Starting phenix.real_space_refine
on Mon Apr 28 13:55:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hjc_52212/04_2025/9hjc_52212_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hjc_52212/04_2025/9hjc_52212.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hjc_52212/04_2025/9hjc_52212.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hjc_52212/04_2025/9hjc_52212.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hjc_52212/04_2025/9hjc_52212_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hjc_52212/04_2025/9hjc_52212_trim.cif"
  }
  resolution = 2.1
  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=  -0.003 sd=   0.222
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
     Mg      2      5.21       5
     S      26      5.16       5
     C    2472      2.51       5
     N     640      2.21       5
     O     728      1.98       5
     H    3806      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7674
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 3819
          Classifications: {'peptide': 243}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 230}
    Chain: "B"
      Number of atoms: 3817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 3817
          Classifications: {'peptide': 243}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 230}
    Chain: "A"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 19
          Unusual residues: {' MG': 1, 'VIB': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 19
          Unusual residues: {' MG': 1, 'VIB': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.72, per 1000 atoms: 0.75
  Number of scatterers: 7674
  At special positions: 0
  Unit cell: (67.1504, 85.8357, 62.4791, 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      26     16.00
     Mg      2     11.99
     O     728      8.00
     N     640      7.00
     C    2472      6.00
     H    3806      1.00
    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: 2.19
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  900

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 4 sheets defined
      30.5% alpha, 25.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 12
    Processing helix  chain 'A' and resid 30 through 37
      removed outlier: 3.833A  pdb=" N   HIS A  34 " --> pdb=" O   ASN A  30 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   ASN A  37 " --> pdb=" O   ARG A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 56
      removed outlier: 4.197A  pdb=" N   ASN A  50 " --> pdb=" O   ASP A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 63
    Processing helix  chain 'A' and resid 76 through 86
    Processing helix  chain 'A' and resid 99 through 116
    Processing helix  chain 'A' and resid 131 through 146
      removed outlier: 3.548A  pdb=" N   LEU A 142 " --> pdb=" O   SER A 138 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   PHE A 143 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   THR A 146 " --> pdb=" O   LEU A 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 12
    Processing helix  chain 'B' and resid 30 through 37
      removed outlier: 3.856A  pdb=" N   HIS B  34 " --> pdb=" O   ASN B  30 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   ASN B  37 " --> pdb=" O   ARG B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 56
      removed outlier: 4.057A  pdb=" N   ASN B  50 " --> pdb=" O   ASP B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 63
    Processing helix  chain 'B' and resid 76 through 86
    Processing helix  chain 'B' and resid 99 through 116
    Processing helix  chain 'B' and resid 131 through 146
      removed outlier: 3.541A  pdb=" N   LEU B 142 " --> pdb=" O   SER B 138 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   PHE B 143 " --> pdb=" O   VAL B 139 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   THR B 146 " --> pdb=" O   LEU B 142 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5
      removed outlier: 6.174A  pdb=" N   HIS A   3 " --> pdb=" O   ARG A 171 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   HIS A 173 " --> pdb=" O   HIS A   3 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   PHE A   5 " --> pdb=" O   HIS A 173 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   GLN A 194 " --> pdb=" O   ASP A 207 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   ASP A 207 " --> pdb=" O   GLN A 194 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 92
      removed outlier: 6.233A  pdb=" N   ILE A  68 " --> pdb=" O   ILE A  91 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ASN A  69 " --> pdb=" O   CYS A  44 " (cutoff:3.500A)
