Starting phenix.real_space_refine
on Mon Feb 10 23:09:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qig_13989/02_2025/7qig_13989.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qig_13989/02_2025/7qig_13989.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qig_13989/02_2025/7qig_13989.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qig_13989/02_2025/7qig_13989.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qig_13989/02_2025/7qig_13989.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qig_13989/02_2025/7qig_13989.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    2007      2.51       5
     N     570      2.21       5
     O     609      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3213
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1071
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1071
          Classifications: {'peptide': 132}
          Link IDs: {'PTRANS': 5, 'TRANS': 126}
    Chain: "B"
      Number of atoms: 1071
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1071
          Classifications: {'peptide': 132}
          Link IDs: {'PTRANS': 5, 'TRANS': 126}
    Chain: "C"
      Number of atoms: 1071
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1071
          Classifications: {'peptide': 132}
          Link IDs: {'PTRANS': 5, 'TRANS': 126}
  Time building chain proxies: 3.47, per 1000 atoms: 1.08
  Number of scatterers: 3213
  At special positions: 0
  Unit cell: (90.695, 124.839, 39.479, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O     609      8.00
     N     570      7.00
     C    2007      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 178 " - pdb=" SG  CYS A 213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 178 " - pdb=" SG  CYS B 213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 178 " - pdb=" SG  CYS C 213 " distance=2.03

  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: 0.81
  Conformation dependent library (CDL) restraints added in 350.5 milliseconds
  

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  738

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 14 sheets defined
      0.0% alpha, 71.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 95 through 99
      removed outlier: 6.310A  pdb=" N   HIS A  95 " --> pdb=" O   ASN B  96 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   TRP B  98 " --> pdb=" O   HIS A  95 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   GLN A  97 " --> pdb=" O   TRP B  98 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 105 through 115
      removed outlier: 6.880A  pdb=" N   VAL B 111 " --> pdb=" O   HIS A 110 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   ALA A 112 " --> pdb=" O   VAL B 111 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   GLY B 113 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   VAL A 111 " --> pdb=" O   HIS C 110 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ALA C 112 " --> pdb=" O   VAL A 111 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   GLY A 113 " --> pdb=" O   ALA C 112 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 120 through 121
      removed outlier: 6.584A  pdb=" N   VAL A 120 " --> pdb=" O   VAL C 121 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 127 through 134
      removed outlier: 6.324A  pdb=" N   TYR A 127 " --> pdb=" O   MET B 128 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   GLY B 130 " --> pdb=" O   TYR A 127 " (cutoff:3.500A)
      removed outlier: 8.873A  pdb=" N   LEU A 129 " --> pdb=" O   GLY B 130 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   ALA B 132 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
      removed outlier: 9.012A  pdb=" N   SER A 131 " --> pdb=" O   ALA B 132 " (cutoff:3.500A)
      removed outlier: 10.401A  pdb=" N   SER B 134 " --> pdb=" O   SER A 131 " (cutoff:3.500A)
      removed outlier: 8.986A  pdb=" N   MET A 133 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   SER C 131 " --> pdb=" O   GLY A 130 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   ALA A 132 " --> pdb=" O   SER C 131 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   MET C 133 " --> pdb=" O   ALA A 132 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   SER A 134 " --> pdb=" O   MET C 133 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 137 through 139
      removed outlier: 6.350A  pdb=" N   ILE A 138 " --> pdb=" O   HIS B 139 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 142 through 146
      removed outlier: 6.237A  pdb=" N   ASN A 142 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   GLU B 145 " --> pdb=" O   ASN A 142 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   TRP A 144 " --> pdb=" O   GLU B 145 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 150
