Starting phenix.real_space_refine
on Sun May 11 06:28:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hjc_52212/05_2025/9hjc_52212_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hjc_52212/05_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_52212/05_2025/9hjc_52212.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hjc_52212/05_2025/9hjc_52212.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hjc_52212/05_2025/9hjc_52212_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hjc_52212/05_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-5687/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: 5.21, per 1000 atoms: 0.68
  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: 2.08
  Conformation dependent library (CDL) restraints added in 754.1 milliseconds
  

  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: 0.63
  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: 2.78

  Time building geometry restraints manager: 2.39 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:             2.930
  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:             0.130
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.840
  Find NCS groups from input model:        0.180
  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:14.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.690
-------------------------------------------------------------------------------
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  : 0.625 
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: 2.3245
  time to fit residues: 151.8707
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  : 0.666 
-------------------------------------------------------------------------------
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 = 0.178149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.165345 restraints weight = 8602.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3917 rms_B_bonded: 0.93
r_work: 0.3847 rms_B_bonded: 1.12 restraints_weight: 0.5000
r_work: 0.3762 rms_B_bonded: 2.00 restraints_weight: 0.2500
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
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       6.28245 (  405)
  covalent geometry    : bond        0.00255 ( 3954)
  covalent geometry    : angle       0.50111 ( 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  : 0.661 
Fit side-chains
REVERT: A  107 MET cc_start: 0.6808 (tpp) cc_final: 0.6401 (mmp)
REVERT: A  110 LYS cc_start: 0.7647 (mmtm) cc_final: 0.7070 (mmtm)
REVERT: B    3 HIS cc_start: 0.6394 (m90) cc_final: 0.5941 (t70)
REVERT: B  107 MET cc_start: 0.6803 (tpp) cc_final: 0.6388 (mmp)
REVERT: B  110 LYS cc_start: 0.7635 (mmtm) cc_final: 0.7087 (mmtm)
  outliers start: 2
  outliers final: 0
  residues processed: 59
  average time/residue: 2.3122
  time to fit residues: 141.6729
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  : 0.680 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0170
   chunk 20 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.7018

-------------------------------------------------------------------------------
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 = 0.4059 r_free = 0.4059 target = 0.178383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.165542 restraints weight = 8687.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 0.94
r_work: 0.3849 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3763 rms_B_bonded: 2.01 restraints_weight: 0.2500
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.0836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3954  Z= 0.119
  Angle     :  0.485   3.769   5378  Z= 0.263
  Chirality :  0.043   0.160    614
  Planarity :  0.003   0.029    684
  Dihedral  :  7.207  87.859    522
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 1.56
  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:  0.98 (0.37), residues: 482
  helix:  1.61 (0.50), residues: 110
  sheet:  0.35 (0.48), residues: 102
  loop :  0.50 (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   0.001   PHE A  67 
 TYR   0.013   0.002   TYR A  53 
 ARG   0.002   0.000   ARG A  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04404 (  151)
  hydrogen bonds       : angle       6.00505 (  405)
  covalent geometry    : bond        0.00253 ( 3954)
  covalent geometry    : angle       0.48466 ( 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  : 0.587 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7386 (mtt-85)
REVERT: A  107 MET cc_start: 0.6831 (tpp) cc_final: 0.6418 (mmp)
REVERT: A  110 LYS cc_start: 0.7642 (mmtm) cc_final: 0.7050 (mmtm)
REVERT: B    3 HIS cc_start: 0.6391 (m90) cc_final: 0.5960 (t70)
REVERT: B  107 MET cc_start: 0.6822 (tpp) cc_final: 0.6406 (mmp)
REVERT: B  110 LYS cc_start: 0.7638 (mmtm) cc_final: 0.7094 (mmtm)
  outliers start: 2
  outliers final: 0
  residues processed: 56
  average time/residue: 2.2938
  time to fit residues: 133.3177
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  : 0.645 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0870
   chunk 8 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    1.1562