      removed outlier: 8.924A  pdb=" N   ALA A  43 " --> pdb=" O   TYR A  19 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   LEU A  21 " --> pdb=" O   ALA A  43 " (cutoff:3.500A)
      removed outlier: 7.820A  pdb=" N   ALA A  45 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   ILE A  23 " --> pdb=" O   ALA A  45 " (cutoff:3.500A)
      removed outlier: 6.061A  pdb=" N   CYS A  20 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
      removed outlier: 7.623A  pdb=" N   LEU A 125 " --> pdb=" O   CYS A  20 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   VAL A  22 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ILE A 153 " --> pdb=" O   LEU A 164 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   LEU A 164 " --> pdb=" O   ILE A 153 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   TRP A 182 " --> pdb=" O   ALA A 240 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   LEU A 185 " --> pdb=" O   THR A 217 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   THR A 217 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 5
      removed outlier: 6.175A  pdb=" N   HIS B   3 " --> pdb=" O   ARG B 171 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   HIS B 173 " --> pdb=" O   HIS B   3 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   PHE B   5 " --> pdb=" O   HIS B 173 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   GLN B 194 " --> pdb=" O   ASP B 207 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   ASP B 207 " --> pdb=" O   GLN B 194 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 92
      removed outlier: 6.261A  pdb=" N   ILE B  68 " --> pdb=" O   ILE B  91 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   PHE B  67 " --> pdb=" O   ARG B  42 " (cutoff:3.500A)
      removed outlier: 8.963A  pdb=" N   ALA B  43 " --> pdb=" O   TYR B  19 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   LEU B  21 " --> pdb=" O   ALA B  43 " (cutoff:3.500A)
      removed outlier: 7.660A  pdb=" N   ALA B  45 " --> pdb=" O   LEU B  21 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   ILE B  23 " --> pdb=" O   ALA B  45 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   CYS B  20 " --> pdb=" O   VAL B 123 " (cutoff:3.500A)
      removed outlier: 7.621A  pdb=" N   LEU B 125 " --> pdb=" O   CYS B  20 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   VAL B  22 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   ILE B 153 " --> pdb=" O   LEU B 164 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   LEU B 164 " --> pdb=" O   ILE B 153 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   TRP B 182 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   LEU B 185 " --> pdb=" O   THR B 217 " (cutoff:3.500A)
      removed outlier: 5.243A  pdb=" N   THR B 217 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)

    151 hydrogen bonds defined for protein.
    405 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: 2.79

  Time building geometry restraints manager: 2.59 seconds

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

  Histogram of bond lengths:
        0.82 -     1.02: 3794
        1.02 -     1.21: 2
        1.21 -     1.41: 1604
        1.41 -     1.61: 2320
        1.61 -     1.81: 40
  Bond restraints: 7760
  Sorted by residual:
  bond pdb=" SG  CYS A 183 "
       pdb=" HG  CYS A 183 "
    ideal  model  delta    sigma   weight residual
    1.200  1.341 -0.141 2.00e-02 2.50e+03 4.97e+01
  bond pdb=" SG  CYS B  44 "
       pdb=" HG  CYS B  44 "
    ideal  model  delta    sigma   weight residual
    1.200  1.341 -0.141 2.00e-02 2.50e+03 4.94e+01
  bond pdb=" SG  CYS B 104 "
       pdb=" HG  CYS B 104 "
    ideal  model  delta    sigma   weight residual
    1.200  1.340 -0.140 2.00e-02 2.50e+03 4.93e+01
  bond pdb=" SG  CYS A  44 "
       pdb=" HG  CYS A  44 "
    ideal  model  delta    sigma   weight residual
    1.200  1.340 -0.140 2.00e-02 2.50e+03 4.91e+01
  bond pdb=" SG  CYS A 104 "
       pdb=" HG  CYS A 104 "
    ideal  model  delta    sigma   weight residual
    1.200  1.340 -0.140 2.00e-02 2.50e+03 4.90e+01
  ... (remaining 7755 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 13831
        1.76 -     3.53: 179
        3.53 -     5.29: 31
        5.29 -     7.06: 5
        7.06 -     8.82: 2
  Bond angle restraints: 14048
  Sorted by residual:
  angle pdb=" N   ASN A  37 "
        pdb=" CA  ASN A  37 "
        pdb=" C   ASN A  37 "
      ideal   model   delta    sigma   weight residual
     112.54  119.47   -6.93 1.22e+00 6.72e-01 3.23e+01
  angle pdb=" N   ASN B  37 "
        pdb=" CA  ASN B  37 "
