Starting phenix.real_space_refine
on Sat May 10 18:27:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ul9_42357/05_2025/8ul9_42357.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ul9_42357/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ul9_42357/05_2025/8ul9_42357.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ul9_42357/05_2025/8ul9_42357.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ul9_42357/05_2025/8ul9_42357.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ul9_42357/05_2025/8ul9_42357.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.71, per 1000 atoms: 1.16
  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: 2.07
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 0.55
  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: 1.74

  Time building geometry restraints manager: 2.31 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 388 or resid 1001 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 388 or resid 1001 through 1004 or (resid 1005 and (na \ 
me N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or n \ 
ame C16 or name C17 or name C18 or name C19 or name C2 or name C20 or name C21 o \ 
r name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C \ 
28 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or nam \ 
e 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 name C44 or name C45 or name C46 or name C5 or name C6 o \ 
r name C7 or name C8 or name O11 or name O1P or name O2 or name O2P or name O3 o \ 
r 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:             2.000
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.870
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.030
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.220
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.012   0.001   TRP A 160 
 HIS   0.004   0.001   HIS A 164 
 PHE   0.013   0.001   PHE A 275 
 TYR   0.015   0.001   TYR A 274 
 ARG   0.001   0.000   ARG B  32 

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

*********************** 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  : 0.742 
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: 0.1409
  time to fit residues: 23.5099
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  : 0.692 
-------------------------------------------------------------------------------
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 64 optimal weight:    0.7980
   chunk 57 optimal weight:    0.2980
   chunk 31 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.5380

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.211437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.163879 restraints weight = 17567.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 5.02
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3749
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3749 r_free = 0.3749    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3748 r_free = 0.3748    target_work(ls_wunit_k1) = 0.157         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3748
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.0868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6868  Z= 0.126
  Angle     :  0.497   6.728   9282  Z= 0.257
  Chirality :  0.040   0.127   1004
  Planarity :  0.004   0.037   1113
  Dihedral  : 21.622 179.744   1206
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.16 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  8.72 %
    Favored  : 89.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.30), residues: 776
  helix:  2.29 (0.21), residues: 568
  sheet:  None (None), residues: 0
  loop : -1.42 (0.44), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 160 
 HIS   0.004   0.001   HIS A 164 
 PHE   0.012   0.001   PHE A  61 
 TYR   0.010   0.001   TYR A 274 
 ARG   0.003   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03835 (  441)
  hydrogen bonds       : angle       4.26218 ( 1310)
  covalent geometry    : bond        0.00293 ( 6868)
  covalent geometry    : angle       0.49720 ( 9282)

*********************** 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
  99 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 PHE cc_start: 0.6745 (OUTLIER) cc_final: 0.6495 (t80)
REVERT: A  290 SER cc_start: 0.8132 (t) cc_final: 0.7839 (p)
REVERT: A  369 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7795 (tp)
REVERT: B   70 ASP cc_start: 0.7811 (t0) cc_final: 0.7601 (t0)
REVERT: B  224 PHE cc_start: 0.7761 (t80) cc_final: 0.7455 (t80)
REVERT: B  290 SER cc_start: 0.8263 (t) cc_final: 0.7953 (p)
REVERT: B  320 MET cc_start: 0.8715 (tpp) cc_final: 0.8409 (mmt)
  outliers start: 9
  outliers final: 5
  residues processed: 95
  average time/residue: 0.1401
  time to fit residues: 19.4517
Evaluate side-chains
  95 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
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  168 LEU
Chi-restraints excluded: chain A residue  369 ILE
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  101 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.1980
   chunk 9 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 74 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4267 r_free = 0.4267 target = 0.210510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.156090 restraints weight = 19743.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 7.11
r_work: 0.3106 rms_B_bonded: 6.07 restraints_weight: 2.0000
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2928
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2928 r_free = 0.2928    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2928 r_free = 0.2928    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2928
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.1077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6868  Z= 0.138
  Angle     :  0.501   6.428   9282  Z= 0.257
  Chirality :  0.040   0.134   1004
  Planarity :  0.004   0.036   1113
  Dihedral  : 19.971 179.647   1200
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.03 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  :  9.74 %
    Favored  : 88.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.31), residues: 776
  helix:  2.39 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -1.48 (0.43), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 160 
 HIS   0.004   0.001   HIS A 164 
 PHE   0.013   0.001   PHE B 275 
 TYR   0.014   0.001   TYR B 156 
 ARG   0.004   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03858 (  441)
  hydrogen bonds       : angle       4.17232 ( 1310)
  covalent geometry    : bond        0.00336 ( 6868)
  covalent geometry    : angle       0.50085 ( 9282)

