Starting phenix.real_space_refine
on Tue Mar  3 11:26:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qig_13989/03_2026/7qig_13989.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qig_13989/03_2026/7qig_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_13989/03_2026/7qig_13989.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qig_13989/03_2026/7qig_13989.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qig_13989/03_2026/7qig_13989.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qig_13989/03_2026/7qig_13989.cif"
  }
  resolution = 2.7
  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=   0.001
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.88, per 1000 atoms: 0.27
  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: 0.26
  Conformation dependent library (CDL) restraints added in 124.8 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: 0.12
  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: 0.42

  Time building geometry restraints manager: 0.33 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: 0.00
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:             3.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.850
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  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:6.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.830
-------------------------------------------------------------------------------
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   3297  Z= 0.222
  Angle     :  0.695   5.229   4467  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.008   0.001   ARG C 163 
 TYR   0.025   0.003   TYR A 149 
 PHE   0.021   0.004   PHE B 140 
 TRP   0.017   0.002   TRP A  98 
 HIS   0.004   0.001   HIS C 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 3294)
  covalent geometry    : angle       0.69487 ( 4461)
  SS BOND              : bond        0.00273 (    3)
  SS BOND              : angle       0.58547 (    6)
  hydrogen bonds       : bond        0.16336 (   68)
  hydrogen bonds       : angle       8.53830 (  204)

*********************** 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  : 0.137 
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: 0.8365 (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: 0.8473
  time to fit residues: 74.1275
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  : 0.166 
-------------------------------------------------------------------------------
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 24 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    0.4980
   chunk 32 optimal weight:    0.4980
   chunk 31 optimal weight:    0.4980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3573 r_free = 0.3573 target = 0.110168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.099087 restraints weight = 4307.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.43
r_work: 0.3315 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3297  Z= 0.150
  Angle     :  0.642   5.442   4467  Z= 0.359
  Chirality :  0.050   0.147    456
  Planarity :  0.003   0.021    585
  Dihedral  :  6.177  18.148    447
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.74 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  :  8.70 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.11 (0.29), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.12 (0.22), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 163 
 TYR   0.017   0.002   TYR A 149 
 PHE   0.026   0.005   PHE A 140 
 TRP   0.017   0.003   TRP B  98 
 HIS   0.003   0.001   HIS B 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 3294)
  covalent geometry    : angle       0.64189 ( 4461)
  SS BOND              : bond        0.00254 (    3)
  SS BOND              : angle       0.89791 (    6)
  hydrogen bonds       : bond        0.02863 (   68)
  hydrogen bonds       : angle       6.48862 (  204)

*********************** 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
  86 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8548 (mttt) cc_final: 0.7117 (mtpt)
REVERT: A  155 ARG cc_start: 0.8491 (mtt90) cc_final: 0.7263 (mtt180)
REVERT: A  163 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8361 (ptt90)
REVERT: B  135 ARG cc_start: 0.8941 (ttt180) cc_final: 0.8702 (ttt180)
REVERT: B  147 ARG cc_start: 0.8804 (mtm180) cc_final: 0.8568 (mtm180)
REVERT: B  155 ARG cc_start: 0.7390 (mtt-85) cc_final: 0.6165 (mtp85)
REVERT: B  163 ARG cc_start: 0.8690 (ptt180) cc_final: 0.7652 (pmt-80)
REVERT: B  184 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8484 (ptpp)
REVERT: B  193 LYS cc_start: 0.8833 (tttp) cc_final: 0.8575 (tttm)
REVERT: C  109 LYS cc_start: 0.8819 (mttt) cc_final: 0.7643 (mtpt)
REVERT: C  163 ARG cc_start: 0.6055 (OUTLIER) cc_final: 0.4197 (mmt180)
  outliers start: 10
  outliers final: 2
  residues processed: 78
  average time/residue: 0.8924
  time to fit residues: 70.7780
Evaluate side-chains
  79 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 SER
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0970
   chunk 15 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 32 optimal weight:    0.4980
   chunk 7 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 = 0.3590 r_free = 0.3590 target = 0.111181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.100190 restraints weight = 4323.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 1.43
r_work: 0.3329 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
moved from start:          0.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3297  Z= 0.129
  Angle     :  0.605   5.277   4467  Z= 0.337
  Chirality :  0.048   0.140    456
  Planarity :  0.003   0.018    585
  Dihedral  :  5.891  17.966    444
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  :  9.57 %
    Favored  : 87.54 %
  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 are not related in a simple way.
  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
 ARG   0.003   0.000   ARG A 150 
 TYR   0.016   0.002   TYR A 148 
 PHE   0.024   0.005   PHE A 140 
 TRP   0.012   0.002   TRP A  98 
 HIS   0.003   0.001   HIS C 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 3294)
  covalent geometry    : angle       0.60464 ( 4461)
  SS BOND              : bond        0.00263 (    3)
  SS BOND              : angle       0.88404 (    6)
  hydrogen bonds       : bond        0.02831 (   68)
  hydrogen bonds       : angle       6.09180 (  204)