        pdb=" C   ASN B  37 "
      ideal   model   delta    sigma   weight residual
     111.82  117.29   -5.47 1.16e+00 7.43e-01 2.22e+01
  angle pdb=" N   ASP B  73 "
        pdb=" CA  ASP B  73 "
        pdb=" C   ASP B  73 "
      ideal   model   delta    sigma   weight residual
     113.38  107.80    5.58 1.23e+00 6.61e-01 2.06e+01
  angle pdb=" N   ASP A  73 "
        pdb=" CA  ASP A  73 "
        pdb=" C   ASP A  73 "
      ideal   model   delta    sigma   weight residual
     113.23  108.20    5.03 1.24e+00 6.50e-01 1.64e+01
  angle pdb=" N   ASN B 219 "
        pdb=" CA  ASN B 219 "
        pdb=" C   ASN B 219 "
      ideal   model   delta    sigma   weight residual
     110.59  105.90    4.69 1.45e+00 4.76e-01 1.05e+01
  ... (remaining 14043 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 3308
       17.44 -    34.88: 224
       34.88 -    52.32: 69
       52.32 -    69.77: 30
       69.77 -    87.21: 7
  Dihedral angle restraints: 3638
    sinusoidal: 1993
      harmonic: 1645
  Sorted by residual:
  dihedral pdb=" CG  LYS B 106 "
           pdb=" CD  LYS B 106 "
           pdb=" CE  LYS B 106 "
           pdb=" NZ  LYS B 106 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.75   57.25     3      1.50e+01 4.44e-03 9.43e+00
  dihedral pdb=" CG  LYS A 106 "
           pdb=" CD  LYS A 106 "
           pdb=" CE  LYS A 106 "
           pdb=" NZ  LYS A 106 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.90   57.10     3      1.50e+01 4.44e-03 9.43e+00
  dihedral pdb=" CA  LYS A 115 "
           pdb=" CB  LYS A 115 "
           pdb=" CG  LYS A 115 "
           pdb=" CD  LYS A 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  115.43  -55.43     3      1.50e+01 4.44e-03 9.35e+00
  ... (remaining 3635 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 444
       0.038 -    0.077: 95
       0.077 -    0.115: 58
       0.115 -    0.153: 15
       0.153 -    0.192: 2
  Chirality restraints: 614
  Sorted by residual:
  chirality pdb=" CA  ASN A  37 "
            pdb=" N   ASN A  37 "
            pdb=" C   ASN A  37 "
            pdb=" CB  ASN A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.19e-01
  chirality pdb=" CA  ASN B  37 "
            pdb=" N   ASN B  37 "
            pdb=" C   ASN B  37 "
            pdb=" CB  ASN B  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.61e-01
  chirality pdb=" CA  ILE A  68 "
            pdb=" N   ILE A  68 "
            pdb=" C   ILE A  68 "
            pdb=" CB  ILE A  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.78e-01
  ... (remaining 611 not shown)

  Planarity restraints: 1143
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B  50 "    0.180 2.00e-02 2.50e+03   1.79e-01 4.82e+02
        pdb=" CG  ASN B  50 "   -0.016 2.00e-02 2.50e+03
        pdb=" OD1 ASN B  50 "   -0.169 2.00e-02 2.50e+03
        pdb=" ND2 ASN B  50 "    0.000 2.00e-02 2.50e+03
        pdb="HD21 ASN B  50 "   -0.254 2.00e-02 2.50e+03
        pdb="HD22 ASN B  50 "    0.259 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A  50 "    0.163 2.00e-02 2.50e+03   1.62e-01 3.95e+02
        pdb=" CG  ASN A  50 "   -0.012 2.00e-02 2.50e+03
        pdb=" OD1 ASN A  50 "   -0.155 2.00e-02 2.50e+03
        pdb=" ND2 ASN A  50 "    0.001 2.00e-02 2.50e+03
        pdb="HD21 ASN A  50 "   -0.230 2.00e-02 2.50e+03
        pdb="HD22 ASN A  50 "    0.233 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 219 "   -0.154 2.00e-02 2.50e+03   1.53e-01 3.51e+02
        pdb=" CG  ASN B 219 "    0.014 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 219 "    0.146 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 219 "   -0.003 2.00e-02 2.50e+03
        pdb="HD21 ASN B 219 "    0.217 2.00e-02 2.50e+03
        pdb="HD22 ASN B 219 "   -0.220 2.00e-02 2.50e+03
  ... (remaining 1140 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.28: 1424
        2.28 -     2.86: 17833
        2.86 -     3.44: 21183
        3.44 -     4.02: 30780
        4.02 -     4.60: 44501
  Nonbonded interactions: 115721
  Sorted by model distance:
  nonbonded pdb=" O   GLN B 166 "
            pdb=" HE2 HIS B 170 "
     model   vdw
     1.705 2.450
  nonbonded pdb=" O   GLN A 166 "
            pdb=" HE2 HIS A 170 "
     model   vdw
     1.726 2.450
  nonbonded pdb=" OE1 GLU A  89 "
            pdb=" HZ1 LYS A 111 "
     model   vdw
     1.747 2.450
  nonbonded pdb=" H   LYS A  18 "
            pdb=" OD2 ASP A 120 "
     model   vdw
     1.781 2.450
  nonbonded pdb=" H   GLY A 189 "
            pdb=" H   GLY B 189 "
     model   vdw
     1.786 2.100