      removed outlier: 6.418A  pdb=" N   TYR A 149 " --> pdb=" O   ARG B 150 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 154 through 155
      removed outlier: 6.734A  pdb=" N   TYR A 154 " --> pdb=" O   ARG C 155 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 162
      removed outlier: 6.505A  pdb=" N   GLN A 159 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   TYR B 162 " --> pdb=" O   GLN A 159 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   TYR A 161 " --> pdb=" O   TYR B 162 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 166 through 172
      removed outlier: 7.025A  pdb=" N   GLN B 171 " --> pdb=" O   ASN A 170 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   ASN A 172 " --> pdb=" O   GLN B 171 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   GLN A 167 " --> pdb=" O   TYR C 168 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   ASN C 170 " --> pdb=" O   GLN A 167 " (cutoff:3.500A)
      removed outlier: 8.649A  pdb=" N   SER A 169 " --> pdb=" O   ASN C 170 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   ASN C 172 " --> pdb=" O   SER A 169 " (cutoff:3.500A)
      removed outlier: 9.040A  pdb=" N   GLN A 171 " --> pdb=" O   ASN C 172 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 175 through 191
      removed outlier: 8.937A  pdb=" N   VAL A 175 " --> pdb=" O   HIS B 176 " (cutoff:3.500A)
      removed outlier: 7.908A  pdb=" N   CYS B 178 " --> pdb=" O   VAL A 175 " (cutoff:3.500A)
      removed outlier: 9.127A  pdb=" N   ASP A 177 " --> pdb=" O   CYS B 178 " (cutoff:3.500A)
      removed outlier: 9.686A  pdb=" N   ASN B 180 " --> pdb=" O   ASP A 177 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   VAL A 179 " --> pdb=" O   ASN B 180 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   THR B 182 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   ILE A 181 " --> pdb=" O   THR B 182 " (cutoff:3.500A)
      removed outlier: 8.050A  pdb=" N   LYS B 184 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ILE A 183 " --> pdb=" O   LYS B 184 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   HIS B 186 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   GLN A 185 " --> pdb=" O   HIS B 186 " (cutoff:3.500A)
      removed outlier: 8.089A  pdb=" N   VAL B 188 " --> pdb=" O   GLN A 185 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   THR A 187 " --> pdb=" O   VAL B 188 " (cutoff:3.500A)
      removed outlier: 8.319A  pdb=" N   THR B 190 " --> pdb=" O   THR A 187 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   THR A 189 " --> pdb=" O   THR B 190 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   GLY B 194 " --> pdb=" O   THR A 191 " (cutoff:3.500A)
      removed outlier: 9.087A  pdb=" N   LYS A 193 " --> pdb=" O   GLY B 194 " (cutoff:3.500A)
      removed outlier: 9.696A  pdb=" N   ASN B 196 " --> pdb=" O   LYS A 193 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   GLU A 195 " --> pdb=" O   ASN B 196 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   THR B 198 " --> pdb=" O   GLU A 195 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   PHE A 197 " --> pdb=" O   THR B 198 " (cutoff:3.500A)
      removed outlier: 8.644A  pdb=" N   THR B 200 " --> pdb=" O   PHE A 197 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   GLU A 199 " --> pdb=" O   THR B 200 " (cutoff:3.500A)
      removed outlier: 8.212A  pdb=" N   VAL B 202 " --> pdb=" O   GLU A 199 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ASP A 201 " --> pdb=" O   VAL B 202 " (cutoff:3.500A)
      removed outlier: 8.233A  pdb=" N   MET B 204 " --> pdb=" O   ASP A 201 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   LYS A 203 " --> pdb=" O   MET B 204 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 175 through 191
      removed outlier: 8.937A  pdb=" N   VAL A 175 " --> pdb=" O   HIS B 176 " (cutoff:3.500A)
      removed outlier: 7.908A  pdb=" N   CYS B 178 " --> pdb=" O   VAL A 175 " (cutoff:3.500A)
      removed outlier: 9.127A  pdb=" N   ASP A 177 " --> pdb=" O   CYS B 178 " (cutoff:3.500A)
      removed outlier: 9.686A  pdb=" N   ASN B 180 " --> pdb=" O   ASP A 177 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   VAL A 179 " --> pdb=" O   ASN B 180 " (cutoff:3.500A)
      removed outlier: 8.460A  pdb=" N   THR B 182 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   ILE A 181 " --> pdb=" O   THR B 182 " (cutoff:3.500A)
      removed outlier: 8.050A  pdb=" N   LYS B 184 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   ILE A 183 " --> pdb=" O   LYS B 184 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   HIS B 186 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   GLN A 185 " --> pdb=" O   HIS B 186 " (cutoff:3.500A)
      removed outlier: 8.089A  pdb=" N   VAL B 188 " --> pdb=" O   GLN A 185 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   THR A 187 " --> pdb=" O   VAL B 188 " (cutoff:3.500A)
