Starting phenix.real_space_refine
on Tue Feb  3 16:26:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9r3e_53555/02_2026/9r3e_53555.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9r3e_53555/02_2026/9r3e_53555.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9r3e_53555/02_2026/9r3e_53555.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9r3e_53555/02_2026/9r3e_53555.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9r3e_53555/02_2026/9r3e_53555.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9r3e_53555/02_2026/9r3e_53555.map"
  }
  resolution = 4.8
  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=   0.023
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      18      5.16       5
     C    3062      2.51       5
     N     810      2.21       5
     O     902      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4792
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 2396
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2396
          Classifications: {'peptide': 298}
          Link IDs: {'PTRANS': 8, 'TRANS': 289}
    Chain: "C"
      Number of atoms: 2396
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2396
          Classifications: {'peptide': 298}
          Link IDs: {'PTRANS': 8, 'TRANS': 289}
  Time building chain proxies: 1.25, per 1000 atoms: 0.26
  Number of scatterers: 4792
  At special positions: 0
  Unit cell: (64.603, 62.086, 119.977, 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      18     16.00
     O     902      8.00
     N     810      7.00
     C    3062      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.34
  Conformation dependent library (CDL) restraints added in 204.6 milliseconds
  

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1132

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 2 sheets defined
      60.9% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'B' and resid 32 through 38
      removed outlier: 4.613A  pdb=" N   THR B  37 " --> pdb=" O   PRO B  33 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LYS B  38 " --> pdb=" O   SER B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 55
      removed outlier: 3.661A  pdb=" N   SER B  52 " --> pdb=" O   GLY B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 64
      removed outlier: 3.786A  pdb=" N   LYS B  63 " --> pdb=" O   VAL B  59 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   SER B  64 " --> pdb=" O   PRO B  60 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 59 through 64'
    Processing helix  chain 'B' and resid 64 through 80
      removed outlier: 3.739A  pdb=" N   ILE B  69 " --> pdb=" O   TRP B  65 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLN B  70 " --> pdb=" O   LYS B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 96
      removed outlier: 3.788A  pdb=" N   LEU B  94 " --> pdb=" O   PHE B  90 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   HIS B  95 " --> pdb=" O   GLN B  91 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   GLU B  96 " --> pdb=" O   LYS B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 111
    Processing helix  chain 'B' and resid 123 through 131
      removed outlier: 4.703A  pdb=" N   GLU B 129 " --> pdb=" O   ASP B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 138
    Processing helix  chain 'B' and resid 139 through 156
      removed outlier: 4.679A  pdb=" N   LEU B 145 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU B 146 " --> pdb=" O   GLY B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 176
      removed outlier: 3.744A  pdb=" N   GLN B 175 " --> pdb=" O   TYR B 171 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   GLY B 176 " --> pdb=" O   ALA B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 195
      removed outlier: 4.315A  pdb=" N   GLN B 195 " --> pdb=" O   LEU B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 215
      removed outlier: 3.955A  pdb=" N   ILE B 215 " --> pdb=" O   PRO B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 225
      removed outlier: 3.791A  pdb=" N   ASN B 224 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   VAL B 225 " --> pdb=" O   GLY B 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 220 through 225'
    Processing helix  chain 'B' and resid 228 through 234
    Processing helix  chain 'B' and resid 235 through 240
      removed outlier: 3.726A  pdb=" N   TYR B 239 " --> pdb=" O   ILE B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 262
      removed outlier: 4.344A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 297
    Processing helix  chain 'B' and resid 309 through 325
    Processing helix  chain 'C' and resid 48 through 55
      removed outlier: 3.634A  pdb=" N   SER C  52 " --> pdb=" O   GLY C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 64