*********************** 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
  85 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.100 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8517 (mttt) cc_final: 0.6968 (mtpt)
REVERT: A  155 ARG cc_start: 0.8466 (mtt90) cc_final: 0.7300 (mtt180)
REVERT: A  163 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8333 (ptt90)
REVERT: B  135 ARG cc_start: 0.8925 (ttt180) cc_final: 0.8685 (ttt180)
REVERT: B  147 ARG cc_start: 0.8787 (mtm180) cc_final: 0.8572 (mtm180)
REVERT: B  163 ARG cc_start: 0.8677 (ptt180) cc_final: 0.7518 (pmt-80)
REVERT: B  193 LYS cc_start: 0.8764 (tttp) cc_final: 0.8414 (tttp)
REVERT: C  109 LYS cc_start: 0.8824 (mttt) cc_final: 0.7071 (mttt)
REVERT: C  163 ARG cc_start: 0.6287 (OUTLIER) cc_final: 0.4794 (mmp80)
  outliers start: 10
  outliers final: 4
  residues processed: 75
  average time/residue: 0.8602
  time to fit residues: 65.5739
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  : 0.147 
-------------------------------------------------------------------------------
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 30 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 2 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3560 r_free = 0.3560 target = 0.109013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.097900 restraints weight = 4363.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 1.42
r_work: 0.3305 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3297  Z= 0.200
  Angle     :  0.667   6.082   4467  Z= 0.369
  Chirality :  0.050   0.146    456
  Planarity :  0.004   0.024    585
  Dihedral  :  6.059  18.577    444
  Min Nonbonded Distance : 2.657

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 10.14 %
    Favored  : 86.96 %
  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 are not related in a simple way.
  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
 ARG   0.005   0.001   ARG C 163 
 TYR   0.016   0.002   TYR B 149 
 PHE   0.025   0.006   PHE A 140 
 TRP   0.010   0.002   TRP A  98 
 HIS   0.005   0.001   HIS C 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 3294)
  covalent geometry    : angle       0.66668 ( 4461)
  SS BOND              : bond        0.00201 (    3)
  SS BOND              : angle       0.76402 (    6)
  hydrogen bonds       : bond        0.02718 (   68)
  hydrogen bonds       : angle       6.06042 (  204)

*********************** 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
  84 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8459 (mttt) cc_final: 0.6939 (mtpt)
REVERT: A  155 ARG cc_start: 0.8452 (mtt90) cc_final: 0.7251 (mtt180)
REVERT: A  163 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8316 (ptt90)
REVERT: B  163 ARG cc_start: 0.8721 (ptt180) cc_final: 0.7610 (pmt-80)
REVERT: B  193 LYS cc_start: 0.8803 (tttp) cc_final: 0.8431 (tptp)
REVERT: C  109 LYS cc_start: 0.8818 (mttt) cc_final: 0.7817 (mtpt)
REVERT: C  135 ARG cc_start: 0.9022 (ttt-90) cc_final: 0.8808 (ttt-90)
REVERT: C  163 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.4497 (mmp-170)
  outliers start: 10
  outliers final: 4
  residues processed: 75
  average time/residue: 0.8081
  time to fit residues: 61.6639
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  : 0.115 
-------------------------------------------------------------------------------
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 38 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3541 r_free = 0.3541 target = 0.107175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.096062 restraints weight = 4382.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 1.40
r_work: 0.3282 rms_B_bonded: 1.52 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 2.63 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   3297  Z= 0.269
  Angle     :  0.721   6.784   4467  Z= 0.398
  Chirality :  0.051   0.155    456
  Planarity :  0.004   0.035    585
  Dihedral  :  6.303  19.877    444
  Min Nonbonded Distance : 2.656

