Starting phenix.real_space_refine
on Fri Aug 22 18:08:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ul9_42357/08_2025/8ul9_42357.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ul9_42357/08_2025/8ul9_42357.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ul9_42357/08_2025/8ul9_42357.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ul9_42357/08_2025/8ul9_42357.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ul9_42357/08_2025/8ul9_42357.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ul9_42357/08_2025/8ul9_42357.map"
  }
  resolution = 3.2
  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=  -0.001 sd=   0.062
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      4      5.21       5
     S      42      5.16       5
     C    4519      2.51       5
     N     959      2.21       5
     O    1144      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6674
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3144
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 388, 3120
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 387, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PTRANS': 17, 'TRANS': 369}
      Conformer: "B"
        Number of residues, atoms: 388, 3120
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 387, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PTRANS': 17, 'TRANS': 369}
          bond proxies already assigned to first conformer: 3191
    Chain: "B"
      Number of atoms: 3127
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 388, 3120
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 387, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PTRANS': 17, 'TRANS': 369}
      Conformer: "B"
        Number of residues, atoms: 388, 3120
          Unusual residues: {'ACE': 1}
          Classifications: {'peptide': 387, 'undetermined': 1}
          Link IDs: {'ACE_C-N': 1, 'PTRANS': 17, 'TRANS': 369}
          bond proxies already assigned to first conformer: 3211
    Chain: "A"
      Number of atoms: 200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 200
          Unusual residues: {' MG': 2, 'DGA': 1, 'PCW': 3}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "B"
      Number of atoms: 202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 202
          Unusual residues: {' MG': 2, 'DGA': 1, 'PCW': 3}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 6
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS A 118 " occ=0.44
      ... (18 atoms not shown)
      pdb=" NE2BHIS A 118 " occ=0.56
  Time building chain proxies: 2.24, per 1000 atoms: 0.34
  Number of scatterers: 6674
  At special positions: 0
  Unit cell: (106.92, 96.12, 74.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      42     16.00
     P       6     15.00
     Mg      4     11.99
     O    1144      8.00
     N     959      7.00
     C    4519      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: 0.54
  Conformation dependent library (CDL) restraints added in 426.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1468

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 3 sheets defined
      77.8% alpha, 1.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 16
      removed outlier: 3.618A  pdb=" N   TYR A  16 " --> pdb=" O   LEU A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 42
      removed outlier: 3.754A  pdb=" N   PHE A  34 " --> pdb=" O   VAL A  30 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   PHE A  42 " --> pdb=" O   PHE A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 70
      removed outlier: 3.683A  pdb=" N   VAL A  51 " --> pdb=" O   ALA A  47 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   TYR A  69 " --> pdb=" O   THR A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 106
      removed outlier: 4.118A  pdb=" N   PHE A  83 " --> pdb=" O   ARG A  79 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ALA A  97 " --> pdb=" O   GLN A  93 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ARG A 104 " --> pdb=" O   GLY A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 128
      removed outlier: 3.616A  pdb=" N   GLU A 114 " --> pdb=" O   GLY A 110 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE A 123 " --> pdb=" O   CYS A 119 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   THR A 126 " --> pdb=" O   SER A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 137
      removed outlier: 4.181A  pdb=" N   VAL A 132 " --> pdb=" O   SER A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 165
      removed outlier: 3.535A  pdb=" N   ILE A 145 " --> pdb=" O   THR A 141 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   PHE A 155 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 193