      removed outlier: 3.830A  pdb=" N   LYS C  63 " --> pdb=" O   VAL C  59 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   SER C  64 " --> pdb=" O   PRO C  60 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 59 through 64'
    Processing helix  chain 'C' and resid 64 through 79
      removed outlier: 3.609A  pdb=" N   ILE C  69 " --> pdb=" O   TRP C  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 96
      removed outlier: 3.654A  pdb=" N   LEU C  94 " --> pdb=" O   PHE C  90 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   HIS C  95 " --> pdb=" O   GLN C  91 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   GLU C  96 " --> pdb=" O   LYS C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 111
    Processing helix  chain 'C' and resid 123 through 131
      removed outlier: 4.668A  pdb=" N   GLU C 129 " --> pdb=" O   ASP C 125 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 134 through 138
    Processing helix  chain 'C' and resid 139 through 156
      removed outlier: 4.660A  pdb=" N   LEU C 145 " --> pdb=" O   SER C 141 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   LEU C 146 " --> pdb=" O   GLY C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 166 through 176
      removed outlier: 3.753A  pdb=" N   GLN C 175 " --> pdb=" O   TYR C 171 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLY C 176 " --> pdb=" O   ALA C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 186 through 194
    Processing helix  chain 'C' and resid 211 through 215
      removed outlier: 3.829A  pdb=" N   ILE C 215 " --> pdb=" O   PRO C 212 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 225
      removed outlier: 3.703A  pdb=" N   ASN C 224 " --> pdb=" O   ALA C 220 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   VAL C 225 " --> pdb=" O   GLY C 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 220 through 225'
    Processing helix  chain 'C' and resid 228 through 234
      removed outlier: 3.562A  pdb=" N   MET C 232 " --> pdb=" O   ASN C 228 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 235 through 241
      removed outlier: 3.738A  pdb=" N   TYR C 239 " --> pdb=" O   ILE C 235 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ASN C 241 " --> pdb=" O   LYS C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 251 through 254
    Processing helix  chain 'C' and resid 255 through 263
      removed outlier: 4.108A  pdb=" N   GLN C 259 " --> pdb=" O   ASP C 255 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 297
    Processing helix  chain 'C' and resid 309 through 325
    Processing sheet with id=AA1, first strand: chain 'B' and resid 181 through 182
      removed outlier: 6.724A  pdb=" N   LEU B 182 " --> pdb=" O   HIS B 204 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU B 203 " --> pdb=" O   VAL B 159 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   LEU B  43 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
      removed outlier: 8.345A  pdb=" N   LEU B 160 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   LEU B  45 " --> pdb=" O   LEU B 160 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   VAL B  44 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   LEU B 247 " --> pdb=" O   VAL B  44 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   VAL B  46 " --> pdb=" O   LEU B 247 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   PHE B 244 " --> pdb=" O   PHE B 275 " (cutoff:3.500A)
      removed outlier: 7.851A  pdb=" N   LEU B 277 " --> pdb=" O   PHE B 244 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   PHE B 246 " --> pdb=" O   LEU B 277 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 181 through 182
      removed outlier: 6.722A  pdb=" N   LEU C 182 " --> pdb=" O   HIS C 204 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LEU C 203 " --> pdb=" O   VAL C 159 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   LEU C  43 " --> pdb=" O   LEU C 158 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   LEU C 160 " --> pdb=" O   LEU C  43 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   LEU C  45 " --> pdb=" O   LEU C 160 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   VAL C  44 " --> pdb=" O   LEU C 245 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   LEU C 247 " --> pdb=" O   VAL C  44 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   VAL C  46 " --> pdb=" O   LEU C 247 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   PHE C 244 " --> pdb=" O   PHE C 275 " (cutoff:3.500A)
      removed outlier: 7.823A  pdb=" N   LEU C 277 " --> pdb=" O   PHE C 244 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   PHE C 246 " --> pdb=" O   LEU C 277 " (cutoff:3.500A)

    188 hydrogen bonds defined for protein.
    540 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: 0.44 seconds