      removed outlier: 8.319A  pdb=" N   THR B 190 " --> pdb=" O   THR A 187 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   THR A 189 " --> pdb=" O   THR B 190 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   ASP C 177 " --> pdb=" O   HIS A 176 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   CYS A 178 " --> pdb=" O   ASP C 177 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   VAL C 179 " --> pdb=" O   CYS A 178 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ASN A 180 " --> pdb=" O   VAL C 179 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   LYS C 193 " --> pdb=" O   THR A 192 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   GLY A 194 " --> pdb=" O   LYS C 193 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   GLU C 195 " --> pdb=" O   GLY A 194 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 211 through 219
      removed outlier: 7.061A  pdb=" N   CYS B 213 " --> pdb=" O   MET A 212 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   VAL A 214 " --> pdb=" O   CYS B 213 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   THR B 215 " --> pdb=" O   VAL A 214 " (cutoff:3.500A)
      removed outlier: 8.686A  pdb=" N   GLN A 211 " --> pdb=" O   MET C 212 " (cutoff:3.500A)
      removed outlier: 5.966A  pdb=" N   VAL C 214 " --> pdb=" O   GLN A 211 " (cutoff:3.500A)
      removed outlier: 8.629A  pdb=" N   CYS A 213 " --> pdb=" O   VAL C 214 " (cutoff:3.500A)
      removed outlier: 9.562A  pdb=" N   GLN C 216 " --> pdb=" O   CYS A 213 " (cutoff:3.500A)
      removed outlier: 5.713A  pdb=" N   THR A 215 " --> pdb=" O   GLN C 216 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   GLN C 218 " --> pdb=" O   THR A 215 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   TYR A 217 " --> pdb=" O   GLN C 218 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 222 through 224
      removed outlier: 6.598A  pdb=" N   ALA A 223 " --> pdb=" O   TYR B 224 " (cutoff:3.500A)

    68 hydrogen bonds defined for protein.
    204 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.80

  Time building geometry restraints manager: 0.94 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: 1065
        1.34 -     1.46: 707
        1.46 -     1.58: 1474
        1.58 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 3294
  Sorted by residual:
  bond pdb=" C   LYS B 103 "
       pdb=" O   LYS B 103 "
    ideal  model  delta    sigma   weight residual
    1.233  1.224  0.009 4.80e-03 4.34e+04 3.61e+00
  bond pdb=" N   THR C  94 "
       pdb=" CA  THR C  94 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.95e+00
  bond pdb=" N   THR A  94 "
       pdb=" CA  THR A  94 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.77e+00
  bond pdb=" N   THR B  94 "
       pdb=" CA  THR B  94 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.64e+00
  bond pdb=" CB  ARG B 207 "
       pdb=" CG  ARG B 207 "
    ideal  model  delta    sigma   weight residual
    1.520  1.494  0.026 3.00e-02 1.11e+03 7.43e-01
  ... (remaining 3289 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.05: 4015
        1.05 -     2.09: 350
        2.09 -     3.14: 73
        3.14 -     4.18: 18
        4.18 -     5.23: 5
  Bond angle restraints: 4461
  Sorted by residual:
  angle pdb=" C   TYR C 162 "
        pdb=" N   ARG C 163 "
        pdb=" CA  ARG C 163 "
      ideal   model   delta    sigma   weight residual
     122.59  117.40    5.19 1.11e+00 8.12e-01 2.19e+01
  angle pdb=" N   ARG A 163 "
        pdb=" CA  ARG A 163 "
        pdb=" C   ARG A 163 "
      ideal   model   delta    sigma   weight residual
     109.30  113.66   -4.36 1.49e+00 4.50e-01 8.57e+00
  angle pdb=" N   ARG C 163 "
        pdb=" CA  ARG C 163 "
        pdb=" C   ARG C 163 "
      ideal   model   delta    sigma   weight residual
     109.30  112.74   -3.44 1.49e+00 4.50e-01 5.33e+00
  angle pdb=" N   GLY C 123 "
        pdb=" CA  GLY C 123 "
        pdb=" C   GLY C 123 "
      ideal   model   delta    sigma   weight residual
     113.18  118.41   -5.23 2.37e+00 1.78e-01 4.87e+00
  angle pdb=" C   GLU A 195 "
        pdb=" CA  GLU A 195 "
        pdb=" CB  GLU A 195 "
      ideal   model   delta    sigma   weight residual
     112.00  108.15    3.85 1.79e+00 3.12e-01 4.63e+00
  ... (remaining 4456 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 1805
       17.96 -    35.93: 102
       35.93 -    53.89: 37
       53.89 -    71.86: 9
       71.86 -    89.82: 6
  Dihedral angle restraints: 1959
    sinusoidal: 795
      harmonic: 1164
  Sorted by residual:
  dihedral pdb=" CA  CYS B 178 "
           pdb=" C   CYS B 178 "
           pdb=" N   VAL B 179 "
           pdb=" CA  VAL B 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.76  -18.24     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  MET C 204 "