    Processing helix  chain 'A' and resid 194 through 200
    Processing helix  chain 'A' and resid 217 through 248
    Processing helix  chain 'A' and resid 255 through 266
      removed outlier: 3.591A  pdb=" N   GLU A 259 " --> pdb=" O   SER A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 285
    Processing helix  chain 'A' and resid 286 through 289
      removed outlier: 3.600A  pdb=" N   ILE A 289 " --> pdb=" O   PRO A 286 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 286 through 289'
    Processing helix  chain 'A' and resid 290 through 314
    Processing helix  chain 'A' and resid 322 through 341
      Proline residue:  A 328  - end of helix
    Processing helix  chain 'A' and resid 347 through 381
    Processing helix  chain 'B' and resid 7 through 14
      removed outlier: 4.383A  pdb=" N   GLY B  11 " --> pdb=" O   SER B   8 " (cutoff:3.500A)
      removed outlier: 5.290A  pdb=" N   ASN B  12 " --> pdb=" O   SER B   9 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU B  13 " --> pdb=" O   LEU B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 31
      removed outlier: 4.520A  pdb=" N   ASN B  28 " --> pdb=" O   SER B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 39
    Processing helix  chain 'B' and resid 47 through 70
      removed outlier: 3.531A  pdb=" N   VAL B  51 " --> pdb=" O   ALA B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 106
      removed outlier: 4.218A  pdb=" N   TYR B  82 " --> pdb=" O   PRO B  78 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   PHE B  83 " --> pdb=" O   ARG B  79 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ARG B 104 " --> pdb=" O   GLY B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 128
      removed outlier: 3.616A  pdb=" N   GLU B 114 " --> pdb=" O   GLY B 110 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ILE B 123 " --> pdb=" O   CYS B 119 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   THR B 126 " --> pdb=" O   SER B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 137
      removed outlier: 4.303A  pdb=" N   VAL B 132 " --> pdb=" O   SER B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 166
      removed outlier: 3.549A  pdb=" N   ILE B 145 " --> pdb=" O   THR B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 193
    Processing helix  chain 'B' and resid 194 through 199
    Processing helix  chain 'B' and resid 217 through 248
    Processing helix  chain 'B' and resid 253 through 285
      removed outlier: 3.940A  pdb=" N   THR B 257 " --> pdb=" O   THR B 253 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLU B 259 " --> pdb=" O   SER B 255 " (cutoff:3.500A)
      Proline residue:  B 270  - end of helix
    Processing helix  chain 'B' and resid 286 through 289
      removed outlier: 3.646A  pdb=" N   ILE B 289 " --> pdb=" O   PRO B 286 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 286 through 289'
    Processing helix  chain 'B' and resid 290 through 315
    Processing helix  chain 'B' and resid 322 through 341
      Proline residue:  B 328  - end of helix
    Processing helix  chain 'B' and resid 345 through 381
      removed outlier: 3.642A  pdb=" N   ILE B 349 " --> pdb=" O   GLN B 345 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   VAL B 350 " --> pdb=" O   LYS B 346 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 204
      removed outlier: 3.787A  pdb=" N   ALA A 204 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 20 through 22
    Processing sheet with id=AA3, first strand: chain 'B' and resid 202 through 204
      removed outlier: 7.389A  pdb=" N   VAL B 215 " --> pdb=" O   VAL B 203 " (cutoff:3.500A)

    441 hydrogen bonds defined for protein.
    1310 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: 0.89

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 939
        1.31 -     1.43: 2072
        1.43 -     1.56: 3777
        1.56 -     1.69: 12
        1.69 -     1.81: 68
  Bond restraints: 6868
  Sorted by residual:
  bond pdb=" C11 PCW A1003 "
       pdb=" O3  PCW A1003 "
    ideal  model  delta    sigma   weight residual
    1.326  1.420 -0.094 2.00e-02 2.50e+03 2.23e+01
  bond pdb=" C11 PCW A1004 "
       pdb=" O3  PCW A1004 "
    ideal  model  delta    sigma   weight residual
    1.326  1.420 -0.094 2.00e-02 2.50e+03 2.21e+01
  bond pdb=" C11 PCW B1004 "
       pdb=" O3  PCW B1004 "
    ideal  model  delta    sigma   weight residual
    1.326  1.419 -0.093 2.00e-02 2.50e+03 2.18e+01
  bond pdb=" C11 PCW A1005 "
       pdb=" O3  PCW A1005 "
    ideal  model  delta    sigma   weight residual
    1.326  1.419 -0.093 2.00e-02 2.50e+03 2.16e+01