  ... (remaining 115716 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 or (resid 2 and (name N or name CA or name C or name O o \ 
r name CB or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 o \ 
r name HB3 or name HG2 or name HG3)) or (resid 3 and (name N or name CA or name  \ 
C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 
2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name H \ 
E2)) or resid 4 through 243 or resid 301 through 302))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.660
  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:             0.170
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     24.650
  Find NCS groups from input model:        0.200
  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:12.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
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      :  0.006   0.127   3954  Z= 0.318
  Angle     :  0.709   6.934   5378  Z= 0.411
  Chirality :  0.045   0.192    614
  Planarity :  0.004   0.031    684
  Dihedral  : 14.740  87.208   1438
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 2.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  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:  1.01 (0.37), residues: 482
  helix:  1.19 (0.49), residues: 110
  sheet:  0.63 (0.47), residues: 102
  loop :  0.62 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  36 
 HIS   0.002   0.001   HIS B 147 
 PHE   0.007   0.001   PHE B   5 
 TYR   0.013   0.002   TYR A  53 
 ARG   0.004   0.001   ARG A  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14087 (  151)
  hydrogen bonds       : angle       7.74475 (  405)
  covalent geometry    : bond        0.00560 ( 3954)
  covalent geometry    : angle       0.70884 ( 5378)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.596 
Fit side-chains
REVERT: A  107 MET cc_start: 0.6826 (tpp) cc_final: 0.6411 (mmp)
REVERT: A  110 LYS cc_start: 0.7698 (mmtm) cc_final: 0.7110 (mmtm)
REVERT: A  114 GLU cc_start: 0.7307 (pt0) cc_final: 0.6977 (pt0)
REVERT: B    3 HIS cc_start: 0.6424 (m90) cc_final: 0.5997 (t70)
REVERT: B  107 MET cc_start: 0.6838 (tpp) cc_final: 0.6422 (mmp)
REVERT: B  110 LYS cc_start: 0.7682 (mmtm) cc_final: 0.7137 (mmtm)
REVERT: B  114 GLU cc_start: 0.7293 (pt0) cc_final: 0.6973 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 63
  average time/residue: 2.3200
  time to fit residues: 151.5222
Evaluate side-chains
  52 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
B  34 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.178150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.165355 restraints weight = 8602.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3917 rms_B_bonded: 0.93
r_work: 0.3848 rms_B_bonded: 1.12 restraints_weight: 0.5000
r_work: 0.3762 rms_B_bonded: 1.99 restraints_weight: 0.2500
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.0743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3954  Z= 0.121
  Angle     :  0.501   3.784   5378  Z= 0.273
  Chirality :  0.044   0.158    614
  Planarity :  0.004   0.030    684
  Dihedral  :  7.111  86.299    522
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  8.88 %
    Favored  : 90.65 %
  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:  1.05 (0.38), residues: 482
  helix:  1.56 (0.50), residues: 110
  sheet:  0.46 (0.48), residues: 102
  loop :  0.57 (0.39), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  36 
 HIS   0.003   0.001   HIS A 173 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.011   0.002   TYR A  53 
 ARG   0.003   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04532 (  151)
  hydrogen bonds       : angle       6.28236 (  405)
  covalent geometry    : bond        0.00255 ( 3954)
  covalent geometry    : angle       0.50112 ( 5378)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.621 
Fit side-chains
REVERT: A  107 MET cc_start: 0.6811 (tpp) cc_final: 0.6404 (mmp)
REVERT: A  110 LYS cc_start: 0.7649 (mmtm) cc_final: 0.7073 (mmtm)
REVERT: B    3 HIS cc_start: 0.6395 (m90) cc_final: 0.5947 (t70)
REVERT: B  107 MET cc_start: 0.6807 (tpp) cc_final: 0.6393 (mmp)
REVERT: B  110 LYS cc_start: 0.7637 (mmtm) cc_final: 0.7091 (mmtm)
  outliers start: 2
  outliers final: 0
  residues processed: 59
  average time/residue: 2.2874
  time to fit residues: 140.1868
Evaluate side-chains
  50 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0870
   chunk 20 optimal weight:    0.9990
   chunk 35 optimal weight:    0.3980
   overall best weight:    0.6560

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
