: 0.8112 (m-30)
REVERT: G   83 MET cc_start: 0.4852 (mmp) cc_final: 0.4549 (mmm)
REVERT: G  135 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7291 (mtp180)
  outliers start: 18
  outliers final: 15
  residues processed: 139
  average time/residue: 0.0868
  time to fit residues: 17.8674
Evaluate side-chains
  144 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain C residue  165 MET
Chi-restraints excluded: chain C residue  205 SER
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  237 TYR
Chi-restraints excluded: chain E residue  105 MET
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain E residue  241 TYR
Chi-restraints excluded: chain G residue  135 ARG
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  183 LEU
Chi-restraints excluded: chain G residue  212 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    0.8980
   chunk 36 optimal weight:    9.9990
   chunk 55 optimal weight:    1.9990
   chunk 106 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   chunk 20 optimal weight:    0.5980
   chunk 96 optimal weight:    2.9990
   chunk 113 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.184697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 95)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.132654 restraints weight = 14458.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.73
r_work: 0.3124 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2894
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2894 r_free = 0.2894    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2894
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9035  Z= 0.126
  Angle     :  0.466  10.143  12169  Z= 0.242
  Chirality :  0.036   0.141   1447
  Planarity :  0.004   0.043   1544
  Dihedral  :  3.331  12.208   1223
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 27.10 %
    Favored  : 71.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.14 (0.24), residues: 1149
  helix:  3.09 (0.16), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.16 (0.52), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G 216 
 TYR   0.011   0.001   TYR D 237 
 PHE   0.027   0.001   PHE A  32 
 TRP   0.003   0.001   TRP B  18 
 HIS   0.002   0.001   HIS D 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 9035)
  covalent geometry    : angle       0.46601 (12169)
  hydrogen bonds       : bond        0.03977 (  812)
  hydrogen bonds       : angle       3.46832 ( 2411)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.285 
Fit side-chains
REVERT: B   56 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.6662 (m-10)
REVERT: C   56 PHE cc_start: 0.7359 (m-10) cc_final: 0.6992 (m-80)
REVERT: C   67 MET cc_start: 0.7356 (ptt) cc_final: 0.6831 (ptp)
REVERT: C   69 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7264 (ptmm)
REVERT: C  179 MET cc_start: 0.7609 (mtt) cc_final: 0.7322 (mtp)
REVERT: D  179 MET cc_start: 0.8038 (tpp) cc_final: 0.7648 (ttt)
REVERT: E   75 ASP cc_start: 0.8457 (m-30) cc_final: 0.7585 (t70)
REVERT: E  148 ASP cc_start: 0.8418 (m-30) cc_final: 0.8165 (m-30)
REVERT: F  148 ASP cc_start: 0.8587 (m-30) cc_final: 0.8139 (m-30)
REVERT: G   83 MET cc_start: 0.4880 (mmp) cc_final: 0.4565 (mmm)
REVERT: G  135 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7351 (mtp180)
  outliers start: 17
  outliers final: 14
  residues processed: 139
  average time/residue: 0.0834
  time to fit residues: 16.9465
Evaluate side-chains
  143 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain C residue  205 SER
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  237 TYR
Chi-restraints excluded: chain E residue  105 MET
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain E residue  241 TYR
Chi-restraints excluded: chain G residue  135 ARG
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  183 LEU
Chi-restraints excluded: chain G residue  212 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 48 optimal weight:   20.0000
   chunk 64 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9990
   chunk 99 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 96 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.185092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 97)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.126949 restraints weight = 10334.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 1.91
r_work: 0.3067 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3034
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3034
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.1407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9035  Z= 0.118
  Angle     :  0.455   8.790  12169  Z= 0.235
  Chirality :  0.036   0.126   1447
  Planarity :  0.003   0.043   1544
  Dihedral  :  3.317  12.989   1223
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 26.99 %
    Favored  : 70.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.18 (0.24), residues: 1149
  helix:  3.11 (0.16), residues: 1011
  sheet:  None (None), residues: 0
  loop : -0.21 (0.53), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G 216 
 TYR   0.011   0.001   TYR D 237 
 PHE   0.015   0.001   PHE A  39 
 TRP   0.002   0.001   TRP A  18 
 HIS   0.002   0.001   HIS D 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9035)
  covalent geometry    : angle       0.45482 (12169)
  hydrogen bonds       : bond        0.03866 (  812)
  hydrogen bonds       : angle       3.44767 ( 2411)

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.349 
Fit side-chains
REVERT: B   56 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.6560 (m-10)
REVERT: C   56 PHE cc_start: 0.7159 (m-10) cc_final: 0.6829 (m-80)
REVERT: C   67 MET cc_start: 0.7324 (ptt) cc_final: 0.6800 (ptp)
REVERT: C   69 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7242 (ptmm)
REVERT: E   75 ASP cc_start: 0.8337 (m-30) cc_final: 0.7463 (t70)
REVERT: E  148 ASP cc_start: 0.8349 (m-30) cc_final: 0.8007 (m-30)
REVERT: F  148 ASP cc_start: 0.8393 (m-30) cc_final: 0.7946 (m-30)
REVERT: G   83 MET cc_start: 0.4857 (mmp) cc_final: 0.4585 (mmm)
REVERT: G  135 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7135 (mtp180)
  outliers start: 19
  outliers final: 14
  residues processed: 139
  average time/residue: 0.0821
  time to fit residues: 16.7230
Evaluate side-chains
  144 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain C residue   69 LYS
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain C residue  165 MET
Chi-restraints excluded: chain C residue  205 SER
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  237 TYR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain E residue  241 TYR
Chi-restraints excluded: chain G residue  135 ARG
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  183 LEU
Chi-restraints excluded: chain G residue  212 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 14 optimal weight:   20.0000
   chunk 2 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 72 optimal weight:   20.0000
   chunk 109 optimal weight:    0.7980
   chunk 97 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 88 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 113 optimal weight:    6.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.185354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.139496 restraints weight = 8771.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.95
r_work: 0.3091 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3052
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3052 r_free = 0.3052    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3052 r_free = 0.3052    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3052
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9035  Z= 0.111
  Angle     :  0.446   8.572  12169  Z= 0.231
  Chirality :  0.036   0.128   1447
  Planarity :  0.003   0.043   1544
  Dihedral  :  3.275  13.218   1223
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 27.31 %
    Favored  : 70.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  4.26 (0.24), residues: 1149
  helix:  3.14 (0.16), residues: 1016
  sheet:  None (None), residues: 0
  loop : -0.19 (0.55), residues: 133

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G 216 
 TYR   0.011   0.001   TYR D 237 
 PHE   0.012   0.001   PHE A  39 
 TRP   0.002   0.001   TRP A  18 
 HIS   0.002   0.001   HIS D 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 9035)
  covalent geometry    : angle       0.44557 (12169)
  hydrogen bonds       : bond        0.03789 (  812)
  hydrogen bonds       : angle       3.41086 ( 2411)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2604.99 seconds
wall clock time: 45 minutes 11.66 seconds (2711.66 seconds total)