*********************** 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
  102 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 SER cc_start: 0.8545 (t) cc_final: 0.8285 (p)
REVERT: B   99 ASP cc_start: 0.7076 (OUTLIER) cc_final: 0.6625 (p0)
REVERT: B  224 PHE cc_start: 0.8266 (t80) cc_final: 0.7899 (t80)
REVERT: B  290 SER cc_start: 0.8689 (t) cc_final: 0.8427 (p)
REVERT: B  320 MET cc_start: 0.8831 (tpp) cc_final: 0.8288 (mmt)
  outliers start: 13
  outliers final: 10
  residues processed: 97
  average time/residue: 0.1459
  time to fit residues: 20.5094
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  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  124 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 54 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 70 optimal weight:    0.3980
   chunk 72 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.210643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.155915 restraints weight = 20814.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 7.15
r_work: 0.3092 rms_B_bonded: 6.30 restraints_weight: 2.0000
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2916
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2916 r_free = 0.2916    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2916
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6868  Z= 0.133
  Angle     :  0.490   6.632   9282  Z= 0.253
  Chirality :  0.040   0.143   1004
  Planarity :  0.004   0.035   1113
  Dihedral  : 18.872 179.606   1198
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.03 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 10.47 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.31), residues: 776
  helix:  2.46 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -1.51 (0.43), residues: 220

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03776 (  441)
  hydrogen bonds       : angle       4.09523 ( 1310)
  covalent geometry    : bond        0.00321 ( 6868)
  covalent geometry    : angle       0.48982 ( 9282)

*********************** 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
  101 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 SER cc_start: 0.8550 (t) cc_final: 0.8309 (p)
REVERT: B   99 ASP cc_start: 0.7025 (OUTLIER) cc_final: 0.6610 (p0)
REVERT: B  224 PHE cc_start: 0.8323 (t80) cc_final: 0.7899 (t80)
REVERT: B  290 SER cc_start: 0.8679 (t) cc_final: 0.8431 (p)
REVERT: B  320 MET cc_start: 0.8840 (tpp) cc_final: 0.8529 (mmt)
  outliers start: 16
  outliers final: 12
  residues processed: 96
  average time/residue: 0.1422
  time to fit residues: 19.8838
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  : 0.690 
-------------------------------------------------------------------------------
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 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  124 ASN
Chi-restraints excluded: chain B residue  135 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 17 optimal weight:    0.0060
   chunk 18 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 25 optimal weight:    9.9990
   chunk 45 optimal weight:    0.0970
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.7796

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.209784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.154232 restraints weight = 21173.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 7.60
r_work: 0.3091 rms_B_bonded: 6.16 restraints_weight: 2.0000
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2910
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2910 r_free = 0.2910    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2910
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.1292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6868  Z= 0.144
  Angle     :  0.498   5.513   9282  Z= 0.258
  Chirality :  0.040   0.141   1004
  Planarity :  0.004   0.035   1113
  Dihedral  : 18.168 179.652   1196
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.03 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 10.17 %
    Favored  : 87.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.31), residues: 776
  helix:  2.42 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -1.52 (0.43), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 160 
 HIS   0.004   0.001   HIS A 164 
 PHE   0.014   0.001   PHE A 275 
 TYR   0.014   0.001   TYR B 156 
 ARG   0.003   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03855 (  441)
  hydrogen bonds       : angle       4.13112 ( 1310)
  covalent geometry    : bond        0.00355 ( 6868)
  covalent geometry    : angle       0.49848 ( 9282)

*********************** 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
  102 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 SER cc_start: 0.8579 (t) cc_final: 0.8348 (p)
REVERT: B   69 TYR cc_start: 0.8863 (m-80) cc_final: 0.8555 (m-80)
REVERT: B   99 ASP cc_start: 0.6877 (OUTLIER) cc_final: 0.6474 (p0)
REVERT: B  224 PHE cc_start: 0.8264 (t80) cc_final: 0.7850 (t80)
REVERT: B  290 SER cc_start: 0.8674 (t) cc_final: 0.8422 (p)
REVERT: B  320 MET cc_start: 0.8795 (tpp) cc_final: 0.8474 (mmt)
  outliers start: 16
  outliers final: 12
  residues processed: 97
  average time/residue: 0.1427
  time to fit residues: 20.0348
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  : 0.707 
-------------------------------------------------------------------------------
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  124 ASN
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 5 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 39 optimal weight:    7.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.4253 r_free = 0.4253 target = 0.209191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.159053 restraints weight = 15408.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 5.39
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3693
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3693 r_free = 0.3693    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3693 r_free = 0.3693    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3693
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.1383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6868  Z= 0.154
  Angle     :  0.508   5.648   9282  Z= 0.264
  Chirality :  0.041   0.142   1004
  Planarity :  0.004   0.034   1113
  Dihedral  : 17.713 179.666   1196
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.03 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.05 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.31), residues: 776
  helix:  2.36 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -1.56 (0.44), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 160 
 HIS   0.003   0.001   HIS A 164 
 PHE   0.015   0.001   PHE A 275 
 TYR   0.014   0.001   TYR B 156 
 ARG   0.003   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03952 (  441)
  hydrogen bonds       : angle       4.17936 ( 1310)
  covalent geometry    : bond        0.00384 ( 6868)
  covalent geometry    : angle       0.50817 ( 9282)