  bond pdb=" C11 PCW B1003 "
       pdb=" O3  PCW B1003 "
    ideal  model  delta    sigma   weight residual
    1.326  1.419 -0.093 2.00e-02 2.50e+03 2.15e+01
  ... (remaining 6863 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.10: 9193
        5.10 -    10.21: 65
       10.21 -    15.31: 15
       15.31 -    20.42: 3
       20.42 -    25.52: 6
  Bond angle restraints: 9282
  Sorted by residual:
  angle pdb=" C19 PCW B1003 "
        pdb=" C20 PCW B1003 "
        pdb=" C21 PCW B1003 "
      ideal   model   delta    sigma   weight residual
     127.82  153.34  -25.52 3.00e+00 1.11e-01 7.24e+01
  angle pdb=" C19 PCW B1005 "
        pdb=" C20 PCW B1005 "
        pdb=" C21 PCW B1005 "
      ideal   model   delta    sigma   weight residual
     127.82  152.95  -25.13 3.00e+00 1.11e-01 7.02e+01
  angle pdb=" C19 PCW A1004 "
        pdb=" C20 PCW A1004 "
        pdb=" C21 PCW A1004 "
      ideal   model   delta    sigma   weight residual
     127.82  152.71  -24.89 3.00e+00 1.11e-01 6.88e+01
  angle pdb=" C19 PCW B1004 "
        pdb=" C20 PCW B1004 "
        pdb=" C21 PCW B1004 "
      ideal   model   delta    sigma   weight residual
     127.82  152.34  -24.52 3.00e+00 1.11e-01 6.68e+01
  angle pdb=" C19 PCW A1005 "
        pdb=" C20 PCW A1005 "
        pdb=" C21 PCW A1005 "
      ideal   model   delta    sigma   weight residual
     127.82  152.27  -24.45 3.00e+00 1.11e-01 6.64e+01
  ... (remaining 9277 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.89: 3865
       35.89 -    71.79: 151
       71.79 -   107.68: 5
      107.68 -   143.58: 3
      143.58 -   179.47: 7
  Dihedral angle restraints: 4031
    sinusoidal: 1737
      harmonic: 2294
  Sorted by residual:
  dihedral pdb=" CH3 ACE B   1 "
           pdb=" C   ACE B   1 "
           pdb=" N   GLY B   2 "
           pdb=" CA  GLY B   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00   -0.53 -179.47     1      5.00e+00 4.00e-02 7.68e+02
  dihedral pdb=" CH3 ACE A   1 "
           pdb=" C   ACE A   1 "
           pdb=" N   GLY A   2 "
           pdb=" CA  GLY A   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00   -0.64 -179.36     1      5.00e+00 4.00e-02 7.68e+02
  dihedral pdb=" N   PCW A1004 "
           pdb=" C4  PCW A1004 "
           pdb=" C5  PCW A1004 "
           pdb=" O4P PCW A1004 "
      ideal   model   delta sinusoidal    sigma   weight residual
     293.34  126.41  166.93     1      3.00e+01 1.11e-03 2.11e+01
  ... (remaining 4028 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 773
       0.047 -    0.094: 192
       0.094 -    0.140: 34
       0.140 -    0.187: 0
       0.187 -    0.234: 5
  Chirality restraints: 1004
  Sorted by residual:
  chirality pdb=" C2  PCW A1003 "
            pdb=" C1  PCW A1003 "
            pdb=" C3  PCW A1003 "
            pdb=" O2  PCW A1003 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.56    0.23 2.00e-01 2.50e+01 1.37e+00
  chirality pdb=" C2  PCW B1005 "
            pdb=" C1  PCW B1005 "
            pdb=" C3  PCW B1005 "
            pdb=" O2  PCW B1005 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.55    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" C2  PCW A1005 "
            pdb=" C1  PCW A1005 "
            pdb=" C3  PCW A1005 "
            pdb=" O2  PCW A1005 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.54    0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1001 not shown)

  Planarity restraints: 1113
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 347 "    0.008 2.00e-02 2.50e+03   1.55e-02 2.42e+00
        pdb=" C   GLY A 347 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   GLY A 347 "    0.010 2.00e-02 2.50e+03
        pdb=" N   SER A 348 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 175 "    0.025 5.00e-02 4.00e+02   3.72e-02 2.21e+00
        pdb=" N   PRO B 176 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B 176 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 176 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 269 "    0.022 5.00e-02 4.00e+02   3.27e-02 1.71e+00
        pdb=" N   PRO B 270 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 270 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 270 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1110 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 57
        2.60 -     3.17: 5721
        3.17 -     3.75: 10261
        3.75 -     4.32: 14183
        4.32 -     4.90: 24343
  Nonbonded interactions: 54565
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 121 "
            pdb="MG    MG A1002 "
     model   vdw
     2.024 2.170
  nonbonded pdb=" OD1 ASP B 121 "
            pdb="MG    MG B1002 "
     model   vdw