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

  Histogram of bond lengths:
        1.14 -     1.27: 827
        1.27 -     1.41: 1124
        1.41 -     1.54: 2836
        1.54 -     1.68: 65
        1.68 -     1.81: 28
  Bond restraints: 4880
  Sorted by residual:
  bond pdb=" CG  PHE C  90 "
       pdb=" CD2 PHE C  90 "
    ideal  model  delta    sigma   weight residual
    1.384  1.252  0.132 2.10e-02 2.27e+03 3.94e+01
  bond pdb=" CG  ASN C 166 "
       pdb=" ND2 ASN C 166 "
    ideal  model  delta    sigma   weight residual
    1.328  1.212  0.116 2.10e-02 2.27e+03 3.04e+01
  bond pdb=" CG  ASN C 166 "
       pdb=" OD1 ASN C 166 "
    ideal  model  delta    sigma   weight residual
    1.231  1.140  0.091 1.90e-02 2.77e+03 2.29e+01
  bond pdb=" CB  PHE C  90 "
       pdb=" CG  PHE C  90 "
    ideal  model  delta    sigma   weight residual
    1.502  1.394  0.108 2.30e-02 1.89e+03 2.20e+01
  bond pdb=" CB  ASN C 166 "
       pdb=" CG  ASN C 166 "
    ideal  model  delta    sigma   weight residual
    1.516  1.400  0.116 2.50e-02 1.60e+03 2.15e+01
  ... (remaining 4875 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.61: 6440
        4.61 -     9.22: 118
        9.22 -    13.84: 18
       13.84 -    18.45: 2
       18.45 -    23.06: 2
  Bond angle restraints: 6580
  Sorted by residual:
  angle pdb=" CB  LYS C 110 "
        pdb=" CG  LYS C 110 "
        pdb=" CD  LYS C 110 "
      ideal   model   delta    sigma   weight residual
     111.30   92.79   18.51 2.30e+00 1.89e-01 6.48e+01
  angle pdb=" CD  LYS B 110 "
        pdb=" CE  LYS B 110 "
        pdb=" NZ  LYS B 110 "
      ideal   model   delta    sigma   weight residual
     111.90   88.84   23.06 3.20e+00 9.77e-02 5.19e+01
  angle pdb=" C   HIS C 274 "
        pdb=" N   PHE C 275 "
        pdb=" CA  PHE C 275 "
      ideal   model   delta    sigma   weight residual
     122.36  111.32   11.04 1.60e+00 3.91e-01 4.76e+01
  angle pdb=" CD  LYS C 299 "
        pdb=" CE  LYS C 299 "
        pdb=" NZ  LYS C 299 "
      ideal   model   delta    sigma   weight residual
     111.90  129.75  -17.85 3.20e+00 9.77e-02 3.11e+01
  angle pdb=" N   ARG B 324 "
        pdb=" CA  ARG B 324 "
        pdb=" C   ARG B 324 "
      ideal   model   delta    sigma   weight residual
     113.28  106.67    6.61 1.22e+00 6.72e-01 2.93e+01
  ... (remaining 6575 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.82: 2673
       16.82 -    33.64: 253
       33.64 -    50.46: 41
       50.46 -    67.27: 7
       67.27 -    84.09: 6
  Dihedral angle restraints: 2980
    sinusoidal: 1238
      harmonic: 1742
  Sorted by residual:
  dihedral pdb=" CA  ARG C 119 "
           pdb=" C   ARG C 119 "
           pdb=" N   SER C 120 "
           pdb=" CA  SER C 120 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.38  -25.62     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" CA  MET B 293 "
           pdb=" C   MET B 293 "
           pdb=" N   LEU B 294 "
           pdb=" CA  LEU B 294 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.52   25.48     0      5.00e+00 4.00e-02 2.60e+01
  dihedral pdb=" CA  MET C 293 "
           pdb=" C   MET C 293 "
           pdb=" N   LEU C 294 "
           pdb=" CA  LEU C 294 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.07   24.93     0      5.00e+00 4.00e-02 2.49e+01
  ... (remaining 2977 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.166: 708
       0.166 -    0.333: 36
       0.333 -    0.499: 2
       0.499 -    0.665: 1
       0.665 -    0.831: 1
  Chirality restraints: 748
  Sorted by residual:
  chirality pdb=" CG  LEU C 200 "
            pdb=" CB  LEU C 200 "
            pdb=" CD1 LEU C 200 "
            pdb=" CD2 LEU C 200 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.76   -0.83 2.00e-01 2.50e+01 1.73e+01
  chirality pdb=" CB  ILE B 215 "
            pdb=" CA  ILE B 215 "
            pdb=" CG1 ILE B 215 "
            pdb=" CG2 ILE B 215 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.14    0.50 2.00e-01 2.50e+01 6.31e+00
  chirality pdb=" CB  ILE C 321 "
            pdb=" CA  ILE C 321 "
            pdb=" CG1 ILE C 321 "
            pdb=" CG2 ILE C 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.21    0.44 2.00e-01 2.50e+01 4.74e+00
  ... (remaining 745 not shown)

