Starting phenix.real_space_refine
on Sat May  2 12:45:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9wxr_66355/05_2026/9wxr_66355.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9wxr_66355/05_2026/9wxr_66355.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9wxr_66355/05_2026/9wxr_66355.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9wxr_66355/05_2026/9wxr_66355.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9wxr_66355/05_2026/9wxr_66355.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9wxr_66355/05_2026/9wxr_66355.map"
  }
  resolution = 4.9
  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=   0.005
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      16      5.16       5
     C    3370      2.51       5
     N     824      2.21       5
     O     956      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5166
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 345, 2563
          Classifications: {'peptide': 345}
          Link IDs: {'PTRANS': 8, 'TRANS': 336}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 20
          Unusual residues: {'RET': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.62, per 1000 atoms: 0.31
  Number of scatterers: 5166
  At special positions: 0
  Unit cell: (64.38, 93.98, 115.44, 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      16     16.00
     O     956      8.00
     N     824      7.00
     C    3370      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 267.8 milliseconds
  

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1244

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 2 sheets defined
      87.2% alpha, 1.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 28
      removed outlier: 3.853A  pdb=" N   VAL A   6 " --> pdb=" O   ASP A   2 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   VAL A   7 " --> pdb=" O   ALA A   3 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   VAL A  22 " --> pdb=" O   GLY A  18 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   GLY A  23 " --> pdb=" O   VAL A  19 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   PHE A  24 " --> pdb=" O   ALA A  20 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   LEU A  25 " --> pdb=" O   ILE A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 39
    Processing helix  chain 'A' and resid 42 through 58
    Processing helix  chain 'A' and resid 71 through 93
      removed outlier: 3.979A  pdb=" N   TRP A  77 " --> pdb=" O   ARG A  73 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL A  78 " --> pdb=" O   TYR A  74 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL A  79 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
      Proline residue:  A  82  - end of helix
      removed outlier: 3.533A  pdb=" N   ILE A  88 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 119
      removed outlier: 4.009A  pdb=" N   ILE A  99 " --> pdb=" O   SER A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 145
      removed outlier: 3.855A  pdb=" N   TRP A 125 " --> pdb=" O   GLY A 121 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ALA A 126 " --> pdb=" O   THR A 122 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   MET A 133 " --> pdb=" O   GLY A 129 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   PHE A 134 " --> pdb=" O   VAL A 130 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   HIS A 135 " --> pdb=" O   SER A 131 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   SER A 137 " --> pdb=" O   MET A 133 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   LEU A 142 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 150
      removed outlier: 3.766A  pdb=" N   VAL A 150 " --> pdb=" O   PRO A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 181
      removed outlier: 4.338A  pdb=" N   ILE A 172 " --> pdb=" O   GLY A 168 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ALA A 173 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   TYR A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
      Proline residue:  A 175  - end of helix
    Processing helix  chain 'A' and resid 189 through 215
      Proline residue:  A 207  - end of helix