B  98 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.178709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.165882 restraints weight = 8681.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 0.94
r_work: 0.3852 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3767 rms_B_bonded: 2.01 restraints_weight: 0.2500
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.0858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3954  Z= 0.114
  Angle     :  0.479   3.764   5378  Z= 0.260
  Chirality :  0.043   0.160    614
  Planarity :  0.003   0.028    684
  Dihedral  :  7.174  87.929    522
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 1.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  9.11 %
    Favored  : 90.42 %
  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:  1.00 (0.37), residues: 482
  helix:  1.64 (0.50), residues: 110
  sheet:  0.36 (0.48), residues: 102
  loop :  0.51 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 237 
 HIS   0.002   0.001   HIS A 173 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.012   0.002   TYR A  53 
 ARG   0.002   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04325 (  151)
  hydrogen bonds       : angle       5.96154 (  405)
  covalent geometry    : bond        0.00245 ( 3954)
  covalent geometry    : angle       0.47944 ( 5378)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.589 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7510 (mtt-85)
REVERT: A  107 MET cc_start: 0.6821 (tpp) cc_final: 0.6401 (mmp)
REVERT: A  110 LYS cc_start: 0.7633 (mmtm) cc_final: 0.7037 (mmtm)
REVERT: B    3 HIS cc_start: 0.6385 (m90) cc_final: 0.5953 (t70)
REVERT: B  107 MET cc_start: 0.6812 (tpp) cc_final: 0.6397 (mmp)
REVERT: B  110 LYS cc_start: 0.7629 (mmtm) cc_final: 0.7053 (mmtm)
REVERT: B  114 GLU cc_start: 0.7247 (pt0) cc_final: 0.6956 (pt0)
  outliers start: 2
  outliers final: 0
  residues processed: 56
  average time/residue: 2.3095
  time to fit residues: 134.4610
Evaluate side-chains
  51 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    0.3980
   chunk 3 optimal weight:    3.9990
   chunk 39 optimal weight:    0.2980
   chunk 8 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B  98 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.177749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.164900 restraints weight = 8665.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3913 rms_B_bonded: 0.94
r_work: 0.3842 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3756 rms_B_bonded: 2.00 restraints_weight: 0.2500
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.0926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3954  Z= 0.130
  Angle     :  0.495   3.762   5378  Z= 0.268
  Chirality :  0.043   0.161    614
  Planarity :  0.004   0.029    684
  Dihedral  :  7.377  88.797    522
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 1.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  8.88 %
    Favored  : 90.89 %
  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:  0.86 (0.37), residues: 482
  helix:  1.49 (0.49), residues: 110
  sheet:  0.25 (0.47), residues: 102
  loop :  0.45 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 237 
 HIS   0.002   0.001   HIS A 173 
 PHE   0.008   0.002   PHE A  67 
 TYR   0.014   0.002   TYR A  53 
 ARG   0.002   0.000   ARG B 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04437 (  151)
  hydrogen bonds       : angle       5.98237 (  405)
  covalent geometry    : bond        0.00279 ( 3954)
  covalent geometry    : angle       0.49542 ( 5378)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.603 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7395 (mtt-85)
REVERT: A  107 MET cc_start: 0.6849 (tpp) cc_final: 0.6436 (mmp)
REVERT: A  110 LYS cc_start: 0.7656 (mmtm) cc_final: 0.7068 (mmtm)
REVERT: B    3 HIS cc_start: 0.6418 (m90) cc_final: 0.5984 (t70)
REVERT: B  107 MET cc_start: 0.6841 (tpp) cc_final: 0.6435 (mmp)
REVERT: B  110 LYS cc_start: 0.7633 (mmtm) cc_final: 0.7101 (mmtm)
  outliers start: 1
  outliers final: 0
  residues processed: 57
  average time/residue: 2.2746
  time to fit residues: 134.6559
Evaluate side-chains
  55 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 47 optimal weight:    0.4980
   chunk 16 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
B  98 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.175586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.162603 restraints weight = 8649.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3889 rms_B_bonded: 0.95
r_work: 0.3817 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3728 rms_B_bonded: 2.02 restraints_weight: 0.2500