  Planarity restraints: 836
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 275 "    0.034 2.00e-02 2.50e+03   5.95e-02 6.19e+01
        pdb=" CG  PHE C 275 "   -0.122 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 275 "    0.081 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 275 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 275 "   -0.030 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 275 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 275 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  90 "    0.061 2.00e-02 2.50e+03   5.71e-02 5.71e+01
        pdb=" CG  PHE B  90 "   -0.132 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  90 "    0.034 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  90 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  90 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  90 "    0.024 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  90 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C 169 "   -0.027 2.00e-02 2.50e+03   6.72e-02 4.52e+01
        pdb=" CD  GLU C 169 "    0.116 2.00e-02 2.50e+03
        pdb=" OE1 GLU C 169 "   -0.045 2.00e-02 2.50e+03
        pdb=" OE2 GLU C 169 "   -0.044 2.00e-02 2.50e+03
  ... (remaining 833 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 277
        2.71 -     3.26: 5491
        3.26 -     3.80: 7839
        3.80 -     4.35: 10113
        4.35 -     4.90: 15348
  Nonbonded interactions: 39068
  Sorted by model distance:
  nonbonded pdb=" O   ARG B 316 "
            pdb=" OE1 GLU B 320 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" O   ARG C 316 "
            pdb=" OE1 GLU C 320 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   ARG B 324 "
            pdb=" NE  ARG B 324 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" N   GLU C  83 "
            pdb=" OE2 GLU C  86 "
     model   vdw
     2.303 3.120
  nonbonded pdb=" O   LYS B  66 "
            pdb=" OE1 GLN B  70 "
     model   vdw
     2.330 3.040
  ... (remaining 39063 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 'B'
  selection = chain 'C'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.390
  Find NCS groups from input model:        0.040
  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:0.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3819
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      :  0.012   0.139   4880  Z= 0.485
  Angle     :  1.556  23.061   6580  Z= 0.779
  Chirality :  0.085   0.831    748
  Planarity :  0.014   0.120    836
  Dihedral  : 13.653  84.093   1848
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 47.56
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  8.28 %
    Favored  : 91.55 %
  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: -2.95 (0.32), residues: 592
  helix: -1.84 (0.27), residues: 292
  sheet: -2.80 (0.70), residues: 48
  loop : -1.73 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.032   0.004   ARG B  41 
 TYR   0.032   0.005   TYR C 222 
 PHE   0.132   0.008   PHE B  90 
 TRP   0.022   0.005   TRP B 193 
 HIS   0.071   0.011   HIS C 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.01171 ( 4880)
  covalent geometry    : angle       1.55574 ( 6580)
  hydrogen bonds       : bond        0.15930 (  188)
  hydrogen bonds       : angle       7.35792 (  540)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.059 
Fit side-chains
REVERT: B   96 GLU cc_start: 0.4381 (mp0) cc_final: 0.4097 (mp0)
REVERT: B  110 LYS cc_start: 0.7117 (pttt) cc_final: 0.6468 (tptt)
REVERT: B  138 MET cc_start: 0.1604 (tpt) cc_final: -0.1863 (mtt)
REVERT: B  154 GLU cc_start: 0.8839 (pt0) cc_final: 0.8165 (pp20)
REVERT: B  237 LYS cc_start: 0.7271 (ptpt) cc_final: 0.6719 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 37
  average time/residue: 0.0619
  time to fit residues: 2.6181
Evaluate side-chains
  18 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    0.0030
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0000
   chunk 2 optimal weight:    0.0570
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0070
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 50 optimal weight:    0.0470
   overall best weight:    0.0228
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 228 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.079120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.075123 restraints weight = 15786.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.076093 restraints weight = 11372.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.076701 restraints weight = 8444.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.077288 restraints weight = 6562.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.077649 restraints weight = 4960.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3179
moved from start:          0.5629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4880  Z= 0.158
  Angle     :  0.797   8.867   6580  Z= 0.414
  Chirality :  0.049   0.173    748
  Planarity :  0.006   0.046    836
  Dihedral  :  5.595  18.125    634
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 18.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  6.74 %
    Favored  : 92.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.07 (0.34), residues: 592
  helix: -0.86 (0.29), residues: 286
  sheet: -2.51 (0.54), residues: 70
  loop : -1.45 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 233 
 TYR   0.014   0.002   TYR B 128 
 PHE   0.024   0.002   PHE C 314 
 TRP   0.007   0.001   TRP B  65 
 HIS   0.008   0.003   HIS C 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 4880)
  covalent geometry    : angle       0.79664 ( 6580)
  hydrogen bonds       : bond        0.04324 (  188)
  hydrogen bonds       : angle       5.27582 (  540)