    Processing helix  chain 'A' and resid 216 through 219
    Processing helix  chain 'A' and resid 248 through 255
    Processing helix  chain 'A' and resid 255 through 279
      removed outlier: 4.150A  pdb=" N   LYS A 259 " --> pdb=" O   SER A 255 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU A 260 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 319
      removed outlier: 3.922A  pdb=" N   ALA A 301 " --> pdb=" O   SER A 297 " (cutoff:3.500A)
      removed outlier: 5.472A  pdb=" N   GLU A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   THR A 303 " --> pdb=" O   ASN A 299 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL A 304 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 370
    Processing helix  chain 'B' and resid 2 through 28
      removed outlier: 3.852A  pdb=" N   VAL B   6 " --> pdb=" O   ASP B   2 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   VAL B   7 " --> pdb=" O   ALA B   3 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   VAL B  22 " --> pdb=" O   GLY B  18 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   GLY B  23 " --> pdb=" O   VAL B  19 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   PHE B  24 " --> pdb=" O   ALA B  20 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   LEU B  25 " --> pdb=" O   ILE B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 39
    Processing helix  chain 'B' and resid 42 through 58
    Processing helix  chain 'B' and resid 71 through 93
      removed outlier: 3.980A  pdb=" N   TRP B  77 " --> pdb=" O   ARG B  73 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   VAL B  78 " --> pdb=" O   TYR B  74 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   VAL B  79 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
      Proline residue:  B  82  - end of helix
      removed outlier: 3.533A  pdb=" N   ILE B  88 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 119
      removed outlier: 4.009A  pdb=" N   ILE B  99 " --> pdb=" O   SER B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 145
      removed outlier: 3.855A  pdb=" N   TRP B 125 " --> pdb=" O   GLY B 121 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ALA B 126 " --> pdb=" O   THR B 122 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   MET B 133 " --> pdb=" O   GLY B 129 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   PHE B 134 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   HIS B 135 " --> pdb=" O   SER B 131 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   SER B 137 " --> pdb=" O   MET B 133 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   LEU B 142 " --> pdb=" O   LEU B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 150
      removed outlier: 3.765A  pdb=" N   VAL B 150 " --> pdb=" O   PRO B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 181
      removed outlier: 4.338A  pdb=" N   ILE B 172 " --> pdb=" O   GLY B 168 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ALA B 173 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   TYR B 174 " --> pdb=" O   LEU B 170 " (cutoff:3.500A)
      Proline residue:  B 175  - end of helix
    Processing helix  chain 'B' and resid 189 through 215
      Proline residue:  B 207  - end of helix
    Processing helix  chain 'B' and resid 216 through 219
    Processing helix  chain 'B' and resid 248 through 255
    Processing helix  chain 'B' and resid 255 through 279
      removed outlier: 4.150A  pdb=" N   LYS B 259 " --> pdb=" O   SER B 255 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU B 260 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 319
      removed outlier: 3.922A  pdb=" N   ALA B 301 " --> pdb=" O   SER B 297 " (cutoff:3.500A)
      removed outlier: 5.472A  pdb=" N   GLU B 302 " --> pdb=" O   ILE B 298 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   THR B 303 " --> pdb=" O   ASN B 299 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL B 304 " --> pdb=" O   ALA B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 370
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 64
    Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 64