     2.029 2.170
  nonbonded pdb=" OD1 ASP B 117 "
            pdb="MG    MG B1002 "
     model   vdw
     2.057 2.170
  nonbonded pdb=" OD1 ASP A  96 "
            pdb="MG    MG A1002 "
     model   vdw
     2.204 2.170
  nonbonded pdb=" OD2 ASP B 117 "
            pdb="MG    MG B1001 "
     model   vdw
     2.209 2.170
  ... (remaining 54560 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 113 or resid 115 through 117 or resid 119 throug \ 
h 271 or resid 273 through 1007))
  selection = (chain 'B' and (resid 1 through 113 or resid 115 through 117 or resid 119 throug \ 
h 271 or resid 273 through 1004 or (resid 1005 and (name N or name C1 or name C1 \ 
1 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or nam \ 
e C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or  \ 
name C24 or name C25 or name C26 or name C27 or name C28 or name C3 or name C31  \ 
or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name  \ 
C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C43 or na \ 
me C44 or name C45 or name C46 or name C5 or name C6 or name C7 or name C8 or na \ 
me O11 or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or  \ 
name O4P or name P )) or resid 1007))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.19 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.380
  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:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.710
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
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      :  0.008   0.094   6868  Z= 0.387
  Angle     :  1.290  25.522   9282  Z= 0.478
  Chirality :  0.042   0.234   1004
  Planarity :  0.004   0.037   1113
  Dihedral  : 19.116 179.471   2563
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  :  5.23 %
    Favored  : 92.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.06 (0.31), residues: 776
  helix:  2.42 (0.22), residues: 552
  sheet:  None (None), residues: 0
  loop : -1.46 (0.42), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  32 
 TYR   0.015   0.001   TYR A 274 
 PHE   0.013   0.001   PHE A 275 
 TRP   0.012   0.001   TRP A 160 
 HIS   0.004   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00799 ( 6868)
  covalent geometry    : angle       1.28993 ( 9282)
  hydrogen bonds       : bond        0.09533 (  441)
  hydrogen bonds       : angle       5.00090 ( 1310)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 PHE cc_start: 0.5544 (OUTLIER) cc_final: 0.5280 (t80)
REVERT: A   92 TYR cc_start: 0.7852 (t80) cc_final: 0.7650 (t80)
REVERT: A  369 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8006 (tp)
REVERT: A  375 ASP cc_start: 0.7427 (t0) cc_final: 0.7019 (t0)
REVERT: B   92 TYR cc_start: 0.7926 (t80) cc_final: 0.7715 (t80)
REVERT: B  224 PHE cc_start: 0.8090 (t80) cc_final: 0.7677 (t80)
REVERT: B  290 SER cc_start: 0.8751 (t) cc_final: 0.8431 (p)
REVERT: B  320 MET cc_start: 0.8872 (tpp) cc_final: 0.8352 (mmt)
  outliers start: 15
  outliers final: 6
  residues processed: 115
  average time/residue: 0.0472
  time to fit residues: 8.1420
Evaluate side-chains
  97 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 PHE
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  167 LYS
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  124 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A 345 GLN
B  75 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.210643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.158262 restraints weight = 18177.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 6.24
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3676
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3676 r_free = 0.3676    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3676 r_free = 0.3676    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3676
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.0871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6868  Z= 0.136
  Angle     :  0.508   6.851   9282  Z= 0.262
  Chirality :  0.040   0.130   1004
  Planarity :  0.004   0.037   1113
  Dihedral  : 21.514 179.693   1206
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.03 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  9.01 %
    Favored  : 89.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.30), residues: 776
  helix:  2.25 (0.21), residues: 568
  sheet:  None (None), residues: 0
  loop : -1.43 (0.44), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 104 
 TYR   0.011   0.001   TYR A 274 
 PHE   0.013   0.001   PHE A  61 
 TRP   0.010   0.001   TRP A 160 
 HIS   0.004   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6868)