*********************** 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
  98 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 SER cc_start: 0.8149 (t) cc_final: 0.7899 (p)
REVERT: B   99 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7266 (p0)
REVERT: B  224 PHE cc_start: 0.7790 (t80) cc_final: 0.7368 (t80)
REVERT: B  290 SER cc_start: 0.8204 (t) cc_final: 0.7953 (p)
  outliers start: 12
  outliers final: 11
  residues processed: 95
  average time/residue: 0.1368
  time to fit residues: 19.1586
Evaluate side-chains
  92 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
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  124 ASN
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 31 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 40 optimal weight:   20.0000
   chunk 24 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9980
   chunk 17 optimal weight:    0.0980
   chunk 39 optimal weight:    7.9990
   chunk 59 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0870
   chunk 8 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.4758

-------------------------------------------------------------------------------
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 = 0.4277 r_free = 0.4277 target = 0.211676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.165553 restraints weight = 15299.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3772 rms_B_bonded: 4.70
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3772
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3772 r_free = 0.3772    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3772 r_free = 0.3772    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3772
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.1469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6868  Z= 0.116
  Angle     :  0.475   7.298   9282  Z= 0.246
  Chirality :  0.039   0.147   1004
  Planarity :  0.004   0.034   1113
  Dihedral  : 17.259 179.597   1196
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.90 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 12.06 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.31), residues: 776
  helix:  2.50 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -1.53 (0.44), residues: 218

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03634 (  441)
  hydrogen bonds       : angle       4.05570 ( 1310)
  covalent geometry    : bond        0.00271 ( 6868)
  covalent geometry    : angle       0.47549 ( 9282)

*********************** 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: 14
    poor density    : 85
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
REVERT: A  287 SER cc_start: 0.8852 (t) cc_final: 0.8547 (m)
REVERT: A  290 SER cc_start: 0.8103 (t) cc_final: 0.7880 (p)
REVERT: B   99 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7433 (p0)
REVERT: B  224 PHE cc_start: 0.7773 (t80) cc_final: 0.7383 (t80)
REVERT: B  290 SER cc_start: 0.8167 (t) cc_final: 0.7939 (p)
  outliers start: 14
  outliers final: 12
  residues processed: 95
  average time/residue: 0.1485
  time to fit residues: 20.4740
Evaluate side-chains
  92 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  338 MET
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  124 ASN
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 50 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 58 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 68 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0970
   chunk 69 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 = 0.4273 r_free = 0.4273 target = 0.211297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.163572 restraints weight = 17227.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3745 rms_B_bonded: 5.05
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 = 0.09   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-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: 0.7657
moved from start:          0.1524

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= 0.121
  Angle     :  0.474   5.220   9282  Z= 0.247
  Chirality :  0.039   0.143   1004
  Planarity :  0.004   0.034   1113
  Dihedral  : 17.000 179.548   1194
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.29 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 11.34 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.31), residues: 776
  helix:  2.51 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -1.56 (0.44), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 160 
 HIS   0.003   0.001   HIS A 164 
 PHE   0.012   0.001   PHE A 275 
 TYR   0.016   0.001   TYR B 156 
 ARG   0.004   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03662 (  441)
  hydrogen bonds       : angle       4.06493 ( 1310)
  covalent geometry    : bond        0.00287 ( 6868)
  covalent geometry    : angle       0.47414 ( 9282)