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

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

  592 Ramachandran restraints generated.
    296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  592 Ramachandran restraints generated.
    296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
REVERT: C  209 TYR cc_start: 0.4688 (p90) cc_final: 0.4286 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 47
  average time/residue: 0.0767
  time to fit residues: 4.1716
Evaluate side-chains
  19 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 30 optimal weight:    0.1980
   chunk 49 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 1 optimal weight:    0.1980
   chunk 28 optimal weight:    6.9990
   chunk 46 optimal weight:    0.0870
   chunk 56 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:    0.4980
   chunk 25 optimal weight:    0.1980
   chunk 48 optimal weight:    0.0470
   overall best weight:    0.1456
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.091147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.088112 restraints weight = 10792.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.088953 restraints weight = 7304.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.089544 restraints weight = 5022.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.090013 restraints weight = 3608.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.090260 restraints weight = 2558.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2978
moved from start:          0.6623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4880  Z= 0.134
  Angle     :  0.722   8.856   6580  Z= 0.374
  Chirality :  0.046   0.146    748
  Planarity :  0.004   0.040    836
  Dihedral  :  5.183  15.570    634
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 16.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  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: -2.20 (0.34), residues: 592
  helix: -0.94 (0.29), residues: 294
  sheet: -2.94 (0.57), residues: 60
  loop : -1.53 (0.42), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 316 
 TYR   0.011   0.002   TYR C 313 
 PHE   0.016   0.002   PHE B 314 
 TRP   0.006   0.001   TRP C 193 
 HIS   0.003   0.001   HIS C 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 4880)
  covalent geometry    : angle       0.72244 ( 6580)
  hydrogen bonds       : bond        0.03753 (  188)
  hydrogen bonds       : angle       4.90078 (  540)

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

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

  592 Ramachandran restraints generated.
    296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  592 Ramachandran restraints generated.
    296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.061 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   96 GLU cc_start: 0.4540 (mp0) cc_final: 0.3580 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0695
  time to fit residues: 2.5247
Evaluate side-chains
  15 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 25 optimal weight:    0.0970
   chunk 46 optimal weight:    0.0050
   chunk 2 optimal weight:    9.9990
   chunk 38 optimal weight:    0.0970
   chunk 47 optimal weight:    0.0670
   chunk 14 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 56 optimal weight:    0.5980
   chunk 28 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.1728
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B  58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 HIS
B 268 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.092082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.087541 restraints weight = 11120.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.088739 restraints weight = 7635.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.089643 restraints weight = 5408.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.090326 restraints weight = 3863.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.090780 restraints weight = 2773.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3036
moved from start:          0.7120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4880  Z= 0.126
  Angle     :  0.714  10.369   6580  Z= 0.359
  Chirality :  0.046   0.216    748
  Planarity :  0.004   0.032    836
  Dihedral  :  4.982  14.794    634
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 15.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  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: -2.37 (0.32), residues: 592
  helix: -1.11 (0.27), residues: 296
  sheet: -2.91 (0.59), residues: 56
  loop : -1.63 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 233 
 TYR   0.010   0.001   TYR C 313 
 PHE   0.011   0.001   PHE C 314 
 TRP   0.004   0.001   TRP B 251 
 HIS   0.006   0.001   HIS C 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 4880)
  covalent geometry    : angle       0.71351 ( 6580)
  hydrogen bonds       : bond        0.03334 (  188)
  hydrogen bonds       : angle       4.85964 (  540)