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.0933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3954  Z= 0.184
  Angle     :  0.558   3.857   5378  Z= 0.304
  Chirality :  0.045   0.161    614
  Planarity :  0.004   0.031    684
  Dihedral  :  7.768  89.512    522
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  8.41 %
    Favored  : 90.89 %
  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:  0.61 (0.37), residues: 482
  helix:  1.11 (0.47), residues: 110
  sheet:  0.07 (0.47), residues: 102
  loop :  0.38 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 202 
 HIS   0.003   0.001   HIS A 173 
 PHE   0.010   0.002   PHE B   5 
 TYR   0.016   0.003   TYR A  53 
 ARG   0.003   0.001   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05171 (  151)
  hydrogen bonds       : angle       6.24903 (  405)
  covalent geometry    : bond        0.00404 ( 3954)
  covalent geometry    : angle       0.55774 ( 5378)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.606 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7455 (mtt-85)
REVERT: A  107 MET cc_start: 0.6892 (tpp) cc_final: 0.6461 (mmp)
REVERT: A  110 LYS cc_start: 0.7683 (mmtm) cc_final: 0.7113 (mmtm)
REVERT: B    3 HIS cc_start: 0.6459 (m90) cc_final: 0.6009 (t70)
REVERT: B  107 MET cc_start: 0.6895 (tpp) cc_final: 0.6469 (mmp)
REVERT: B  110 LYS cc_start: 0.7676 (mmtm) cc_final: 0.7159 (mmtm)
  outliers start: 3
  outliers final: 0
  residues processed: 58
  average time/residue: 2.2704
  time to fit residues: 136.8261
Evaluate side-chains
  48 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0770
   chunk 31 optimal weight:    0.0870
   chunk 9 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.7718

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

Flipped N/Q/H residues before XYZ refinement:
B  98 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.177555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.164745 restraints weight = 8655.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3911 rms_B_bonded: 0.94
r_work: 0.3839 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3753 rms_B_bonded: 2.01 restraints_weight: 0.2500
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.0997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3954  Z= 0.124
  Angle     :  0.493   3.753   5378  Z= 0.267
  Chirality :  0.043   0.159    614
  Planarity :  0.003   0.031    684
  Dihedral  :  7.510  89.350    522
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 1.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  9.58 %
    Favored  : 90.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.73 (0.37), residues: 482
  helix:  1.45 (0.49), residues: 110
  sheet:  0.04 (0.46), residues: 102
  loop :  0.39 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 237 
 HIS   0.002   0.001   HIS A 173 
 PHE   0.008   0.002   PHE A  67 
 TYR   0.013   0.002   TYR A  53 
 ARG   0.002   0.000   ARG B 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04361 (  151)
  hydrogen bonds       : angle       5.95993 (  405)
  covalent geometry    : bond        0.00267 ( 3954)
  covalent geometry    : angle       0.49320 ( 5378)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.641 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7440 (mtt-85)
REVERT: A  107 MET cc_start: 0.6853 (tpp) cc_final: 0.6431 (mmp)
REVERT: A  110 LYS cc_start: 0.7658 (mmtm) cc_final: 0.7083 (mmtm)
REVERT: B    3 HIS cc_start: 0.6430 (m90) cc_final: 0.5988 (t70)
REVERT: B  107 MET cc_start: 0.6835 (tpp) cc_final: 0.6412 (mmp)
REVERT: B  110 LYS cc_start: 0.7669 (mmtm) cc_final: 0.7131 (mmtm)
  outliers start: 1
  outliers final: 0
  residues processed: 52
  average time/residue: 2.2872
  time to fit residues: 123.7000
Evaluate side-chains
  50 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 21 optimal weight:    0.4980
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 14 optimal weight:    0.3980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
B  98 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.177834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.164902 restraints weight = 8689.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.3912 rms_B_bonded: 0.95
r_work: 0.3842 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3754 rms_B_bonded: 2.02 restraints_weight: 0.2500
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.1040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3954  Z= 0.123
  Angle     :  0.487   3.722   5378  Z= 0.263
  Chirality :  0.043   0.158    614
  Planarity :  0.003   0.031    684
  Dihedral  :  7.448  89.297    522