           pdb=" C   MET C 204 "
           pdb=" N   MET C 205 "
           pdb=" CA  MET C 205 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.78   18.22     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  CYS A 178 "
           pdb=" C   CYS A 178 "
           pdb=" N   VAL A 179 "
           pdb=" CA  VAL A 179 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.05  -17.95     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 1956 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 238
       0.033 -    0.066: 149
       0.066 -    0.098: 33
       0.098 -    0.131: 22
       0.131 -    0.163: 14
  Chirality restraints: 456
  Sorted by residual:
  chirality pdb=" CA  ILE B 183 "
            pdb=" N   ILE B 183 "
            pdb=" C   ILE B 183 "
            pdb=" CB  ILE B 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.67e-01
  chirality pdb=" CA  VAL C 175 "
            pdb=" N   VAL C 175 "
            pdb=" C   VAL C 175 "
            pdb=" CB  VAL C 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.77e-01
  chirality pdb=" CA  VAL A 175 "
            pdb=" N   VAL A 175 "
            pdb=" C   VAL A 175 "
            pdb=" CB  VAL A 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.70e-01
  ... (remaining 453 not shown)

  Planarity restraints: 585
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 207 "    0.277 9.50e-02 1.11e+02   1.24e-01 9.44e+00
        pdb=" NE  ARG B 207 "   -0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 207 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 207 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 207 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 163 "   -0.194 9.50e-02 1.11e+02   8.71e-02 4.86e+00
        pdb=" NE  ARG C 163 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 163 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 163 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 163 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 146 "    0.009 2.00e-02 2.50e+03   1.74e-02 3.04e+00
        pdb=" CG  ASP A 146 "   -0.030 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 146 "    0.011 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 146 "    0.011 2.00e-02 2.50e+03
  ... (remaining 582 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 37
        2.69 -     3.24: 2767
        3.24 -     3.80: 5117
        3.80 -     4.35: 6629
        4.35 -     4.90: 11919
  Nonbonded interactions: 26469
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B 193 "
            pdb=" OE2 GLU B 195 "
     model   vdw
     2.138 3.120
  nonbonded pdb=" O   THR B 191 "
            pdb=" OG1 THR B 191 "
     model   vdw
     2.483 3.040
  nonbonded pdb=" OG1 THR A 215 "
            pdb=" O   THR B 215 "
     model   vdw
     2.498 3.040
  nonbonded pdb=" O   HIS B 176 "
            pdb=" OD1 ASP B 177 "
     model   vdw
     2.501 3.040
  nonbonded pdb=" O   HIS A 176 "
            pdb=" OD1 ASP A 177 "
     model   vdw
     2.501 3.040
  ... (remaining 26464 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.710
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.670
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
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      :  0.005   0.033   3294  Z= 0.317
  Angle     :  0.695   5.229   4461  Z= 0.401
  Chirality :  0.051   0.163    456
  Planarity :  0.007   0.124    585
  Dihedral  : 14.668  89.822   1212
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.18 (0.28), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.21), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  98 
 HIS   0.004   0.001   HIS C 139 
 PHE   0.021   0.004   PHE B 140 
 TYR   0.025   0.003   TYR A 149 
 ARG   0.008   0.001   ARG C 163 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8529 (mttt) cc_final: 0.6756 (mttt)
REVERT: A  128 MET cc_start: 0.9142 (mtp) cc_final: 0.8867 (mtp)
REVERT: A  155 ARG cc_start: 0.7644 (mtt90) cc_final: 0.7017 (mtt-85)
REVERT: A  205 MET cc_start: 0.9202 (mtt) cc_final: 0.8666 (mtt)
REVERT: B  135 ARG cc_start: 0.8588 (ttt180) cc_final: 0.8366 (ttt180)
REVERT: B  147 ARG cc_start: 0.8447 (mtm180) cc_final: 0.8226 (mtm180)
REVERT: B  155 ARG cc_start: 0.6889 (mtt-85) cc_final: 0.6180 (mtp85)
REVERT: B  163 ARG cc_start: 0.8024 (ptt180) cc_final: 0.7414 (pmt-80)
REVERT: C  109 LYS cc_start: 0.8666 (mttt) cc_final: 0.6750 (mttt)
REVERT: C  135 ARG cc_start: 0.8685 (ttt180) cc_final: 0.8438 (ttt180)
  outliers start: 0
  outliers final: 1
  residues processed: 86
  average time/residue: 1.8124
  time to fit residues: 158.7706
Evaluate side-chains
  75 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  204 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    0.4980