    428 hydrogen bonds defined for protein.
    1266 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: 0.73

  Time building geometry restraints manager: 0.63 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1304
        1.33 -     1.45: 987
        1.45 -     1.57: 2937
        1.57 -     1.69: 0
        1.69 -     1.81: 32
  Bond restraints: 5260
  Sorted by residual:
  bond pdb=" CB  MET A 109 "
       pdb=" CG  MET A 109 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.54e-01
  bond pdb=" CB  MET B 109 "
       pdb=" CG  MET B 109 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.49e-01
  bond pdb=" CD  GLN A 364 "
       pdb=" OE1 GLN A 364 "
    ideal  model  delta    sigma   weight residual
    1.231  1.215  0.016 1.90e-02 2.77e+03 6.98e-01
  bond pdb=" CD  GLN B 364 "
       pdb=" OE1 GLN B 364 "
    ideal  model  delta    sigma   weight residual
    1.231  1.216  0.015 1.90e-02 2.77e+03 6.35e-01
  bond pdb=" SD  MET B 109 "
       pdb=" CE  MET B 109 "
    ideal  model  delta    sigma   weight residual
    1.791  1.772  0.019 2.50e-02 1.60e+03 6.03e-01
  ... (remaining 5255 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 7033
        1.89 -     3.78: 107
        3.78 -     5.67: 30
        5.67 -     7.56: 4
        7.56 -     9.45: 4
  Bond angle restraints: 7178
  Sorted by residual:
  angle pdb=" N   GLN A 364 "
        pdb=" CA  GLN A 364 "
        pdb=" CB  GLN A 364 "
      ideal   model   delta    sigma   weight residual
     110.28  115.25   -4.97 1.55e+00 4.16e-01 1.03e+01
  angle pdb=" N   GLN B 364 "
        pdb=" CA  GLN B 364 "
        pdb=" CB  GLN B 364 "
      ideal   model   delta    sigma   weight residual
     110.28  115.23   -4.95 1.55e+00 4.16e-01 1.02e+01
  angle pdb=" CB  MET A 109 "
        pdb=" CG  MET A 109 "
        pdb=" SD  MET A 109 "
      ideal   model   delta    sigma   weight residual
     112.70  103.25    9.45 3.00e+00 1.11e-01 9.93e+00
  angle pdb=" CB  MET B 109 "
        pdb=" CG  MET B 109 "
        pdb=" SD  MET B 109 "
      ideal   model   delta    sigma   weight residual
     112.70  103.29    9.41 3.00e+00 1.11e-01 9.84e+00
  angle pdb=" CA  MET B 355 "
        pdb=" CB  MET B 355 "
        pdb=" CG  MET B 355 "
      ideal   model   delta    sigma   weight residual
     114.10  119.05   -4.95 2.00e+00 2.50e-01 6.12e+00
  ... (remaining 7173 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.50: 2778
       17.50 -    35.00: 216
       35.00 -    52.50: 26
       52.50 -    70.00: 0
       70.00 -    87.50: 8
  Dihedral angle restraints: 3028
    sinusoidal: 1068
      harmonic: 1960
  Sorted by residual:
  dihedral pdb=" CA  ALA B 132 "
           pdb=" C   ALA B 132 "
           pdb=" N   MET B 133 "
           pdb=" CA  MET B 133 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.77  -20.23     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  ALA A 132 "
           pdb=" C   ALA A 132 "
           pdb=" N   MET A 133 "
           pdb=" CA  MET A 133 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.78  -20.22     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  ALA B 300 "
           pdb=" C   ALA B 300 "
           pdb=" N   ALA B 301 "
           pdb=" CA  ALA B 301 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.75  -18.25     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 3025 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 567
       0.033 -    0.067: 219
       0.067 -    0.100: 64
       0.100 -    0.133: 22
       0.133 -    0.167: 6
  Chirality restraints: 878
  Sorted by residual:
  chirality pdb=" CG  LEU B 352 "
            pdb=" CB  LEU B 352 "
            pdb=" CD1 LEU B 352 "
            pdb=" CD2 LEU B 352 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 6.93e-01
  chirality pdb=" CG  LEU A 352 "
            pdb=" CB  LEU A 352 "
            pdb=" CD1 LEU A 352 "
            pdb=" CD2 LEU A 352 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 6.89e-01
  chirality pdb=" CG  LEU B 292 "
            pdb=" CB  LEU B 292 "
            pdb=" CD1 LEU B 292 "
            pdb=" CD2 LEU B 292 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.27e-01
  ... (remaining 875 not shown)

  Planarity restraints: 894
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 355 "    0.007 2.00e-02 2.50e+03   1.43e-02 2.04e+00
        pdb=" C   MET B 355 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   MET B 355 "    0.009 2.00e-02 2.50e+03
        pdb=" N   GLU B 356 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 355 "   -0.007 2.00e-02 2.50e+03   1.42e-02 2.01e+00
        pdb=" C   MET A 355 "    0.025 2.00e-02 2.50e+03
        pdb=" O   MET A 355 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLU A 356 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 208 "    0.014 2.00e-02 2.50e+03   9.34e-03 1.74e+00
        pdb=" CG  TYR B 208 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 208 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 208 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 208 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 208 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 208 "    0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR B 208 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 891 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 2090
        2.89 -     3.39: 6168
        3.39 -     3.90: 8536
        3.90 -     4.40: 9733
        4.40 -     4.90: 15006
  Nonbonded interactions: 41533
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 360 "
            pdb=" OE1 GLN A 364 "
     model   vdw
     2.391 3.040
  nonbonded pdb=" O   ALA B 360 "
            pdb=" OE1 GLN B 364 "
     model   vdw
     2.392 3.040
  nonbonded pdb=" O   ASP A 321 "
            pdb=" OD1 ASP A 321 "
     model   vdw
     2.553 3.040
  nonbonded pdb=" O   ASP B 321 "
            pdb=" OD1 ASP B 321 "
     model   vdw
     2.554 3.040
  nonbonded pdb=" O   MET B 103 "
            pdb=" OD1 ASP B 106 "
     model   vdw
     2.580 3.040
  ... (remaining 41528 not shown)