  covalent geometry    : angle       0.50797 ( 9282)
  hydrogen bonds       : bond        0.03882 (  441)
  hydrogen bonds       : angle       4.28592 ( 1310)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 PHE cc_start: 0.6554 (OUTLIER) cc_final: 0.6344 (t80)
REVERT: A  290 SER cc_start: 0.8159 (t) cc_final: 0.7847 (p)
REVERT: A  369 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7748 (tp)
REVERT: B   70 ASP cc_start: 0.7871 (t0) cc_final: 0.7646 (t0)
REVERT: B  224 PHE cc_start: 0.7799 (t80) cc_final: 0.7447 (t80)
REVERT: B  290 SER cc_start: 0.8271 (t) cc_final: 0.7944 (p)
REVERT: B  320 MET cc_start: 0.8718 (tpp) cc_final: 0.8378 (mmt)
  outliers start: 9
  outliers final: 5
  residues processed: 94
  average time/residue: 0.0493
  time to fit residues: 6.8993
Evaluate side-chains
  93 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 PHE
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  167 LYS
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  124 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 13 optimal weight:    0.0070
   chunk 46 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 72 optimal weight:    0.0770
   chunk 19 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.4556

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.212247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.156510 restraints weight = 21437.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 8.22
r_work: 0.3141 rms_B_bonded: 5.91 restraints_weight: 2.0000
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3119
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3119
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.1122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6868  Z= 0.114
  Angle     :  0.474   6.482   9282  Z= 0.244
  Chirality :  0.039   0.126   1004
  Planarity :  0.004   0.036   1113
  Dihedral  : 19.817 179.647   1202
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.90 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  9.30 %
    Favored  : 88.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.11 (0.31), residues: 776
  helix:  2.33 (0.21), residues: 572
  sheet:  None (None), residues: 0
  loop : -1.42 (0.45), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  79 
 TYR   0.013   0.001   TYR B 156 
 PHE   0.012   0.001   PHE B  95 
 TRP   0.011   0.001   TRP A 160 
 HIS   0.004   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 6868)
  covalent geometry    : angle       0.47414 ( 9282)
  hydrogen bonds       : bond        0.03643 (  441)
  hydrogen bonds       : angle       4.08660 ( 1310)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 PHE cc_start: 0.6021 (OUTLIER) cc_final: 0.5798 (t80)
REVERT: A  196 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8478 (mm110)
REVERT: A  287 SER cc_start: 0.9248 (t) cc_final: 0.8935 (m)
REVERT: A  290 SER cc_start: 0.8518 (t) cc_final: 0.8268 (p)
REVERT: B   99 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6685 (p0)
REVERT: B  224 PHE cc_start: 0.8278 (t80) cc_final: 0.7915 (t80)
REVERT: B  290 SER cc_start: 0.8648 (t) cc_final: 0.8395 (p)
REVERT: B  320 MET cc_start: 0.8827 (tpp) cc_final: 0.8284 (mmt)
  outliers start: 13
  outliers final: 9
  residues processed: 98
  average time/residue: 0.0487
  time to fit residues: 6.9954
Evaluate side-chains
  96 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 PHE
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  167 LYS
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  343 ASP
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  101 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 20 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 63 optimal weight:    5.9990
   chunk 61 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 345 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.209065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.162426 restraints weight = 15846.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 4.68
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3741 r_free = 0.3741    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.1164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6868  Z= 0.159
  Angle     :  0.518   6.633   9282  Z= 0.266
  Chirality :  0.041   0.140   1004
  Planarity :  0.004   0.036   1113
  Dihedral  : 19.149 179.645   1200
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.16 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 10.76 %
    Favored  : 87.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.31), residues: 776
  helix:  2.38 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -1.52 (0.43), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  79 