   chunk 29 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0980
   chunk 10 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 30 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.4980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.110983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.099995 restraints weight = 4248.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 1.42
r_work: 0.3334 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3248 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3294  Z= 0.196
  Angle     :  0.625   5.180   4461  Z= 0.350
  Chirality :  0.049   0.143    456
  Planarity :  0.003   0.022    585
  Dihedral  :  6.103  17.930    447
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  :  8.99 %
    Favored  : 88.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.12 (0.29), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.13 (0.22), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP B  98 
 HIS   0.003   0.001   HIS C 186 
 PHE   0.025   0.005   PHE C 140 
 TYR   0.017   0.002   TYR A 149 
 ARG   0.003   0.000   ARG C 163 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8558 (mttt) cc_final: 0.7034 (mtpt)
REVERT: A  128 MET cc_start: 0.9308 (mtp) cc_final: 0.9037 (mtp)
REVERT: A  155 ARG cc_start: 0.8472 (mtt90) cc_final: 0.7280 (mtt180)
REVERT: A  163 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8365 (ptt90)
REVERT: B  147 ARG cc_start: 0.8804 (mtm180) cc_final: 0.8560 (mtm180)
REVERT: B  155 ARG cc_start: 0.7384 (mtt-85) cc_final: 0.6187 (mtp85)
REVERT: B  163 ARG cc_start: 0.8684 (ptt180) cc_final: 0.7641 (pmt-80)
REVERT: B  184 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8408 (ptpp)
REVERT: B  193 LYS cc_start: 0.8829 (tttp) cc_final: 0.8564 (tttm)
REVERT: C  109 LYS cc_start: 0.8817 (mttt) cc_final: 0.7632 (mtpt)
REVERT: C  163 ARG cc_start: 0.5968 (OUTLIER) cc_final: 0.4151 (mmt180)
REVERT: C  204 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7983 (tpt)
  outliers start: 9
  outliers final: 1
  residues processed: 78
  average time/residue: 1.9202
  time to fit residues: 152.3208
Evaluate side-chains
  78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain B residue  184 LYS
Chi-restraints excluded: chain C residue  163 ARG
Chi-restraints excluded: chain C residue  204 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 33 optimal weight:    0.1980
   chunk 17 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0870
   chunk 8 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.5560

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.111326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.100228 restraints weight = 4292.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.42
r_work: 0.3331 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3294  Z= 0.201
  Angle     :  0.604   5.232   4461  Z= 0.336
  Chirality :  0.048   0.141    456
  Planarity :  0.003   0.017    585
  Dihedral  :  5.893  17.985    444
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  :  9.86 %
    Favored  : 87.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.16 (0.29), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.16 (0.22), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  98 
 HIS   0.003   0.001   HIS C 139 
 PHE   0.023   0.005   PHE A 140 
 TYR   0.017   0.002   TYR A 148 
 ARG   0.003   0.000   ARG C 163 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.390 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8516 (mttt) cc_final: 0.6968 (mtpt)
REVERT: A  128 MET cc_start: 0.9319 (mtp) cc_final: 0.9039 (mtp)
REVERT: A  155 ARG cc_start: 0.8478 (mtt90) cc_final: 0.7289 (mtt180)
REVERT: A  163 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8333 (ptt90)
REVERT: B  147 ARG cc_start: 0.8756 (mtm180) cc_final: 0.8539 (mtm180)
REVERT: B  155 ARG cc_start: 0.7477 (mtt-85) cc_final: 0.6178 (mtp85)
REVERT: B  163 ARG cc_start: 0.8682 (ptt180) cc_final: 0.7527 (pmt-80)
REVERT: B  193 LYS cc_start: 0.8766 (tttp) cc_final: 0.8424 (tttp)
REVERT: C  109 LYS cc_start: 0.8826 (mttt) cc_final: 0.7072 (mttt)
REVERT: C  163 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.4801 (mmp80)
REVERT: C  204 MET cc_start: 0.8356 (mmm) cc_final: 0.7825 (mmm)
  outliers start: 10
  outliers final: 4
  residues processed: 77
  average time/residue: 1.8878
  time to fit residues: 148.0772
Evaluate side-chains
  80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  153 MET
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain C residue  163 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A  99 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.108516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.097301 restraints weight = 4382.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 1.42