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.23 %
    Favored  : 90.77 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 13.33 %
    Favored  : 84.06 %
  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 are not related in a simple way.
  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
 ARG   0.006   0.001   ARG C 163 
 TYR   0.017   0.002   TYR C 149 
 PHE   0.026   0.006   PHE A 174 
 TRP   0.009   0.002   TRP C 144 
 HIS   0.005   0.002   HIS C 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00625 ( 3294)
  covalent geometry    : angle       0.72051 ( 4461)
  SS BOND              : bond        0.00261 (    3)
  SS BOND              : angle       0.86107 (    6)
  hydrogen bonds       : bond        0.02919 (   68)
  hydrogen bonds       : angle       6.13050 (  204)

*********************** 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
  83 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8441 (mttt) cc_final: 0.6978 (mtpt)
REVERT: A  155 ARG cc_start: 0.8366 (mtt90) cc_final: 0.7155 (mtt180)
REVERT: A  163 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8336 (ptt90)
REVERT: B  163 ARG cc_start: 0.8806 (ptt180) cc_final: 0.7778 (pmt-80)
REVERT: B  193 LYS cc_start: 0.8764 (tttp) cc_final: 0.8417 (tttm)
REVERT: C  109 LYS cc_start: 0.8839 (mttt) cc_final: 0.7840 (mtpt)
REVERT: C  163 ARG cc_start: 0.6198 (OUTLIER) cc_final: 0.5890 (mmp-170)
  outliers start: 9
  outliers final: 3
  residues processed: 75
  average time/residue: 0.8219
  time to fit residues: 62.6818
Evaluate side-chains
  79 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
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 5 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0970
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 0 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.5778

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.110385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.099571 restraints weight = 4344.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.39
r_work: 0.3333 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3252 rms_B_bonded: 2.62 restraints_weight: 0.2500
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3297  Z= 0.138
  Angle     :  0.615   5.554   4467  Z= 0.340
  Chirality :  0.048   0.141    456
  Planarity :  0.003   0.021    585
  Dihedral  :  5.986  18.797    444
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 12.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.004   0.001   ARG C 135 
 TYR   0.017   0.002   TYR B 149 
 PHE   0.025   0.005   PHE A 140 
 TRP   0.010   0.002   TRP C 144 
 HIS   0.003   0.001   HIS C 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 3294)
  covalent geometry    : angle       0.61446 ( 4461)
  SS BOND              : bond        0.00249 (    3)
  SS BOND              : angle       0.91476 (    6)
  hydrogen bonds       : bond        0.02585 (   68)
  hydrogen bonds       : angle       5.92272 (  204)

*********************** 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
  84 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.113 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8413 (mttt) cc_final: 0.6897 (mtpt)
REVERT: A  155 ARG cc_start: 0.8333 (mtt90) cc_final: 0.7251 (mtt-85)
REVERT: A  204 MET cc_start: 0.8392 (mtt) cc_final: 0.7791 (tpt)
REVERT: B  163 ARG cc_start: 0.8782 (ptt180) cc_final: 0.7704 (pmt-80)
REVERT: B  184 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8531 (ptpp)
REVERT: B  193 LYS cc_start: 0.8764 (tttp) cc_final: 0.8353 (tptp)
REVERT: C  109 LYS cc_start: 0.8761 (mttt) cc_final: 0.7724 (mtpt)
REVERT: C  163 ARG cc_start: 0.6132 (OUTLIER) cc_final: 0.5355 (mmp-170)
  outliers start: 10
  outliers final: 4
  residues processed: 76
  average time/residue: 0.8110
  time to fit residues: 62.6751
Evaluate side-chains
  78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
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  146 ASP
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 36 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0270
   chunk 29 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 22 optimal weight:    0.1980
   chunk 33 optimal weight:    0.9990
   chunk 18 optimal weight:    0.3980
   overall best weight:    0.4238

-------------------------------------------------------------------------------
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 = 0.3610 r_free = 0.3610 target = 0.112144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.101312 restraints weight = 4447.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.43
r_work: 0.3357 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3275 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.2263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   3297  Z= 0.112
  Angle     :  0.582   4.962   4467  Z= 0.322
  Chirality :  0.047   0.144    456
  Planarity :  0.003   0.024    585
  Dihedral  :  5.769  18.620    444
  Min Nonbonded Distance : 2.658

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.49 %
    Favored  : 90.51 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.78 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.16 (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
 ARG   0.002   0.000   ARG C 147 
 TYR   0.015   0.002   TYR A 148 
 PHE   0.023   0.005   PHE A 140 
 TRP   0.009   0.002   TRP C 144 
 HIS   0.002   0.001   HIS C 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 3294)
  covalent geometry    : angle       0.58190 ( 4461)
  SS BOND              : bond        0.00295 (    3)
  SS BOND              : angle       0.86881 (    6)
  hydrogen bonds       : bond        0.02376 (   68)
  hydrogen bonds       : angle       5.74086 (  204)