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

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
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:             7.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.620
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
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      :  0.003   0.028   5262  Z= 0.152
  Angle     :  0.664   9.452   7178  Z= 0.346
  Chirality :  0.042   0.167    878
  Planarity :  0.004   0.032    894
  Dihedral  : 12.809  87.499   1784
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  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:  1.31 (0.31), residues: 682
  helix:  1.08 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop :  0.45 (0.47), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 351 
 TYR   0.021   0.002   TYR B 208 
 PHE   0.008   0.001   PHE A 212 
 TRP   0.012   0.001   TRP A 171 
 HIS   0.002   0.001   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 5260)
  covalent geometry    : angle       0.66411 ( 7178)
  hydrogen bonds       : bond        0.11735 (  428)
  hydrogen bonds       : angle       6.06796 ( 1266)
  Misc. bond           : bond        0.00051 (    2)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 MET cc_start: 0.9570 (mmm) cc_final: 0.9363 (mmm)
REVERT: A  293 LEU cc_start: 0.9780 (mm) cc_final: 0.9441 (tt)
REVERT: A  328 SER cc_start: 0.7899 (t) cc_final: 0.7570 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0535
  time to fit residues: 5.3147
Evaluate side-chains
  64 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    1.1184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 135 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.066677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.049823 restraints weight = 18692.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.050979 restraints weight = 14041.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.051820 restraints weight = 11463.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.052553 restraints weight = 9965.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.053122 restraints weight = 8898.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5262  Z= 0.134
  Angle     :  0.596   8.084   7178  Z= 0.305
  Chirality :  0.041   0.128    878
  Planarity :  0.004   0.030    894
  Dihedral  :  6.565  86.061    764
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  2.28 %
    Favored  : 97.34 %
  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:  1.48 (0.31), residues: 682
  helix:  1.12 (0.21), residues: 564
  sheet:  None (None), residues: 0
  loop :  0.78 (0.50), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 351 
 TYR   0.023   0.002   TYR B 208 
 PHE   0.007   0.001   PHE B 212 
 TRP   0.008   0.001   TRP B 171 
 HIS   0.005   0.002   HIS A 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 5260)
  covalent geometry    : angle       0.59647 ( 7178)
  hydrogen bonds       : bond        0.04213 (  428)
  hydrogen bonds       : angle       4.49935 ( 1266)
  Misc. bond           : bond        0.00016 (    2)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 MET cc_start: 0.9151 (mmt) cc_final: 0.8225 (mmt)
REVERT: A  135 HIS cc_start: 0.9445 (t-90) cc_final: 0.9052 (m90)
REVERT: A  199 PHE cc_start: 0.9350 (t80) cc_final: 0.9133 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 68
  average time/residue: 0.0588
  time to fit residues: 4.9148
Evaluate side-chains
  55 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 8 optimal weight:    0.3980
   chunk 67 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 49 optimal weight:    5.9990
   chunk 3 optimal weight:    8.9990
   chunk 14 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0020
   chunk 15 optimal weight:    6.9990
   overall best weight:    0.6188
-------------------------------------------------------------------------------
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 = 0.3335 r_free = 0.3335 target = 0.068510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.052168 restraints weight = 19162.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.053456 restraints weight = 13869.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.054488 restraints weight = 11120.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.055244 restraints weight = 9425.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.055688 restraints weight = 8329.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.2762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5262  Z= 0.137
  Angle     :  0.667   6.786   7178  Z= 0.330
  Chirality :  0.040   0.133    878
  Planarity :  0.004   0.028    894
  Dihedral  :  6.251  59.135    764
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  5.32 %
    Favored  : 93.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.31 (0.32), residues: 682
  helix:  0.97 (0.22), residues: 558
  sheet:  None (None), residues: 0
  loop :  0.91 (0.55), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 351 
 TYR   0.019   0.002   TYR B 208 
 PHE   0.012   0.001   PHE B 212 
 TRP   0.007   0.001   TRP B  77 
 HIS   0.007   0.004   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 5260)
  covalent geometry    : angle       0.66706 ( 7178)
  hydrogen bonds       : bond        0.04010 (  428)
  hydrogen bonds       : angle       4.34181 ( 1266)
  Misc. bond           : bond        0.00206 (    2)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 LEU cc_start: 0.9289 (mm) cc_final: 0.9089 (mm)
REVERT: A  171 TRP cc_start: 0.8574 (t-100) cc_final: 0.8209 (t-100)
REVERT: A  199 PHE cc_start: 0.9230 (t80) cc_final: 0.8850 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 63
  average time/residue: 0.0631
  time to fit residues: 4.7347
Evaluate side-chains
  52 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 65 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 4 optimal weight:    0.0870
   chunk 53 optimal weight:    2.9990
   chunk 63 optimal weight:    6.9990
   chunk 6 optimal weight:    0.0670
   chunk 25 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 58 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0040
   overall best weight:    1.2312
-------------------------------------------------------------------------------
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 = 0.3353 r_free = 0.3353 target = 0.069276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.053557 restraints weight = 22069.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.054876 restraints weight = 16447.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.055808 restraints weight = 13187.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.056487 restraints weight = 11162.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.057027 restraints weight = 9835.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.3367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5262  Z= 0.162
  Angle     :  0.753   9.137   7178  Z= 0.371
  Chirality :  0.042   0.126    878
  Planarity :  0.004   0.031    894
  Dihedral  :  7.167  86.710    764
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