r_work: 0.3294 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 2.69 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3294  Z= 0.349
  Angle     :  0.687   6.359   4461  Z= 0.380
  Chirality :  0.051   0.153    456
  Planarity :  0.004   0.025    585
  Dihedral  :  6.161  18.762    444
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.51 %
    Favored  : 89.49 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 10.72 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.17 (0.29), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.17 (0.22), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  98 
 HIS   0.005   0.002   HIS C 139 
 PHE   0.026   0.006   PHE A 140 
 TYR   0.017   0.002   TYR B 149 
 ARG   0.005   0.001   ARG C 163 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8432 (mttt) cc_final: 0.6975 (mtpt)
REVERT: A  155 ARG cc_start: 0.8488 (mtt90) cc_final: 0.7240 (mtt180)
REVERT: A  163 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8324 (ptt90)
REVERT: B  163 ARG cc_start: 0.8749 (ptt180) cc_final: 0.7653 (pmt-80)
REVERT: B  193 LYS cc_start: 0.8804 (tttp) cc_final: 0.8478 (tttm)
REVERT: C  109 LYS cc_start: 0.8824 (mttt) cc_final: 0.7822 (mtpt)
REVERT: C  135 ARG cc_start: 0.9029 (ttt-90) cc_final: 0.8822 (ttt-90)
REVERT: C  163 ARG cc_start: 0.6235 (OUTLIER) cc_final: 0.4515 (mmp-170)
REVERT: C  204 MET cc_start: 0.8410 (mmm) cc_final: 0.7822 (mmm)
  outliers start: 9
  outliers final: 4
  residues processed: 74
  average time/residue: 1.8237
  time to fit residues: 137.4313
Evaluate side-chains
  79 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain C residue  163 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    1.1786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.108064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.096948 restraints weight = 4396.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 1.42
r_work: 0.3290 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035   3294  Z= 0.377
  Angle     :  0.701   6.566   4461  Z= 0.388
  Chirality :  0.051   0.151    456
  Planarity :  0.004   0.036    585
  Dihedral  :  6.268  19.696    444
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.74 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 12.46 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.22 (0.29), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.21 (0.22), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A  98 
 HIS   0.005   0.002   HIS C 139 
 PHE   0.025   0.006   PHE A 140 
 TYR   0.016   0.002   TYR A 217 
 ARG   0.005   0.001   ARG C 163 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8475 (mttt) cc_final: 0.7016 (mtpt)
REVERT: A  155 ARG cc_start: 0.8397 (mtt90) cc_final: 0.7194 (mtt180)
REVERT: A  163 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8328 (ptt90)
REVERT: B  163 ARG cc_start: 0.8824 (ptt180) cc_final: 0.7762 (pmt-80)
REVERT: B  193 LYS cc_start: 0.8761 (tttp) cc_final: 0.8409 (tttm)
REVERT: C  109 LYS cc_start: 0.8833 (mttt) cc_final: 0.7827 (mtpt)
REVERT: C  163 ARG cc_start: 0.6175 (OUTLIER) cc_final: 0.5812 (mmt180)
  outliers start: 10
  outliers final: 3
  residues processed: 76
  average time/residue: 1.8446
  time to fit residues: 142.6467
Evaluate side-chains
  80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain C residue  163 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0570
   overall best weight:    0.7500

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.109907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.098798 restraints weight = 4434.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 1.43
r_work: 0.3313 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3294  Z= 0.255
  Angle     :  0.640   5.817   4461  Z= 0.353
  Chirality :  0.049   0.142    456
  Planarity :  0.003   0.023    585
  Dihedral  :  6.078  18.839    444
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.49 %
    Favored  : 90.51 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 12.46 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.21 (0.29), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.22), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 144 
 HIS   0.004   0.001   HIS C 139 
 PHE   0.025   0.005   PHE A 140 
 TYR   0.018   0.002   TYR B 149 
 ARG   0.004   0.001   ARG C 135 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8428 (mttt) cc_final: 0.7002 (mtpt)
REVERT: A  155 ARG cc_start: 0.8374 (mtt90) cc_final: 0.7264 (mtt-85)
REVERT: A  163 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8335 (ptt90)
REVERT: A  204 MET cc_start: 0.8419 (mtt) cc_final: 0.7886 (tpt)
REVERT: B  163 ARG cc_start: 0.8804 (ptt180) cc_final: 0.7752 (pmt-80)
REVERT: B  193 LYS cc_start: 0.8785 (tttp) cc_final: 0.8377 (tptp)
REVERT: C  109 LYS cc_start: 0.8768 (mttt) cc_final: 0.7721 (mtpt)