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

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

  592 Ramachandran restraints generated.
    296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  592 Ramachandran restraints generated.
    296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.069 
Fit side-chains
REVERT: B  110 LYS cc_start: 0.6825 (pttt) cc_final: 0.6530 (tptt)
REVERT: B  153 MET cc_start: 0.7479 (mmp) cc_final: 0.7170 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 19
  average time/residue: 0.1273
  time to fit residues: 2.7210
Evaluate side-chains
  11 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 32 optimal weight:    0.0170
   chunk 30 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0030
   chunk 24 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 48 optimal weight:    0.3980
   chunk 52 optimal weight:    0.2980
   chunk 29 optimal weight:    9.9990
   overall best weight:    0.2828
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  58 GLN
** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.094850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.091528 restraints weight = 10584.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.092386 restraints weight = 7514.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.093054 restraints weight = 5399.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.093529 restraints weight = 3915.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.093842 restraints weight = 2824.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.4074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2986
moved from start:          0.7548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4880  Z= 0.131
  Angle     :  0.699   8.443   6580  Z= 0.354
  Chirality :  0.045   0.193    748
  Planarity :  0.004   0.030    836
  Dihedral  :  4.903  16.777    634
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  4.49 %
    Favored  : 95.13 %
  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: -2.45 (0.32), residues: 592
  helix: -1.12 (0.27), residues: 294
  sheet: -2.72 (0.65), residues: 56
  loop : -1.82 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 233 
 TYR   0.010   0.001   TYR B 303 
 PHE   0.010   0.001   PHE B 286 
 TRP   0.003   0.001   TRP B 193 
 HIS   0.005   0.001   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 4880)
  covalent geometry    : angle       0.69912 ( 6580)
  hydrogen bonds       : bond        0.03395 (  188)
  hydrogen bonds       : angle       4.82365 (  540)

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

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

  592 Ramachandran restraints generated.
    296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  592 Ramachandran restraints generated.
    296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 18
  time to evaluate  : 0.099 
Fit side-chains
REVERT: B  110 LYS cc_start: 0.6983 (pttt) cc_final: 0.6582 (tptt)
REVERT: B  153 MET cc_start: 0.7314 (mmp) cc_final: 0.6993 (mmp)
REVERT: B  210 THR cc_start: 0.7109 (p) cc_final: 0.6519 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 19
  average time/residue: 0.0743
  time to fit residues: 1.7384
Evaluate side-chains
  12 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 38 optimal weight:    0.0050
   chunk 14 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0050
   chunk 16 optimal weight:    0.8980
   chunk 1 optimal weight:    0.2980
   chunk 10 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.4008
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.094233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.091351 restraints weight = 10344.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.092075 restraints weight = 7339.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.092644 restraints weight = 5214.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.093043 restraints weight = 3775.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.093322 restraints weight = 2758.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.4048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2969
moved from start:          0.7746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4880  Z= 0.124
  Angle     :  0.700  10.344   6580  Z= 0.353
  Chirality :  0.045   0.156    748
  Planarity :  0.004   0.026    836
  Dihedral  :  4.809  16.651    634
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  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: -2.43 (0.32), residues: 592
  helix: -1.08 (0.27), residues: 294
  sheet: -2.62 (0.67), residues: 56
  loop : -1.87 (0.38), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 233 
 TYR   0.010   0.001   TYR C 313 
 PHE   0.008   0.001   PHE C 244 
 TRP   0.003   0.001   TRP B 251 
 HIS   0.006   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 4880)
  covalent geometry    : angle       0.70040 ( 6580)
  hydrogen bonds       : bond        0.03292 (  188)
  hydrogen bonds       : angle       4.90297 (  540)