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:  1.00 (0.32), residues: 682
  helix:  0.79 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop :  0.63 (0.56), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 351 
 TYR   0.020   0.002   TYR B 208 
 PHE   0.009   0.001   PHE A 212 
 TRP   0.020   0.002   TRP B 171 
 HIS   0.007   0.004   HIS B 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 5260)
  covalent geometry    : angle       0.75327 ( 7178)
  hydrogen bonds       : bond        0.04141 (  428)
  hydrogen bonds       : angle       4.57653 ( 1266)
  Misc. bond           : bond        0.00722 (    2)

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

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

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1364 Ramachandran restraints generated.
    682 Oldfield, 0 Emsley, 682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 LEU cc_start: 0.9326 (mm) cc_final: 0.9096 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0594
  time to fit residues: 4.4829
Evaluate side-chains
  47 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 64 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.7980
-------------------------------------------------------------------------------
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 = 0.3319 r_free = 0.3319 target = 0.067620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.051897 restraints weight = 19096.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.053267 restraints weight = 13714.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 14)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.054155 restraints weight = 10779.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.054937 restraints weight = 9167.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.055524 restraints weight = 8033.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.3670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5262  Z= 0.131
  Angle     :  0.681   7.523   7178  Z= 0.337
  Chirality :  0.042   0.174    878
  Planarity :  0.004   0.031    894
  Dihedral  :  6.416  74.857    764
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  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:  0.89 (0.32), residues: 682
  helix:  0.66 (0.22), residues: 562
  sheet:  None (None), residues: 0
  loop :  0.88 (0.58), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 351 
 TYR   0.018   0.001   TYR A 208 
 PHE   0.019   0.001   PHE B 199 
 TRP   0.004   0.001   TRP B  77 
 HIS   0.005   0.002   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 5260)
  covalent geometry    : angle       0.68119 ( 7178)
  hydrogen bonds       : bond        0.04011 (  428)
  hydrogen bonds       : angle       4.46992 ( 1266)
  Misc. bond           : bond        0.00422 (    2)

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

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

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 LEU cc_start: 0.9679 (tp) cc_final: 0.9445 (tp)
REVERT: B  111 LEU cc_start: 0.9348 (mm) cc_final: 0.9132 (mm)
REVERT: B  212 PHE cc_start: 0.9230 (m-80) cc_final: 0.8929 (m-80)
REVERT: B  295 LEU cc_start: 0.9662 (pp) cc_final: 0.9373 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0661
  time to fit residues: 4.8216
Evaluate side-chains
  50 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0470
   chunk 42 optimal weight:    0.0970
   chunk 30 optimal weight:    0.0980
   chunk 28 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 11 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.3876
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 166 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.070763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.055554 restraints weight = 21429.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.056912 restraints weight = 15552.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.057904 restraints weight = 12276.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.058591 restraints weight = 10279.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.059176 restraints weight = 8970.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.4233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5262  Z= 0.128
  Angle     :  0.717   9.125   7178  Z= 0.343
  Chirality :  0.042   0.212    878
  Planarity :  0.004   0.033    894
  Dihedral  :  6.760  76.338    764
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 14.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