REVERT: C  163 ARG cc_start: 0.6159 (OUTLIER) cc_final: 0.5364 (mmp-170)
  outliers start: 11
  outliers final: 4
  residues processed: 78
  average time/residue: 1.8380
  time to fit residues: 145.9035
Evaluate side-chains
  79 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  218 GLN
Chi-restraints excluded: chain C residue  163 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 7 optimal weight:    0.4980
   chunk 17 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.9782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.108690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.097630 restraints weight = 4324.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.40
r_work: 0.3297 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3294  Z= 0.322
  Angle     :  0.677   6.160   4461  Z= 0.373
  Chirality :  0.050   0.142    456
  Planarity :  0.004   0.035    585
  Dihedral  :  6.163  19.062    444
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.74 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 13.91 %
    Favored  : 83.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.19 (0.29), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.19 (0.22), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A  98 
 HIS   0.004   0.001   HIS C 139 
 PHE   0.025   0.006   PHE A 140 
 TYR   0.016   0.002   TYR A 217 
 ARG   0.005   0.001   ARG C 163 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.385 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8402 (mttt) cc_final: 0.6950 (mtpt)
REVERT: A  155 ARG cc_start: 0.8369 (mtt90) cc_final: 0.7211 (mtt-85)
REVERT: A  163 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8326 (ptt90)
REVERT: A  204 MET cc_start: 0.8405 (mtt) cc_final: 0.7842 (tpt)
REVERT: B  163 ARG cc_start: 0.8831 (ptt180) cc_final: 0.7744 (pmt-80)
REVERT: B  184 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8591 (ptpt)
REVERT: B  193 LYS cc_start: 0.8780 (tttp) cc_final: 0.8383 (tttm)
REVERT: C  109 LYS cc_start: 0.8779 (mttt) cc_final: 0.7719 (mtpt)
REVERT: C  163 ARG cc_start: 0.6144 (OUTLIER) cc_final: 0.5829 (mmt180)
  outliers start: 10
  outliers final: 4
  residues processed: 77
  average time/residue: 1.8289
  time to fit residues: 143.4375
Evaluate side-chains
  80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  184 LYS
Chi-restraints excluded: chain B residue  218 GLN
Chi-restraints excluded: chain C residue  163 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 27 optimal weight:    0.3980
   chunk 12 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.110841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.099888 restraints weight = 4377.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 1.42
r_work: 0.3335 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3253 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3294  Z= 0.218
  Angle     :  0.616   5.343   4461  Z= 0.341
  Chirality :  0.048   0.138    456
  Planarity :  0.003   0.036    585
  Dihedral  :  5.943  18.826    444
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.74 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.65 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.19 (0.29), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.19 (0.22), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 144 
 HIS   0.003   0.001   HIS C 139 
 PHE   0.025   0.005   PHE A 140 
 TYR   0.018   0.002   TYR B 149 
 ARG   0.004   0.000   ARG C 135 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8386 (mttt) cc_final: 0.6940 (mtpt)
REVERT: A  155 ARG cc_start: 0.8358 (mtt90) cc_final: 0.7250 (mtt-85)
REVERT: A  163 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8300 (ptt90)
REVERT: A  204 MET cc_start: 0.8426 (mtt) cc_final: 0.7901 (tpt)
REVERT: B  163 ARG cc_start: 0.8806 (ptt180) cc_final: 0.7744 (pmt-80)
REVERT: B  184 LYS cc_start: 0.8806 (ptpp) cc_final: 0.8598 (ptpt)
REVERT: B  193 LYS cc_start: 0.8769 (tttp) cc_final: 0.8359 (tttm)
REVERT: C  109 LYS cc_start: 0.8759 (mttt) cc_final: 0.7704 (mtpt)
REVERT: C  163 ARG cc_start: 0.6131 (OUTLIER) cc_final: 0.5344 (mmp-170)
  outliers start: 7
  outliers final: 5
  residues processed: 75
  average time/residue: 1.8785
  time to fit residues: 143.4605
Evaluate side-chains
  80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  218 GLN
Chi-restraints excluded: chain C residue  146 ASP
Chi-restraints excluded: chain C residue  163 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0770
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.6338

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.110955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.099931 restraints weight = 4368.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 1.42
r_work: 0.3340 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3294  Z= 0.225