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 1.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  9.11 %
    Favored  : 90.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.73 (0.37), residues: 482
  helix:  1.46 (0.49), residues: 110
  sheet:  0.07 (0.46), residues: 102
  loop :  0.38 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 237 
 HIS   0.002   0.001   HIS A 173 
 PHE   0.008   0.002   PHE A  67 
 TYR   0.013   0.002   TYR A  53 
 ARG   0.002   0.000   ARG B  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04300 (  151)
  hydrogen bonds       : angle       5.91175 (  405)
  covalent geometry    : bond        0.00264 ( 3954)
  covalent geometry    : angle       0.48672 ( 5378)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.890 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7501 (mtt-85)
REVERT: A  107 MET cc_start: 0.6841 (tpp) cc_final: 0.6423 (mmp)
REVERT: A  110 LYS cc_start: 0.7644 (mmtm) cc_final: 0.7085 (mmtm)
REVERT: B    3 HIS cc_start: 0.6444 (m90) cc_final: 0.5989 (t70)
REVERT: B  107 MET cc_start: 0.6814 (tpp) cc_final: 0.6397 (mmp)
REVERT: B  110 LYS cc_start: 0.7663 (mmtm) cc_final: 0.7111 (mmtm)
  outliers start: 3
  outliers final: 0
  residues processed: 55
  average time/residue: 2.7265
  time to fit residues: 156.4673
Evaluate side-chains
  52 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 37 optimal weight:    0.4980
   chunk 28 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
B  98 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.175477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.162475 restraints weight = 8737.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3887 rms_B_bonded: 0.96
r_work: 0.3816 rms_B_bonded: 1.14 restraints_weight: 0.5000
r_work: 0.3729 rms_B_bonded: 2.01 restraints_weight: 0.2500
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.1039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3954  Z= 0.185
  Angle     :  0.559   3.832   5378  Z= 0.304
  Chirality :  0.045   0.159    614
  Planarity :  0.004   0.031    684
  Dihedral  :  7.781  89.541    522
  Min Nonbonded Distance : 1.836

Molprobity Statistics.
  All-atom Clashscore : 1.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  9.81 %
    Favored  : 89.72 %
  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:  0.56 (0.37), residues: 482
  helix:  1.08 (0.47), residues: 110
  sheet: -0.00 (0.46), residues: 102
  loop :  0.36 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  36 
 HIS   0.003   0.001   HIS A 173 
 PHE   0.010   0.002   PHE B   5 
 TYR   0.016   0.003   TYR B  53 
 ARG   0.003   0.001   ARG B 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05097 (  151)
  hydrogen bonds       : angle       6.20357 (  405)
  covalent geometry    : bond        0.00408 ( 3954)
  covalent geometry    : angle       0.55924 ( 5378)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.679 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7414 (mtt-85)
REVERT: A  107 MET cc_start: 0.6900 (tpp) cc_final: 0.6475 (mmp)
REVERT: A  110 LYS cc_start: 0.7706 (mmtm) cc_final: 0.7147 (mmtm)
REVERT: B    3 HIS cc_start: 0.6467 (m90) cc_final: 0.6025 (t70)
REVERT: B  107 MET cc_start: 0.6878 (tpp) cc_final: 0.6457 (mmp)
REVERT: B  110 LYS cc_start: 0.7699 (mmtm) cc_final: 0.7173 (mmtm)
  outliers start: 2
  outliers final: 0
  residues processed: 54
  average time/residue: 2.7760
  time to fit residues: 156.0655
Evaluate side-chains
  51 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 7 optimal weight:    0.2980
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0770
   chunk 41 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0770
   chunk 31 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
B  98 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.179863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.166977 restraints weight = 8756.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 0.95
r_work: 0.3863 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3778 rms_B_bonded: 2.02 restraints_weight: 0.2500
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.1142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3954  Z= 0.098
  Angle     :  0.461   3.703   5378  Z= 0.247
  Chirality :  0.043   0.157    614
  Planarity :  0.003   0.032    684
  Dihedral  :  7.279  89.610    522
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 1.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 10.05 %
    Favored  : 89.72 %
  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:  0.85 (0.37), residues: 482
  helix:  1.67 (0.50), residues: 110