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

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

  592 Ramachandran restraints generated.
    296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  592 Ramachandran restraints generated.
    296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.061 
Fit side-chains
REVERT: B  110 LYS cc_start: 0.6773 (pttt) cc_final: 0.6375 (tptt)
REVERT: B  153 MET cc_start: 0.7266 (mmp) cc_final: 0.6768 (mmp)
REVERT: B  159 VAL cc_start: 0.4854 (m) cc_final: 0.4587 (t)
REVERT: B  210 THR cc_start: 0.7195 (p) cc_final: 0.6647 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 17
  average time/residue: 0.0534
  time to fit residues: 1.1574
Evaluate side-chains
  14 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0980
   chunk 37 optimal weight:    0.6980
   chunk 22 optimal weight:    0.1980
   chunk 41 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0870
   chunk 9 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   chunk 6 optimal weight:    0.8980
   chunk 49 optimal weight:    0.1980
   overall best weight:    0.2558
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.093828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.090355 restraints weight = 10557.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.091229 restraints weight = 7533.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.091892 restraints weight = 5520.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.092354 restraints weight = 4097.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.092721 restraints weight = 3059.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3005
moved from start:          0.7947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4880  Z= 0.124
  Angle     :  0.679   7.949   6580  Z= 0.349
  Chirality :  0.045   0.138    748
  Planarity :  0.004   0.028    836
  Dihedral  :  4.805  19.248    634
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  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: -2.41 (0.32), residues: 592
  helix: -1.01 (0.27), residues: 294
  sheet: -2.68 (0.67), residues: 56
  loop : -1.92 (0.38), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 233 
 TYR   0.010   0.001   TYR C 313 
 PHE   0.012   0.001   PHE B  90 
 TRP   0.003   0.001   TRP B 193 
 HIS   0.003   0.001   HIS C 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 4880)
  covalent geometry    : angle       0.67897 ( 6580)
  hydrogen bonds       : bond        0.03388 (  188)
  hydrogen bonds       : angle       4.96594 (  540)

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

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

  592 Ramachandran restraints generated.
    296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  592 Ramachandran restraints generated.
    296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.068 
Fit side-chains
REVERT: B  153 MET cc_start: 0.7279 (mmp) cc_final: 0.6724 (mmp)
REVERT: B  159 VAL cc_start: 0.4796 (m) cc_final: 0.4504 (t)
REVERT: B  210 THR cc_start: 0.7309 (p) cc_final: 0.6855 (t)
REVERT: B  233 ARG cc_start: 0.6196 (tpp80) cc_final: 0.5987 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 0.0940
  time to fit residues: 1.7855
Evaluate side-chains
  13 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 47 optimal weight:    0.0050
   chunk 44 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0770
   chunk 54 optimal weight:    6.9990
   chunk 29 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 8 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   overall best weight:    0.6154
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  95 HIS
** B 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.093974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.091029 restraints weight = 10502.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.091762 restraints weight = 7375.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.092342 restraints weight = 5336.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.092769 restraints weight = 3873.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.093044 restraints weight = 2845.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.4039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3010
moved from start:          0.8278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4880  Z= 0.118
  Angle     :  0.655   7.108   6580  Z= 0.336
  Chirality :  0.044   0.139    748
  Planarity :  0.004   0.028    836
  Dihedral  :  4.717  18.642    634
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  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: -2.37 (0.32), residues: 592
  helix: -0.98 (0.27), residues: 300
  sheet: -2.73 (0.67), residues: 56
  loop : -1.89 (0.39), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 233 
 TYR   0.012   0.001   TYR B 313 
 PHE   0.009   0.001   PHE C 314 
 TRP   0.006   0.001   TRP B 193 
 HIS   0.003   0.001   HIS C 204 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 4880)
  covalent geometry    : angle       0.65486 ( 6580)
  hydrogen bonds       : bond        0.03125 (  188)
  hydrogen bonds       : angle       4.88487 (  540)

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

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

  592 Ramachandran restraints generated.
    296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  592 Ramachandran restraints generated.
    296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.102 
Fit side-chains
REVERT: B  153 MET cc_start: 0.7120 (mmp) cc_final: 0.6593 (mmp)
REVERT: B  159 VAL cc_start: 0.5006 (m) cc_final: 0.4645 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 0.0761
  time to fit residues: 1.5276
Evaluate side-chains
  12 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 52 optimal weight:    0.4980
   chunk 19 optimal weight:    0.4980
   chunk 56 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 7 optimal weight:    0.4980
   chunk 35 optimal weight:    0.4980
   chunk 49 optimal weight:    0.3980
   chunk 44 optimal weight:    0.0010
   chunk 48 optimal weight:    0.4980
   overall best weight:    0.3786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.094658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.091574 restraints weight = 10748.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.092369 restraints weight = 7496.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.092983 restraints weight = 5362.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.093401 restraints weight = 3852.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.093715 restraints weight = 2842.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.4055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3004
moved from start:          0.8435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4880  Z= 0.116
  Angle     :  0.669  11.005   6580  Z= 0.335
  Chirality :  0.045   0.287    748
  Planarity :  0.003   0.028    836
  Dihedral  :  4.656  18.191    634
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  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: -2.37 (0.33), residues: 592
  helix: -0.92 (0.28), residues: 300
  sheet: -2.83 (0.68), residues: 56
  loop : -1.96 (0.39), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 233 
 TYR   0.011   0.001   TYR B 313 
 PHE   0.006   0.001   PHE B 286 
 TRP   0.004   0.001   TRP B 193 
 HIS   0.002   0.001   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 4880)
  covalent geometry    : angle       0.66902 ( 6580)
  hydrogen bonds       : bond        0.03074 (  188)
  hydrogen bonds       : angle       4.83454 (  540)