 TYR   0.014   0.001   TYR B 156 
 PHE   0.015   0.001   PHE A 275 
 TRP   0.010   0.001   TRP A 160 
 HIS   0.004   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 6868)
  covalent geometry    : angle       0.51804 ( 9282)
  hydrogen bonds       : bond        0.03987 (  441)
  hydrogen bonds       : angle       4.19248 ( 1310)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 PHE cc_start: 0.6719 (OUTLIER) cc_final: 0.6475 (t80)
REVERT: A  290 SER cc_start: 0.8202 (t) cc_final: 0.7925 (p)
REVERT: B   99 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7486 (p0)
REVERT: B  224 PHE cc_start: 0.7768 (t80) cc_final: 0.7358 (t80)
REVERT: B  290 SER cc_start: 0.8239 (t) cc_final: 0.7967 (p)
  outliers start: 13
  outliers final: 8
  residues processed: 94
  average time/residue: 0.0445
  time to fit residues: 6.3126
Evaluate side-chains
  94 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 PHE
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  167 LYS
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  201 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 63 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 39 optimal weight:    7.9990
   chunk 11 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN
B 102 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.209351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.159495 restraints weight = 18428.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 5.48
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3697
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3697 r_free = 0.3697    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3697 r_free = 0.3697    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3697
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.1267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6868  Z= 0.154
  Angle     :  0.505   5.401   9282  Z= 0.263
  Chirality :  0.041   0.142   1004
  Planarity :  0.004   0.035   1113
  Dihedral  : 18.478 179.676   1198
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.90 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 10.90 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.00 (0.31), residues: 776
  helix:  2.36 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -1.55 (0.43), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  79 
 TYR   0.014   0.001   TYR B 156 
 PHE   0.021   0.001   PHE A  95 
 TRP   0.010   0.001   TRP A 160 
 HIS   0.004   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 6868)
  covalent geometry    : angle       0.50460 ( 9282)
  hydrogen bonds       : bond        0.03942 (  441)
  hydrogen bonds       : angle       4.18209 ( 1310)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 PHE cc_start: 0.6577 (OUTLIER) cc_final: 0.6229 (t80)
REVERT: A  290 SER cc_start: 0.8220 (t) cc_final: 0.7907 (p)
REVERT: B   69 TYR cc_start: 0.8517 (m-80) cc_final: 0.8284 (m-80)
REVERT: B   99 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7168 (p0)
REVERT: B  224 PHE cc_start: 0.7757 (t80) cc_final: 0.7330 (t80)
REVERT: B  290 SER cc_start: 0.8242 (t) cc_final: 0.7928 (p)
  outliers start: 13
  outliers final: 8
  residues processed: 93
  average time/residue: 0.0463
  time to fit residues: 6.4217
Evaluate side-chains
  93 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 PHE
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  167 LYS
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  201 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 69 optimal weight:    0.0050
   chunk 70 optimal weight:    1.9990
   chunk 45 optimal weight:    0.3980
   chunk 68 optimal weight:    0.6980
   chunk 55 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.210988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.163502 restraints weight = 17027.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 4.92
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3745
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3745 r_free = 0.3745    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3745 r_free = 0.3745    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3745
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.1351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6868  Z= 0.123
  Angle     :  0.473   5.256   9282  Z= 0.247
  Chirality :  0.039   0.144   1004
  Planarity :  0.004   0.034   1113
  Dihedral  : 17.759 179.633   1198
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.29 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 11.19 %
    Favored  : 86.63 %
  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 aren not related in a simple way.