*********************** 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
  81 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A  155 ARG cc_start: 0.8349 (mtt90) cc_final: 0.7257 (mtt-85)
REVERT: B  163 ARG cc_start: 0.8764 (ptt180) cc_final: 0.7664 (pmt-80)
REVERT: B  184 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8501 (ptpp)
REVERT: B  193 LYS cc_start: 0.8765 (tttp) cc_final: 0.8340 (tptp)
REVERT: C  109 LYS cc_start: 0.8753 (mttt) cc_final: 0.7709 (mtpt)
REVERT: C  163 ARG cc_start: 0.6108 (OUTLIER) cc_final: 0.4456 (mmp-170)
  outliers start: 7
  outliers final: 5
  residues processed: 76
  average time/residue: 0.8433
  time to fit residues: 65.1560
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  : 0.108 
-------------------------------------------------------------------------------
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 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    0.3980
   chunk 25 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3584 r_free = 0.3584 target = 0.110320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.099349 restraints weight = 4462.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 1.43
r_work: 0.3336 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3297  Z= 0.161
  Angle     :  0.628   5.526   4467  Z= 0.346
  Chirality :  0.048   0.142    456
  Planarity :  0.004   0.040    585
  Dihedral  :  5.888  18.632    444
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.23 %
    Favored  : 90.77 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.78 %
    Favored  : 82.61 %
  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 are not related in a simple way.
  whole: -4.16 (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
 ARG   0.005   0.001   ARG C 135 
 TYR   0.019   0.002   TYR B 149 
 PHE   0.024   0.005   PHE A 174 
 TRP   0.008   0.001   TRP A  98 
 HIS   0.004   0.001   HIS C 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 3294)
  covalent geometry    : angle       0.62798 ( 4461)
  SS BOND              : bond        0.00263 (    3)
  SS BOND              : angle       0.73787 (    6)
  hydrogen bonds       : bond        0.02478 (   68)
  hydrogen bonds       : angle       5.71264 (  204)

*********************** 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
  83 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8463 (mttt) cc_final: 0.7006 (mtpt)
REVERT: A  155 ARG cc_start: 0.8358 (mtt90) cc_final: 0.7246 (mtt-85)
REVERT: A  204 MET cc_start: 0.8477 (mtt) cc_final: 0.8237 (mtp)
REVERT: B  163 ARG cc_start: 0.8804 (ptt180) cc_final: 0.7724 (pmt-80)
REVERT: B  184 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8522 (ptpp)
REVERT: B  193 LYS cc_start: 0.8771 (tttp) cc_final: 0.8364 (tttm)
REVERT: C  109 LYS cc_start: 0.8741 (mttt) cc_final: 0.7706 (mtpt)
REVERT: C  163 ARG cc_start: 0.6130 (OUTLIER) cc_final: 0.5834 (mmt180)
  outliers start: 9
  outliers final: 5
  residues processed: 76
  average time/residue: 0.8555
  time to fit residues: 66.1752
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  : 0.131 
-------------------------------------------------------------------------------
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 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 4 optimal weight:    0.4980
   chunk 11 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 32 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.110923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.099955 restraints weight = 4424.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 1.42
r_work: 0.3341 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: 0.8493
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3297  Z= 0.152
  Angle     :  0.621   5.355   4467  Z= 0.343
  Chirality :  0.048   0.141    456
  Planarity :  0.003   0.022    585
  Dihedral  :  5.884  18.503    444
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.26 %
    Favored  : 89.74 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.36 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.003   0.000   ARG C 163 
 TYR   0.019   0.002   TYR B 149 
 PHE   0.023   0.005   PHE A 140 
 TRP   0.009   0.002   TRP A  98 
 HIS   0.004   0.001   HIS C 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 3294)
  covalent geometry    : angle       0.62063 ( 4461)
  SS BOND              : bond        0.00283 (    3)
  SS BOND              : angle       0.78700 (    6)
  hydrogen bonds       : bond        0.02443 (   68)
  hydrogen bonds       : angle       5.66116 (  204)