  sheet:  0.11 (0.46), residues: 102
  loop :  0.40 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  36 
 HIS   0.002   0.000   HIS B 147 
 PHE   0.006   0.001   PHE B   5 
 TYR   0.010   0.001   TYR A  53 
 ARG   0.002   0.000   ARG B  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03840 (  151)
  hydrogen bonds       : angle       5.69963 (  405)
  covalent geometry    : bond        0.00211 ( 3954)
  covalent geometry    : angle       0.46135 ( 5378)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.644 
Fit side-chains
REVERT: A   61 GLU cc_start: 0.6828 (mp0) cc_final: 0.6597 (mm-30)
REVERT: A  107 MET cc_start: 0.6816 (tpp) cc_final: 0.6387 (mmp)
REVERT: A  110 LYS cc_start: 0.7642 (mmtm) cc_final: 0.7039 (mmtm)
REVERT: A  114 GLU cc_start: 0.7257 (pt0) cc_final: 0.6969 (pt0)
REVERT: B    3 HIS cc_start: 0.6401 (m90) cc_final: 0.5956 (t70)
REVERT: B  107 MET cc_start: 0.6772 (tpp) cc_final: 0.6352 (mmp)
REVERT: B  110 LYS cc_start: 0.7638 (mmtm) cc_final: 0.7032 (mmtm)
REVERT: B  114 GLU cc_start: 0.7233 (pt0) cc_final: 0.6908 (pt0)
  outliers start: 1
  outliers final: 0
  residues processed: 51
  average time/residue: 2.2997
  time to fit residues: 121.9261
Evaluate side-chains
  49 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.177169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.164261 restraints weight = 8721.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3906 rms_B_bonded: 0.95
r_work: 0.3833 rms_B_bonded: 1.14 restraints_weight: 0.5000
r_work: 0.3747 rms_B_bonded: 2.02 restraints_weight: 0.2500
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.1066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3954  Z= 0.145
  Angle     :  0.513   3.758   5378  Z= 0.277
  Chirality :  0.044   0.157    614
  Planarity :  0.004   0.031    684
  Dihedral  :  7.538  89.429    522
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 1.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.05 %
    Favored  : 89.95 %
  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:  0.72 (0.37), residues: 482
  helix:  1.41 (0.49), residues: 110
  sheet:  0.06 (0.46), residues: 102
  loop :  0.40 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 237 
 HIS   0.002   0.001   HIS A 173 
 PHE   0.009   0.002   PHE A  67 
 TYR   0.014   0.002   TYR A  53 
 ARG   0.002   0.000   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04546 (  151)
  hydrogen bonds       : angle       5.97123 (  405)
  covalent geometry    : bond        0.00316 ( 3954)
  covalent geometry    : angle       0.51293 ( 5378)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.670 
Fit side-chains
REVERT: A  107 MET cc_start: 0.6871 (tpp) cc_final: 0.6450 (mmp)
REVERT: A  110 LYS cc_start: 0.7687 (mmtm) cc_final: 0.7138 (mmtm)
REVERT: B    3 HIS cc_start: 0.6475 (m90) cc_final: 0.6012 (t70)
REVERT: B  107 MET cc_start: 0.6835 (tpp) cc_final: 0.6417 (mmp)
REVERT: B  110 LYS cc_start: 0.7677 (mmtm) cc_final: 0.7156 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 2.1087
  time to fit residues: 114.4030
Evaluate side-chains
  52 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 7 optimal weight:    0.4980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.178436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.165492 restraints weight = 8683.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3918 rms_B_bonded: 0.95
r_work: 0.3846 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3761 rms_B_bonded: 2.02 restraints_weight: 0.2500
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3954  Z= 0.116
  Angle     :  0.478   3.716   5378  Z= 0.257
  Chirality :  0.043   0.157    614
  Planarity :  0.003   0.031    684
  Dihedral  :  7.390  89.263    522
  Min Nonbonded Distance : 1.851

Molprobity Statistics.
  All-atom Clashscore : 1.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 10.05 %
    Favored  : 89.72 %
  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:  0.78 (0.37), residues: 482
  helix:  1.56 (0.49), residues: 110
  sheet:  0.06 (0.46), residues: 102
  loop :  0.39 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 237 
 HIS   0.002   0.001   HIS A 173 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.013   0.002   TYR A  53 
 ARG   0.001   0.000   ARG B  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04156 (  151)
  hydrogen bonds       : angle       5.83142 (  405)
  covalent geometry    : bond        0.00249 ( 3954)
  covalent geometry    : angle       0.47842 ( 5378)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7161.76 seconds
wall clock time: 123 minutes 16.53 seconds (7396.53 seconds total)