  Angle     :  0.623   5.358   4461  Z= 0.344
  Chirality :  0.048   0.139    456
  Planarity :  0.003   0.023    585
  Dihedral  :  5.921  18.666    444
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.74 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.65 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.18 (0.29), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.22), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A  98 
 HIS   0.003   0.001   HIS C 139 
 PHE   0.024   0.005   PHE A 140 
 TYR   0.021   0.002   TYR B 149 
 ARG   0.003   0.000   ARG C 163 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8409 (mttt) cc_final: 0.6968 (mtpt)
REVERT: A  155 ARG cc_start: 0.8350 (mtt90) cc_final: 0.7222 (mtt-85)
REVERT: A  163 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8301 (ptt90)
REVERT: A  204 MET cc_start: 0.8410 (mtt) cc_final: 0.7876 (tpt)
REVERT: B  163 ARG cc_start: 0.8811 (ptt180) cc_final: 0.7713 (pmt-80)
REVERT: B  184 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8602 (ptpt)
REVERT: B  193 LYS cc_start: 0.8756 (tttp) cc_final: 0.8336 (tttm)
REVERT: C  109 LYS cc_start: 0.8760 (mttt) cc_final: 0.7694 (mtpt)
REVERT: C  163 ARG cc_start: 0.6132 (OUTLIER) cc_final: 0.5840 (mmt180)
  outliers start: 8
  outliers final: 4
  residues processed: 74
  average time/residue: 1.7917
  time to fit residues: 135.0662
Evaluate side-chains
  78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  184 LYS
Chi-restraints excluded: chain B residue  218 GLN
Chi-restraints excluded: chain C residue  163 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 16 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9980
   chunk 19 optimal weight:    0.3980
   chunk 25 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.111461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.100546 restraints weight = 4331.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.41
r_work: 0.3349 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 2.65 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3294  Z= 0.208
  Angle     :  0.610   5.176   4461  Z= 0.337
  Chirality :  0.048   0.138    456
  Planarity :  0.003   0.033    585
  Dihedral  :  5.846  18.682    444
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.74 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 15.94 %
    Favored  : 82.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.18 (0.29), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.22), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A  98 
 HIS   0.003   0.001   HIS C 139 
 PHE   0.024   0.005   PHE A 140 
 TYR   0.021   0.002   TYR B 149 
 ARG   0.003   0.000   ARG C 163 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8394 (mttt) cc_final: 0.6875 (mtpt)
REVERT: A  155 ARG cc_start: 0.8363 (mtt90) cc_final: 0.7241 (mtt-85)
REVERT: A  204 MET cc_start: 0.8378 (mtt) cc_final: 0.7867 (tpt)
REVERT: B  163 ARG cc_start: 0.8773 (ptt180) cc_final: 0.7716 (pmt-80)
REVERT: B  184 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8607 (ptpt)
REVERT: B  193 LYS cc_start: 0.8742 (tttp) cc_final: 0.8315 (tttm)
REVERT: C  109 LYS cc_start: 0.8756 (mttt) cc_final: 0.7694 (mtpt)
REVERT: C  163 ARG cc_start: 0.6114 (OUTLIER) cc_final: 0.5825 (mmt180)
  outliers start: 7
  outliers final: 3
  residues processed: 71
  average time/residue: 1.8367
  time to fit residues: 132.7622
Evaluate side-chains
  76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain B residue  102 SER
Chi-restraints excluded: chain B residue  184 LYS
Chi-restraints excluded: chain C residue  163 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0870
   chunk 36 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 22 optimal weight:    0.2980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.5758

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.111645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.100653 restraints weight = 4384.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 1.43
r_work: 0.3351 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3294  Z= 0.209
  Angle     :  0.611   5.170   4461  Z= 0.338
  Chirality :  0.048   0.139    456
  Planarity :  0.004   0.037    585
  Dihedral  :  5.837  18.578    444
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.74 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 15.07 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.18 (0.29), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.18 (0.22), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A  98 
 HIS   0.003   0.001   HIS C 139 
 PHE   0.023   0.005   PHE A 140 
 TYR   0.014   0.002   TYR A 217 
 ARG   0.003   0.000   ARG C 163 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3521.72 seconds
wall clock time: 62 minutes 51.99 seconds (3771.99 seconds total)