  whole:  2.14 (0.31), residues: 776
  helix:  2.49 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -1.54 (0.43), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  79 
 TYR   0.012   0.001   TYR B 156 
 PHE   0.012   0.001   PHE B 275 
 TRP   0.011   0.001   TRP A 160 
 HIS   0.004   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6868)
  covalent geometry    : angle       0.47317 ( 9282)
  hydrogen bonds       : bond        0.03717 (  441)
  hydrogen bonds       : angle       4.10023 ( 1310)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 PHE cc_start: 0.6702 (OUTLIER) cc_final: 0.6343 (t80)
REVERT: A  290 SER cc_start: 0.8116 (t) cc_final: 0.7887 (p)
REVERT: B   99 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7332 (p0)
REVERT: B  224 PHE cc_start: 0.7798 (t80) cc_final: 0.7435 (t80)
REVERT: B  290 SER cc_start: 0.8191 (t) cc_final: 0.7952 (p)
  outliers start: 14
  outliers final: 10
  residues processed: 95
  average time/residue: 0.0444
  time to fit residues: 6.2814
Evaluate side-chains
  94 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 PHE
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  167 LYS
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  201 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 24 optimal weight:    0.7980
   chunk 10 optimal weight:   10.0000
   chunk 65 optimal weight:    0.8980
   chunk 58 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 36 optimal weight:    0.5980
   chunk 60 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.209271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.161998 restraints weight = 17002.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 4.90
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3732
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3732 r_free = 0.3732    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3732 r_free = 0.3732    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3732
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6868  Z= 0.150
  Angle     :  0.504   5.685   9282  Z= 0.261
  Chirality :  0.041   0.142   1004
  Planarity :  0.004   0.036   1113
  Dihedral  : 17.553 179.588   1198
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.16 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 11.48 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.03 (0.31), residues: 776
  helix:  2.39 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -1.56 (0.44), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  79 
 TYR   0.013   0.001   TYR B 156 
 PHE   0.015   0.001   PHE A 275 
 TRP   0.010   0.001   TRP A 160 
 HIS   0.004   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 6868)
  covalent geometry    : angle       0.50360 ( 9282)
  hydrogen bonds       : bond        0.03917 (  441)
  hydrogen bonds       : angle       4.15399 ( 1310)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 PHE cc_start: 0.6771 (OUTLIER) cc_final: 0.6413 (t80)
REVERT: A  290 SER cc_start: 0.8145 (t) cc_final: 0.7893 (p)
REVERT: B   99 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7388 (p0)
REVERT: B  224 PHE cc_start: 0.7755 (t80) cc_final: 0.7379 (t80)
REVERT: B  290 SER cc_start: 0.8221 (t) cc_final: 0.7973 (p)
  outliers start: 15
  outliers final: 11
  residues processed: 94
  average time/residue: 0.0514
  time to fit residues: 7.2085
Evaluate side-chains
  94 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 PHE
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  167 LYS
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  343 ASP
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  201 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 48 optimal weight:    6.9990
   chunk 67 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 20 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 59 optimal weight:    0.3980
   chunk 42 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0670
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.211069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.155586 restraints weight = 21430.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 7.74
r_work: 0.3115 rms_B_bonded: 6.13 restraints_weight: 2.0000
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3094
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3094
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6868  Z= 0.121
  Angle     :  0.480   6.949   9282  Z= 0.249
  Chirality :  0.040   0.145   1004
  Planarity :  0.004   0.036   1113
  Dihedral  : 17.203 179.628   1198
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.03 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 11.77 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.15 (0.31), residues: 776
  helix:  2.49 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -1.55 (0.44), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  79 
 TYR   0.012   0.001   TYR B 156 
 PHE   0.012   0.001   PHE B 275 
 TRP   0.011   0.001   TRP A 160 
 HIS   0.003   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6868)
  covalent geometry    : angle       0.48028 ( 9282)
  hydrogen bonds       : bond        0.03679 (  441)
  hydrogen bonds       : angle       4.08040 ( 1310)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 PHE cc_start: 0.6193 (OUTLIER) cc_final: 0.5823 (t80)
REVERT: A  290 SER cc_start: 0.8541 (t) cc_final: 0.8326 (p)
REVERT: B   99 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6569 (p0)
REVERT: B  224 PHE cc_start: 0.8290 (t80) cc_final: 0.7854 (t80)
REVERT: B  290 SER cc_start: 0.8658 (t) cc_final: 0.8416 (p)
  outliers start: 13
  outliers final: 9
  residues processed: 90
  average time/residue: 0.0482
  time to fit residues: 6.5286
Evaluate side-chains
  88 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ASN
Chi-restraints excluded: chain A residue   38 PHE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  167 LYS
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  343 ASP
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  101 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0040
   chunk 24 optimal weight:    0.7980
   chunk 14 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 72 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 71 optimal weight:    0.8980
   chunk 40 optimal weight:   20.0000