-------------------------------------------------------------------------------
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 = 0.4041 r_free = 0.4041 target = 0.176371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.163466 restraints weight = 8675.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3899 rms_B_bonded: 0.95
r_work: 0.3826 rms_B_bonded: 1.14 restraints_weight: 0.5000
r_work: 0.3739 rms_B_bonded: 2.03 restraints_weight: 0.2500
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.0894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3954  Z= 0.156
  Angle     :  0.527   3.799   5378  Z= 0.287
  Chirality :  0.044   0.162    614
  Planarity :  0.004   0.030    684
  Dihedral  :  7.568  89.138    522
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 1.43
  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:  0.75 (0.37), residues: 482
  helix:  1.28 (0.48), residues: 110
  sheet:  0.20 (0.47), residues: 102
  loop :  0.43 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 202 
 HIS   0.002   0.001   HIS A 173 
 PHE   0.009   0.002   PHE A  67 
 TYR   0.015   0.002   TYR A  53 
 ARG   0.002   0.000   ARG B 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04839 (  151)
  hydrogen bonds       : angle       6.14407 (  405)
  covalent geometry    : bond        0.00339 ( 3954)
  covalent geometry    : angle       0.52687 ( 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
  57 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.663 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7433 (mtt-85)
REVERT: A  107 MET cc_start: 0.6864 (tpp) cc_final: 0.6439 (mmp)
REVERT: A  110 LYS cc_start: 0.7660 (mmtm) cc_final: 0.7068 (mmtm)
REVERT: B    3 HIS cc_start: 0.6427 (m90) cc_final: 0.5978 (t70)
REVERT: B  107 MET cc_start: 0.6862 (tpp) cc_final: 0.6441 (mmp)
REVERT: B  110 LYS cc_start: 0.7655 (mmtm) cc_final: 0.7130 (mmtm)
  outliers start: 2
  outliers final: 0
  residues processed: 57
  average time/residue: 2.3688
  time to fit residues: 140.4507
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  : 0.766 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.4037 r_free = 0.4037 target = 0.176043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.163162 restraints weight = 8649.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3894 rms_B_bonded: 0.95
r_work: 0.3821 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3734 rms_B_bonded: 2.02 restraints_weight: 0.2500
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.0943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3954  Z= 0.162
  Angle     :  0.535   3.819   5378  Z= 0.291
  Chirality :  0.044   0.160    614
  Planarity :  0.004   0.031    684
  Dihedral  :  7.679  89.448    522
  Min Nonbonded Distance : 1.856

Molprobity Statistics.
  All-atom Clashscore : 1.43
  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:  0.66 (0.37), residues: 482
  helix:  1.21 (0.48), residues: 110
  sheet:  0.11 (0.47), residues: 102
  loop :  0.38 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  36 
 HIS   0.002   0.001   HIS A 173 
 PHE   0.009   0.002   PHE B   5 
 TYR   0.015   0.002   TYR A  53 
 ARG   0.002   0.001   ARG B 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04882 (  151)
  hydrogen bonds       : angle       6.15555 (  405)
  covalent geometry    : bond        0.00354 ( 3954)
  covalent geometry    : angle       0.53469 ( 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
  57 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.596 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7443 (mtt-85)
REVERT: A  107 MET cc_start: 0.6868 (tpp) cc_final: 0.6439 (mmp)
REVERT: A  110 LYS cc_start: 0.7676 (mmtm) cc_final: 0.7106 (mmtm)
REVERT: B    3 HIS cc_start: 0.6440 (m90) cc_final: 0.5993 (t70)
REVERT: B  107 MET cc_start: 0.6852 (tpp) cc_final: 0.6433 (mmp)
REVERT: B  110 LYS cc_start: 0.7668 (mmtm) cc_final: 0.7140 (mmtm)
  outliers start: 2
  outliers final: 0
  residues processed: 56
  average time/residue: 2.2090
  time to fit residues: 128.6863
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  : 0.591 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0980
   chunk 9 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.4040 r_free = 0.4040 target = 0.176378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.163455 restraints weight = 8644.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3897 rms_B_bonded: 0.95
r_work: 0.3825 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3738 rms_B_bonded: 2.01 restraints_weight: 0.2500
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.0998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3954  Z= 0.153
  Angle     :  0.524   3.793   5378  Z= 0.285
  Chirality :  0.044   0.159    614
  Planarity :  0.004   0.032    684
  Dihedral  :  7.673  89.484    522
  Min Nonbonded Distance : 1.851

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:  0.63 (0.37), residues: 482
  helix:  1.25 (0.48), residues: 110
  sheet:  0.04 (0.47), residues: 102
  loop :  0.35 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 202 
 HIS   0.002   0.001   HIS A 173 
 PHE   0.009   0.002   PHE B   5 
 TYR   0.015   0.002   TYR A  53 
 ARG   0.002   0.000   ARG B 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04759 (  151)
  hydrogen bonds       : angle       6.10832 (  405)
  covalent geometry    : bond        0.00333 ( 3954)
  covalent geometry    : angle       0.52353 ( 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
  56 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.600 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7457 (mtt-85)
REVERT: A   61 GLU cc_start: 0.6836 (mp0) cc_final: 0.6627 (mm-30)
REVERT: A  107 MET cc_start: 0.6864 (tpp) cc_final: 0.6437 (mmp)
REVERT: A  110 LYS cc_start: 0.7672 (mmtm) cc_final: 0.7102 (mmtm)
REVERT: B    3 HIS cc_start: 0.6445 (m90) cc_final: 0.6005 (t70)
REVERT: B  107 MET cc_start: 0.6850 (tpp) cc_final: 0.6433 (mmp)
REVERT: B  110 LYS cc_start: 0.7665 (mmtm) cc_final: 0.7140 (mmtm)
  outliers start: 3
  outliers final: 0
  residues processed: 56
  average time/residue: 2.1542
  time to fit residues: 125.4598
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  : 0.589 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.4051 r_free = 0.4051 target = 0.177489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.164620 restraints weight = 8690.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3911 rms_B_bonded: 0.95
r_work: 0.3839 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3752 rms_B_bonded: 2.02 restraints_weight: 0.2500
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1042