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

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

  592 Ramachandran restraints generated.
    296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  592 Ramachandran restraints generated.
    296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  12 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.100 
Fit side-chains
REVERT: B  153 MET cc_start: 0.7107 (mmp) cc_final: 0.6546 (mmp)
REVERT: B  159 VAL cc_start: 0.4889 (m) cc_final: 0.4407 (t)
REVERT: B  233 ARG cc_start: 0.5954 (tpp80) cc_final: 0.4898 (tpp-160)
  outliers start: 0
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0756
  time to fit residues: 1.1819
Evaluate side-chains
  12 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 42 optimal weight:    0.0470
   chunk 22 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9980
   chunk 7 optimal weight:    0.2980
   chunk 10 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0370
   chunk 15 optimal weight:    0.0010
   chunk 32 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 2 optimal weight:    8.9990
   chunk 46 optimal weight:    0.0050
   overall best weight:    0.0776
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.096579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.093621 restraints weight = 10766.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.094206 restraints weight = 8190.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.094717 restraints weight = 6354.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.095174 restraints weight = 4919.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.095439 restraints weight = 3770.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.4099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2866
moved from start:          0.8670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4880  Z= 0.117
  Angle     :  0.665  10.215   6580  Z= 0.332
  Chirality :  0.045   0.244    748
  Planarity :  0.003   0.029    836
  Dihedral  :  4.560  17.850    634
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  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: -2.39 (0.33), residues: 592
  helix: -0.86 (0.28), residues: 308
  sheet: -2.81 (0.68), residues: 56
  loop : -2.13 (0.39), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 233 
 TYR   0.011   0.001   TYR B 313 
 PHE   0.008   0.001   PHE B 314 
 TRP   0.004   0.001   TRP B 251 
 HIS   0.003   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 4880)
  covalent geometry    : angle       0.66454 ( 6580)
  hydrogen bonds       : bond        0.03165 (  188)
  hydrogen bonds       : angle       4.76879 (  540)

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

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

  592 Ramachandran restraints generated.
    296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  592 Ramachandran restraints generated.
    296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.103 
Fit side-chains
REVERT: B  153 MET cc_start: 0.6826 (mmp) cc_final: 0.6528 (mmp)
REVERT: B  233 ARG cc_start: 0.5739 (tpp80) cc_final: 0.4713 (tpp-160)
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0689
  time to fit residues: 1.2591
Evaluate side-chains
  11 residues out of total 267 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 49 optimal weight:    0.0870
   chunk 21 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0670
   chunk 35 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0040
   chunk 12 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0170
   overall best weight:    0.1746
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.095568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.093034 restraints weight = 10416.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.093661 restraints weight = 7532.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.094095 restraints weight = 5574.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.094506 restraints weight = 4235.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.094774 restraints weight = 3137.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2851
moved from start:          0.8798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4880  Z= 0.117
  Angle     :  0.672  10.077   6580  Z= 0.337
  Chirality :  0.045   0.225    748
  Planarity :  0.003   0.028    836
  Dihedral  :  4.604  18.342    634
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  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: -2.48 (0.33), residues: 592
  helix: -0.90 (0.28), residues: 306
  sheet: -2.79 (0.70), residues: 56
  loop : -2.23 (0.38), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 233 
 TYR   0.011   0.001   TYR B 313 
 PHE   0.006   0.001   PHE C 286 
 TRP   0.003   0.000   TRP B 251 
 HIS   0.002   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 4880)
  covalent geometry    : angle       0.67190 ( 6580)
  hydrogen bonds       : bond        0.03099 (  188)
  hydrogen bonds       : angle       4.86261 (  540)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 846.68 seconds
wall clock time: 15 minutes 22.79 seconds (922.79 seconds total)