*********************** 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
  97 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 SER cc_start: 0.8182 (t) cc_final: 0.7959 (p)
REVERT: B   99 ASP cc_start: 0.7568 (OUTLIER) cc_final: 0.7354 (p0)
REVERT: B  224 PHE cc_start: 0.7801 (t80) cc_final: 0.7407 (t80)
REVERT: B  290 SER cc_start: 0.8160 (t) cc_final: 0.7951 (p)
  outliers start: 16
  outliers final: 14
  residues processed: 92
  average time/residue: 0.1440
  time to fit residues: 19.4211
Evaluate side-chains
  91 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
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  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  338 MET
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  124 ASN
Chi-restraints excluded: chain B residue  135 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 28 optimal weight:    0.2980
   chunk 0 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 17 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0980
   chunk 20 optimal weight:    6.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.4257 r_free = 0.4257 target = 0.209453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.156980 restraints weight = 18277.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3655 rms_B_bonded: 6.26
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3656
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3656 r_free = 0.3656    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3656 r_free = 0.3656    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.1516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6868  Z= 0.154
  Angle     :  0.513   6.422   9282  Z= 0.266
  Chirality :  0.041   0.140   1004
  Planarity :  0.004   0.039   1113
  Dihedral  : 17.071 179.584   1194
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.42 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 11.77 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.31), residues: 776
  helix:  2.40 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -1.58 (0.44), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 199 
 HIS   0.003   0.001   HIS A 164 
 PHE   0.015   0.001   PHE A 275 
 TYR   0.021   0.001   TYR B 156 
 ARG   0.006   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03935 (  441)
  hydrogen bonds       : angle       4.16317 ( 1310)
  covalent geometry    : bond        0.00385 ( 6868)
  covalent geometry    : angle       0.51334 ( 9282)

*********************** 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
  96 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
REVERT: A  290 SER cc_start: 0.8156 (t) cc_final: 0.7912 (p)
REVERT: B   99 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.7084 (p0)
REVERT: B  224 PHE cc_start: 0.7868 (t80) cc_final: 0.7424 (t80)
REVERT: B  290 SER cc_start: 0.8209 (t) cc_final: 0.7964 (p)
  outliers start: 15
  outliers final: 13
  residues processed: 91
  average time/residue: 0.1417
  time to fit residues: 18.8919
Evaluate side-chains
  94 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
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  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  338 MET
Chi-restraints excluded: chain A residue  343 ASP
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  124 ASN
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 51 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 15 optimal weight:    0.2980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.2980
   chunk 10 optimal weight:    8.9990
   chunk 35 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 72 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.4279 r_free = 0.4279 target = 0.211926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.162127 restraints weight = 17863.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 5.53
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3725 r_free = 0.3725    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3725 r_free = 0.3725    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3725
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.1599

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= 0.115
  Angle     :  0.467   5.808   9282  Z= 0.244
  Chirality :  0.039   0.141   1004
  Planarity :  0.004   0.034   1113
  Dihedral  : 16.662 179.679   1194
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.16 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 12.21 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.31), residues: 776
  helix:  2.53 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -1.60 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 160 
 HIS   0.003   0.001   HIS A 164 
 PHE   0.016   0.001   PHE A  95 
 TYR   0.016   0.001   TYR B 156 
 ARG   0.007   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03603 (  441)
  hydrogen bonds       : angle       4.03401 ( 1310)
  covalent geometry    : bond        0.00267 ( 6868)
  covalent geometry    : angle       0.46741 ( 9282)

********************** 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
  95 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
REVERT: A  287 SER cc_start: 0.8865 (t) cc_final: 0.8566 (m)
REVERT: A  290 SER cc_start: 0.8158 (t) cc_final: 0.7939 (p)
REVERT: B   99 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7280 (p0)
REVERT: B  224 PHE cc_start: 0.7862 (t80) cc_final: 0.7462 (t80)
  outliers start: 13
  outliers final: 12
  residues processed: 91
  average time/residue: 0.1499
  time to fit residues: 19.8872
Evaluate side-chains
  89 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
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  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  338 MET
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
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 21 optimal weight:    0.4980
   chunk 15 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 7 optimal weight:    0.3980
   chunk 26 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0970
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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 = 0.4283 r_free = 0.4283 target = 0.212407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.157487 restraints weight = 20849.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 7.55
r_work: 0.3112 rms_B_bonded: 6.44 restraints_weight: 2.0000
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3088
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3088 r_free = 0.3088    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3088
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6868  Z= 0.114
  Angle     :  0.473   6.931   9282  Z= 0.246
  Chirality :  0.039   0.136   1004
  Planarity :  0.004   0.034   1113
  Dihedral  : 16.452 179.601   1194
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.03 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 12.21 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.21 (0.31), residues: 776
  helix:  2.55 (0.21), residues: 558
  sheet:  None (None), residues: 0
  loop : -1.58 (0.43), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 160 
 HIS   0.003   0.001   HIS A 164 
 PHE   0.012   0.001   PHE B 275 
 TYR   0.016   0.001   TYR B 156 
 ARG   0.007   0.000   ARG B  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03576 (  441)
  hydrogen bonds       : angle       4.01887 ( 1310)
  covalent geometry    : bond        0.00265 ( 6868)
  covalent geometry    : angle       0.47283 ( 9282)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3384.30 seconds
wall clock time: 59 minutes 28.52 seconds (3568.52 seconds total)