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: -0.06 (0.30), residues: 682
  helix: -0.03 (0.21), residues: 562
  sheet:  None (None), residues: 0
  loop :  0.76 (0.54), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 351 
 TYR   0.014   0.001   TYR A 208 
 PHE   0.004   0.001   PHE A 212 
 TRP   0.010   0.002   TRP B 171 
 HIS   0.005   0.002   HIS A 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 5260)
  covalent geometry    : angle       0.71739 ( 7178)
  hydrogen bonds       : bond        0.03972 (  428)
  hydrogen bonds       : angle       4.39200 ( 1266)
  Misc. bond           : bond        0.00400 (    2)

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

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

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 LEU cc_start: 0.9675 (tp) cc_final: 0.9435 (tp)
REVERT: B  169 LEU cc_start: 0.9799 (mt) cc_final: 0.9576 (tt)
REVERT: B  199 PHE cc_start: 0.9337 (t80) cc_final: 0.8727 (t80)
REVERT: B  212 PHE cc_start: 0.9241 (m-80) cc_final: 0.8861 (m-80)
REVERT: B  270 LEU cc_start: 0.9856 (tt) cc_final: 0.9403 (mt)
REVERT: B  295 LEU cc_start: 0.9674 (pp) cc_final: 0.9404 (tp)
REVERT: B  344 MET cc_start: 0.9725 (tmm) cc_final: 0.9417 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0657
  time to fit residues: 4.9339
Evaluate side-chains
  46 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 41 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 8 optimal weight:    0.4980
   chunk 50 optimal weight:    2.9990
   chunk 9 optimal weight:    8.9990
   chunk 21 optimal weight:    0.4980
   chunk 2 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0270
   chunk 28 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0670
   overall best weight:    0.3976
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 135 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 = 0.3402 r_free = 0.3402 target = 0.070770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.055411 restraints weight = 21396.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.056760 restraints weight = 15553.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.057785 restraints weight = 12270.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.058481 restraints weight = 10207.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.059105 restraints weight = 8935.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.4558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5262  Z= 0.118
  Angle     :  0.672   7.882   7178  Z= 0.325
  Chirality :  0.041   0.156    878
  Planarity :  0.004   0.034    894
  Dihedral  :  6.757  82.749    764
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  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: -0.32 (0.30), residues: 682
  helix: -0.24 (0.20), residues: 562
  sheet:  None (None), residues: 0
  loop :  0.89 (0.55), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 330 
 TYR   0.010   0.001   TYR B 208 
 PHE   0.007   0.001   PHE B 199 
 TRP   0.005   0.001   TRP B 171 
 HIS   0.004   0.002   HIS A 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 5260)
  covalent geometry    : angle       0.67227 ( 7178)
  hydrogen bonds       : bond        0.03724 (  428)
  hydrogen bonds       : angle       4.26588 ( 1266)
  Misc. bond           : bond        0.00059 (    2)