*********************** 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  : 0.084 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8406 (mttt) cc_final: 0.6882 (mtpt)
REVERT: A  155 ARG cc_start: 0.8353 (mtt90) cc_final: 0.7259 (mtt-85)
REVERT: A  204 MET cc_start: 0.8412 (mtt) cc_final: 0.8163 (mtp)
REVERT: B  163 ARG cc_start: 0.8807 (ptt180) cc_final: 0.7724 (pmt-80)
REVERT: B  184 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8515 (ptpp)
REVERT: B  193 LYS cc_start: 0.8759 (tttp) cc_final: 0.8344 (tttm)
REVERT: C  109 LYS cc_start: 0.8745 (mttt) cc_final: 0.7624 (mtpt)
REVERT: C  163 ARG cc_start: 0.6130 (OUTLIER) cc_final: 0.5831 (mmt180)
  outliers start: 8
  outliers final: 5
  residues processed: 73
  average time/residue: 0.8242
  time to fit residues: 61.2432
Evaluate side-chains
  79 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
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 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    0.0040
   chunk 36 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0020
   chunk 33 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0270
   chunk 18 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.3058

-------------------------------------------------------------------------------
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 = 0.3651 r_free = 0.3651 target = 0.114948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.104267 restraints weight = 4356.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.41
r_work: 0.3404 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.3323 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   3297  Z= 0.093
  Angle     :  0.549   4.332   4467  Z= 0.304
  Chirality :  0.046   0.141    456
  Planarity :  0.003   0.031    585
  Dihedral  :  5.555  18.757    444
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.23 %
    Favored  : 90.77 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.16 (0.30), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.16 (0.23), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 147 
 TYR   0.014   0.001   TYR A 148 
 PHE   0.022   0.004   PHE A 140 
 TRP   0.011   0.002   TRP C 144 
 HIS   0.002   0.001   HIS C 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 3294)
  covalent geometry    : angle       0.54850 ( 4461)
  SS BOND              : bond        0.00328 (    3)
  SS BOND              : angle       0.96283 (    6)
  hydrogen bonds       : bond        0.02186 (   68)
  hydrogen bonds       : angle       5.52585 (  204)

********************** 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
  79 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A  109 LYS cc_start: 0.8401 (mttt) cc_final: 0.6875 (mtpt)
REVERT: A  155 ARG cc_start: 0.8332 (mtt90) cc_final: 0.7259 (mtt-85)
REVERT: A  163 ARG cc_start: 0.8542 (ptt180) cc_final: 0.8222 (ptt90)
REVERT: A  204 MET cc_start: 0.8416 (mtt) cc_final: 0.7837 (tpp)
REVERT: B  163 ARG cc_start: 0.8758 (ptt180) cc_final: 0.7685 (pmt-80)
REVERT: B  184 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8435 (ptpt)
REVERT: B  193 LYS cc_start: 0.8780 (tttp) cc_final: 0.8344 (tptp)
REVERT: C  109 LYS cc_start: 0.8724 (mttt) cc_final: 0.7513 (mtpt)
REVERT: C  163 ARG cc_start: 0.6404 (OUTLIER) cc_final: 0.4689 (mmp-170)
  outliers start: 8
  outliers final: 6
  residues processed: 73
  average time/residue: 0.8288
  time to fit residues: 61.5858
Evaluate side-chains
  76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 68
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
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 B residue  218 GLN
Chi-restraints excluded: chain C residue  145 GLU
Chi-restraints excluded: chain C residue  146 ASP
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:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0980
   chunk 9 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0470
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.4478

-------------------------------------------------------------------------------
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 = 0.3633 r_free = 0.3633 target = 0.113669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.102665 restraints weight = 4418.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 1.44
r_work: 0.3378 rms_B_bonded: 1.58 restraints_weight: 0.5000
r_work: 0.3298 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3297  Z= 0.113
  Angle     :  0.572   4.593   4467  Z= 0.316
  Chirality :  0.047   0.139    456
  Planarity :  0.003   0.034    585
  Dihedral  :  5.593  18.226    444
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.74 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 16.81 %
    Favored  : 81.45 %
  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 are not related in a simple way.
  whole: -4.13 (0.30), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.14 (0.23), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 163 
 TYR   0.019   0.002   TYR B 149 
 PHE   0.021   0.004   PHE A 140 
 TRP   0.008   0.001   TRP A  98 
 HIS   0.003   0.001   HIS C 139 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 3294)
  covalent geometry    : angle       0.57141 ( 4461)
  SS BOND              : bond        0.00298 (    3)
  SS BOND              : angle       0.75991 (    6)
  hydrogen bonds       : bond        0.02204 (   68)
  hydrogen bonds       : angle       5.51516 (  204)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1721.70 seconds
wall clock time: 30 minutes 0.10 seconds (1800.10 seconds total)