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= 0.125
  Angle     :  0.493   3.714   5378  Z= 0.267
  Chirality :  0.043   0.158    614
  Planarity :  0.003   0.032    684
  Dihedral  :  7.509  89.360    522
  Min Nonbonded Distance : 1.856

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  9.58 %
    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:  0.73 (0.37), residues: 482
  helix:  1.48 (0.49), residues: 110
  sheet:  0.07 (0.47), residues: 102
  loop :  0.36 (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 B  53 
 ARG   0.002   0.000   ARG B 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04345 (  151)
  hydrogen bonds       : angle       5.95389 (  405)
  covalent geometry    : bond        0.00270 ( 3954)
  covalent geometry    : angle       0.49297 ( 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
  56 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.598 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7432 (mtt-85)
REVERT: A  107 MET cc_start: 0.6856 (tpp) cc_final: 0.6433 (mmp)
REVERT: A  110 LYS cc_start: 0.7664 (mmtm) cc_final: 0.7071 (mmtm)
REVERT: A  114 GLU cc_start: 0.7277 (pt0) cc_final: 0.6936 (pt0)
REVERT: B    3 HIS cc_start: 0.6440 (m90) cc_final: 0.5990 (t70)
REVERT: B  107 MET cc_start: 0.6824 (tpp) cc_final: 0.6401 (mmp)
REVERT: B  110 LYS cc_start: 0.7662 (mmtm) cc_final: 0.7122 (mmtm)
  outliers start: 2
  outliers final: 0
  residues processed: 56
  average time/residue: 2.1711
  time to fit residues: 126.6471
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 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.4036 r_free = 0.4036 target = 0.175997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.163019 restraints weight = 8740.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 0.95
r_work: 0.3821 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3735 rms_B_bonded: 2.02 restraints_weight: 0.2500
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.1034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3954  Z= 0.169
  Angle     :  0.540   3.811   5378  Z= 0.293
  Chirality :  0.044   0.158    614
  Planarity :  0.004   0.031    684
  Dihedral  :  7.721  89.535    522
  Min Nonbonded Distance : 1.841

Molprobity Statistics.
  All-atom Clashscore : 1.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  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:  0.59 (0.37), residues: 482
  helix:  1.19 (0.48), residues: 110
  sheet:  0.03 (0.47), residues: 102
  loop :  0.34 (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   0.002   TYR A  53 
 ARG   0.002   0.001   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04894 (  151)
  hydrogen bonds       : angle       6.14493 (  405)
  covalent geometry    : bond        0.00369 ( 3954)
  covalent geometry    : angle       0.54001 ( 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
  53 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 52
  time to evaluate  : 0.665 
Fit side-chains
REVERT: A   33 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7473 (mtt-85)
REVERT: A  107 MET cc_start: 0.6874 (tpp) cc_final: 0.6445 (mmp)
REVERT: A  110 LYS cc_start: 0.7686 (mmtm) cc_final: 0.7103 (mmtm)
REVERT: A  114 GLU cc_start: 0.7306 (pt0) cc_final: 0.6975 (pt0)
REVERT: B    3 HIS cc_start: 0.6456 (m90) cc_final: 0.6015 (t70)
REVERT: B  107 MET cc_start: 0.6859 (tpp) cc_final: 0.6438 (mmp)
REVERT: B  110 LYS cc_start: 0.7694 (mmtm) cc_final: 0.7151 (mmtm)
  outliers start: 1
  outliers final: 0
  residues processed: 53
  average time/residue: 2.2729
  time to fit residues: 125.1521
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  : 0.618 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 39 optimal weight:    0.3980
   chunk 31 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4056 r_free = 0.4056 target = 0.178079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.165140 restraints weight = 8743.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3914 rms_B_bonded: 0.95
r_work: 0.3844 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3757 rms_B_bonded: 2.02 restraints_weight: 0.2500
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1074

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= 0.119
  Angle     :  0.486   3.746   5378  Z= 0.262
  Chirality :  0.043   0.157    614
  Planarity :  0.003   0.032    684
  Dihedral  :  7.466  89.341    522
  Min Nonbonded Distance : 1.856