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.211523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.163454 restraints weight = 17254.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 5.08
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3745
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3745 r_free = 0.3745    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3745 r_free = 0.3745    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3745
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.1568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6868  Z= 0.119
  Angle     :  0.471   5.223   9282  Z= 0.246
  Chirality :  0.039   0.143   1004
  Planarity :  0.004   0.036   1113
  Dihedral  : 16.849 179.585   1196
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.16 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 12.06 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.18 (0.31), residues: 776
  helix:  2.52 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -1.57 (0.44), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  79 
 TYR   0.012   0.001   TYR B 156 
 PHE   0.012   0.001   PHE B 275 
 TRP   0.011   0.001   TRP A 160 
 HIS   0.003   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6868)
  covalent geometry    : angle       0.47067 ( 9282)
  hydrogen bonds       : bond        0.03639 (  441)
  hydrogen bonds       : angle       4.06019 ( 1310)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 PHE cc_start: 0.6755 (OUTLIER) cc_final: 0.6385 (t80)
REVERT: A  290 SER cc_start: 0.8171 (t) cc_final: 0.7954 (p)
REVERT: B   99 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7344 (p0)
REVERT: B  224 PHE cc_start: 0.7821 (t80) cc_final: 0.7422 (t80)
  outliers start: 11
  outliers final: 9
  residues processed: 90
  average time/residue: 0.0468
  time to fit residues: 6.2484
Evaluate side-chains
  89 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ASN
Chi-restraints excluded: chain A residue   38 PHE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  167 LYS
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  135 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 59 optimal weight:    0.0050
   chunk 49 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0980
   chunk 66 optimal weight:    0.4980
   chunk 32 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 55 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.3594

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.213244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.160110 restraints weight = 19951.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 6.70
r_work: 0.3132 rms_B_bonded: 6.45 restraints_weight: 2.0000
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3111
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3111
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.1680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6868  Z= 0.104
  Angle     :  0.455   5.143   9282  Z= 0.238
  Chirality :  0.039   0.140   1004
  Planarity :  0.004   0.034   1113
  Dihedral  : 16.502 179.637   1196
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.03 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 12.35 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.31), residues: 776
  helix:  2.61 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -1.56 (0.44), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  79 
 TYR   0.011   0.001   TYR B 156 
 PHE   0.011   0.001   PHE B 275 
 TRP   0.011   0.001   TRP A 160 
 HIS   0.003   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 6868)
  covalent geometry    : angle       0.45469 ( 9282)
  hydrogen bonds       : bond        0.03468 (  441)
  hydrogen bonds       : angle       3.98884 ( 1310)

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

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

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1552 Ramachandran restraints generated.
    776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 PHE cc_start: 0.6164 (OUTLIER) cc_final: 0.5866 (t80)
REVERT: A  287 SER cc_start: 0.9271 (t) cc_final: 0.8977 (m)
REVERT: B   99 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6505 (p0)
REVERT: B  224 PHE cc_start: 0.8324 (t80) cc_final: 0.7891 (t80)
  outliers start: 11
  outliers final: 8
  residues processed: 88
  average time/residue: 0.0463
  time to fit residues: 6.1128
Evaluate side-chains
  88 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ASN
Chi-restraints excluded: chain A residue   38 PHE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  167 LYS
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  101 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 40 optimal weight:   20.0000
   chunk 27 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 2 optimal weight:    8.9990
   chunk 8 optimal weight:    0.5980
   chunk 63 optimal weight:    0.0870
   chunk 69 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.5558

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.212149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.164741 restraints weight = 17938.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 5.09
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3758
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3758 r_free = 0.3758    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3758 r_free = 0.3758    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3758
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6868  Z= 0.122
  Angle     :  0.479   5.573   9282  Z= 0.248
  Chirality :  0.039   0.135   1004
  Planarity :  0.004   0.035   1113
  Dihedral  : 16.426 179.523   1196
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.03 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 12.50 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.23 (0.31), residues: 776
  helix:  2.56 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -1.57 (0.44), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  79 
 TYR   0.016   0.001   TYR B 156 
 PHE   0.014   0.001   PHE A  61 
 TRP   0.011   0.001   TRP A 160 
 HIS   0.003   0.001   HIS A 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 6868)
  covalent geometry    : angle       0.47947 ( 9282)
  hydrogen bonds       : bond        0.03615 (  441)
  hydrogen bonds       : angle       4.03135 ( 1310)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1260.01 seconds
wall clock time: 22 minutes 19.60 seconds (1339.60 seconds total)