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

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

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.064 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 LEU cc_start: 0.9661 (tp) cc_final: 0.9417 (tp)
REVERT: B  169 LEU cc_start: 0.9772 (mt) cc_final: 0.9524 (tt)
REVERT: B  199 PHE cc_start: 0.9379 (t80) cc_final: 0.8702 (t80)
REVERT: B  212 PHE cc_start: 0.9148 (m-80) cc_final: 0.8841 (m-80)
REVERT: B  270 LEU cc_start: 0.9856 (tt) cc_final: 0.9396 (mt)
REVERT: B  295 LEU cc_start: 0.9691 (pp) cc_final: 0.9405 (mt)
REVERT: B  344 MET cc_start: 0.9725 (tmm) cc_final: 0.9406 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0559
  time to fit residues: 4.3151
Evaluate side-chains
  51 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0010
   chunk 55 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0170
   chunk 11 optimal weight:    6.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    0.5024
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 165 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 = 0.3418 r_free = 0.3418 target = 0.071621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.056083 restraints weight = 21529.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.057388 restraints weight = 15941.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.058402 restraints weight = 12754.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.059173 restraints weight = 10718.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.059639 restraints weight = 9372.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.4734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5262  Z= 0.126
  Angle     :  0.726   8.661   7178  Z= 0.346
  Chirality :  0.042   0.212    878
  Planarity :  0.004   0.033    894
  Dihedral  :  5.872  63.781    764
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

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: -0.42 (0.30), residues: 682
  helix: -0.35 (0.20), residues: 574
  sheet:  None (None), residues: 0
  loop :  1.25 (0.59), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 351 
 TYR   0.013   0.001   TYR B 208 
 PHE   0.006   0.001   PHE A 212 
 TRP   0.008   0.001   TRP B 171 
 HIS   0.007   0.003   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 5260)
  covalent geometry    : angle       0.72603 ( 7178)
  hydrogen bonds       : bond        0.03633 (  428)
  hydrogen bonds       : angle       4.20839 ( 1266)
  Misc. bond           : bond        0.00449 (    2)

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

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

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 LEU cc_start: 0.9669 (tp) cc_final: 0.9421 (tp)
REVERT: B  167 VAL cc_start: 0.9545 (m) cc_final: 0.9008 (m)
REVERT: B  169 LEU cc_start: 0.9781 (mt) cc_final: 0.9552 (tt)
REVERT: B  171 TRP cc_start: 0.8994 (m-10) cc_final: 0.8487 (m-10)
REVERT: B  199 PHE cc_start: 0.9371 (t80) cc_final: 0.8570 (t80)
REVERT: B  212 PHE cc_start: 0.9117 (m-80) cc_final: 0.8818 (m-10)
REVERT: B  270 LEU cc_start: 0.9853 (tt) cc_final: 0.9319 (mt)
REVERT: B  295 LEU cc_start: 0.9679 (pp) cc_final: 0.9381 (mt)
REVERT: B  344 MET cc_start: 0.9713 (tmm) cc_final: 0.9401 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.0530
  time to fit residues: 4.0191
Evaluate side-chains
  49 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0870
   chunk 51 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0670
   chunk 54 optimal weight:    0.5980
   chunk 15 optimal weight:    0.1980
   chunk 1 optimal weight:    0.7980
   chunk 9 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   overall best weight:    0.3496
-------------------------------------------------------------------------------
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 = 0.3427 r_free = 0.3427 target = 0.073309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.057274 restraints weight = 21507.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.058645 restraints weight = 15998.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.059669 restraints weight = 12821.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.060450 restraints weight = 10786.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.060928 restraints weight = 9441.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.4945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   5262  Z= 0.121
  Angle     :  0.701  11.236   7178  Z= 0.336
  Chirality :  0.041   0.126    878
  Planarity :  0.004   0.032    894
  Dihedral  :  5.989  72.413    764
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  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: -0.49 (0.30), residues: 682
  helix: -0.40 (0.20), residues: 574
  sheet:  None (None), residues: 0
  loop :  1.21 (0.59), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 351 
 TYR   0.011   0.001   TYR A 264 
 PHE   0.006   0.001   PHE B 199 
 TRP   0.008   0.001   TRP B 171 
 HIS   0.002   0.001   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 5260)
  covalent geometry    : angle       0.70092 ( 7178)
  hydrogen bonds       : bond        0.03499 (  428)
  hydrogen bonds       : angle       4.23859 ( 1266)
  Misc. bond           : bond        0.00152 (    2)