Molprobity Statistics.
  All-atom Clashscore : 1.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  9.81 %
    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:  0.77 (0.37), residues: 482
  helix:  1.55 (0.50), residues: 110
  sheet:  0.10 (0.47), residues: 102
  loop :  0.37 (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 B 147 
 PHE   0.007   0.001   PHE B   5 
 TYR   0.013   0.002   TYR A  53 
 ARG   0.001   0.000   ARG B  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04227 (  151)
  hydrogen bonds       : angle       5.90132 (  405)
  covalent geometry    : bond        0.00258 ( 3954)
  covalent geometry    : angle       0.48645 ( 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  : 0.501 
Fit side-chains
REVERT: A  107 MET cc_start: 0.6838 (tpp) cc_final: 0.6410 (mmp)
REVERT: A  110 LYS cc_start: 0.7671 (mmtm) cc_final: 0.7119 (mmtm)
REVERT: B    3 HIS cc_start: 0.6440 (m90) cc_final: 0.5992 (t70)
REVERT: B  107 MET cc_start: 0.6801 (tpp) cc_final: 0.6382 (mmp)
REVERT: B  110 LYS cc_start: 0.7664 (mmtm) cc_final: 0.7108 (mmtm)
  outliers start: 1
  outliers final: 0
  residues processed: 51
  average time/residue: 2.3297
  time to fit residues: 123.2826
Evaluate side-chains
  48 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.2386

-------------------------------------------------------------------------------
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 = 0.4039 r_free = 0.4039 target = 0.176279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.163342 restraints weight = 8715.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 0.95
r_work: 0.3824 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.3737 rms_B_bonded: 2.02 restraints_weight: 0.2500
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.1036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3954  Z= 0.162
  Angle     :  0.535   3.784   5378  Z= 0.290
  Chirality :  0.044   0.158    614
  Planarity :  0.004   0.031    684
  Dihedral  :  7.676  89.476    522
  Min Nonbonded Distance : 1.835

Molprobity Statistics.
  All-atom Clashscore : 1.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  9.81 %
    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:  0.61 (0.37), residues: 482
  helix:  1.23 (0.48), residues: 110
  sheet:  0.04 (0.47), residues: 102
  loop :  0.34 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  36 
 HIS   0.003   0.001   HIS A 173 
 PHE   0.009   0.002   PHE B   5 
 TYR   0.015   0.002   TYR A  53 
 ARG   0.003   0.001   ARG B  60 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04796 (  151)
  hydrogen bonds       : angle       6.09585 (  405)
  covalent geometry    : bond        0.00357 ( 3954)
  covalent geometry    : angle       0.53465 ( 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: 1
    poor density    : 51
  time to evaluate  : 0.514 
Fit side-chains
REVERT: A  107 MET cc_start: 0.6876 (tpp) cc_final: 0.6446 (mmp)
REVERT: A  110 LYS cc_start: 0.7683 (mmtm) cc_final: 0.7126 (mmtm)
REVERT: A  114 GLU cc_start: 0.7320 (pt0) cc_final: 0.6977 (pt0)
REVERT: B    3 HIS cc_start: 0.6449 (m90) cc_final: 0.6008 (t70)
REVERT: B  107 MET cc_start: 0.6857 (tpp) cc_final: 0.6438 (mmp)
REVERT: B  110 LYS cc_start: 0.7685 (mmtm) cc_final: 0.7139 (mmtm)
  outliers start: 1
  outliers final: 0
  residues processed: 52
  average time/residue: 2.1676
  time to fit residues: 117.2463
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  : 0.640 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 2 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4056 r_free = 0.4056 target = 0.178076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.165229 restraints weight = 8688.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3913 rms_B_bonded: 0.94
r_work: 0.3843 rms_B_bonded: 1.12 restraints_weight: 0.5000
r_work: 0.3758 rms_B_bonded: 2.00 restraints_weight: 0.2500
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1093

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= 0.118
  Angle     :  0.487   3.700   5378  Z= 0.263
  Chirality :  0.043   0.157    614
  Planarity :  0.003   0.032    684
  Dihedral  :  7.447  89.372    522
  Min Nonbonded Distance : 1.852

Molprobity Statistics.
  All-atom Clashscore : 1.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.51 %
    Favored  : 89.49 %
  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:  0.77 (0.37), residues: 482
  helix:  1.53 (0.50), residues: 110
  sheet:  0.11 (0.47), residues: 102
  loop :  0.37 (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 B 147 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.013   0.002   TYR A  53 
 ARG   0.002   0.000   ARG A  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04201 (  151)
  hydrogen bonds       : angle       5.88148 (  405)
  covalent geometry    : bond        0.00255 ( 3954)
  covalent geometry    : angle       0.48724 ( 5378)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6537.25 seconds
wall clock time: 112 minutes 36.35 seconds (6756.35 seconds total)