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

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

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 LEU cc_start: 0.9661 (tp) cc_final: 0.9406 (tp)
REVERT: B  167 VAL cc_start: 0.9531 (m) cc_final: 0.9049 (m)
REVERT: B  169 LEU cc_start: 0.9782 (mt) cc_final: 0.9545 (tt)
REVERT: B  171 TRP cc_start: 0.9013 (m-10) cc_final: 0.8518 (m-10)
REVERT: B  212 PHE cc_start: 0.9099 (m-80) cc_final: 0.8859 (m-80)
REVERT: B  295 LEU cc_start: 0.9691 (pp) cc_final: 0.9376 (mt)
REVERT: B  344 MET cc_start: 0.9706 (tmm) cc_final: 0.9398 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 0.0455
  time to fit residues: 3.5233
Evaluate side-chains
  48 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0870
   chunk 66 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 20 optimal weight:    0.0060
   chunk 65 optimal weight:    0.6980
   chunk 43 optimal weight:    7.9990
   chunk 6 optimal weight:    0.0870
   overall best weight:    0.3352
-------------------------------------------------------------------------------
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 = 0.3449 r_free = 0.3449 target = 0.074849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.058670 restraints weight = 21197.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.059978 restraints weight = 15941.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.060933 restraints weight = 12887.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.061706 restraints weight = 10967.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.062288 restraints weight = 9646.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.5184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5262  Z= 0.135
  Angle     :  0.781  12.532   7178  Z= 0.371
  Chirality :  0.043   0.216    878
  Planarity :  0.004   0.032    894
  Dihedral  :  5.346  52.853    764
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

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: -0.64 (0.30), residues: 682
  helix: -0.48 (0.20), residues: 574
  sheet:  None (None), residues: 0
  loop :  1.06 (0.58), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 330 
 TYR   0.009   0.001   TYR A 264 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.008   0.001   TRP B 171 
 HIS   0.005   0.002   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 5260)
  covalent geometry    : angle       0.78069 ( 7178)
  hydrogen bonds       : bond        0.03718 (  428)
  hydrogen bonds       : angle       4.29213 ( 1266)
  Misc. bond           : bond        0.00491 (    2)

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

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

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  682 Ramachandran restraints generated.
    341 Oldfield, 0 Emsley, 341 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 LEU cc_start: 0.9659 (tp) cc_final: 0.9403 (tp)
REVERT: B  167 VAL cc_start: 0.9396 (m) cc_final: 0.8990 (m)
REVERT: B  169 LEU cc_start: 0.9781 (mt) cc_final: 0.9542 (tt)
REVERT: B  171 TRP cc_start: 0.8955 (m-10) cc_final: 0.8458 (m-10)
REVERT: B  199 PHE cc_start: 0.9490 (t80) cc_final: 0.9213 (t80)
REVERT: B  295 LEU cc_start: 0.9682 (pp) cc_final: 0.9361 (mt)
REVERT: B  344 MET cc_start: 0.9699 (tmm) cc_final: 0.9402 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 61
  average time/residue: 0.0578
  time to fit residues: 4.2543
Evaluate side-chains
  52 residues out of total 263 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0470
   chunk 7 optimal weight:    0.0980
   chunk 56 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.4880
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 166 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.074520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.058540 restraints weight = 21112.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.059828 restraints weight = 15945.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.060751 restraints weight = 12936.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.061489 restraints weight = 11047.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.062084 restraints weight = 9764.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.5367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5262  Z= 0.128
  Angle     :  0.766  14.149   7178  Z= 0.364
  Chirality :  0.043   0.191    878
  Planarity :  0.004   0.031    894
  Dihedral  :  4.966  43.362    764
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.30 %

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: -0.67 (0.30), residues: 682
  helix: -0.50 (0.20), residues: 574
  sheet:  None (None), residues: 0
  loop :  1.05 (0.58), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B 330 
 TYR   0.016   0.001   TYR A   8 
 PHE   0.014   0.001   PHE A 199 
 TRP   0.007   0.001   TRP B 171 
 HIS   0.003   0.001   HIS B 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 5260)
  covalent geometry    : angle       0.76621 ( 7178)
  hydrogen bonds       : bond        0.03694 (  428)
  hydrogen bonds       : angle       4.30671 ( 1266)
  Misc. bond           : bond        0.00452 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 946.06 seconds
wall clock time: 17 minutes 10.78 seconds (1030.78 seconds total)