Starting phenix.real_space_refine
on Wed Jul 23 09:41:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6y1a_10669/07_2025/6y1a_10669.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6y1a_10669/07_2025/6y1a_10669.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6y1a_10669/07_2025/6y1a_10669.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6y1a_10669/07_2025/6y1a_10669.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6y1a_10669/07_2025/6y1a_10669.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6y1a_10669/07_2025/6y1a_10669.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
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: 3
    Type Number    sf(0)   Gaussians
     C    1824      2.51       5
     N     528      2.21       5
     O     608      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 2960
  Number of models: 1
  Model: ""
    Number of chains: 32
    Chain: "A"
      Number of atoms: 184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 184
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "B"
      Number of atoms: 184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 184
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "C"
      Number of atoms: 184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 184
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "D"
      Number of atoms: 184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 184
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "E"
      Number of atoms: 184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 184
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "F"
      Number of atoms: 184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 184
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "G"
      Number of atoms: 184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 184
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "H"
      Number of atoms: 184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 184
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "I"
      Number of atoms: 184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 184
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "J"
      Number of atoms: 184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 184
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "K"
      Number of atoms: 184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 184
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "L"
      Number of atoms: 184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 184
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "M"
      Number of atoms: 184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 184
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "N"
      Number of atoms: 184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 184
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "O"
      Number of atoms: 184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 184
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "P"
      Number of atoms: 184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 184
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "G"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "H"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "I"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "J"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "K"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "L"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "M"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "N"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "O"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "P"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.40, per 1000 atoms: 0.81
  Number of scatterers: 2960
  At special positions: 0
  Unit cell: (61.71, 66.385, 55.165, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     608      8.00
     N     528      7.00
     C    1824      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=16, symmetry=0
  Number of additional bonds: simple=16, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 366.6 milliseconds
  

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  736

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 7 sheets defined
      0.0% alpha, 40.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 18
      removed outlier: 5.958A  pdb=" N   PHE A  15 " --> pdb=" O   LEU C  16 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   HIS C  18 " --> pdb=" O   PHE A  15 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   VAL A  17 " --> pdb=" O   HIS C  18 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   PHE C  15 " --> pdb=" O   LEU E  16 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   HIS E  18 " --> pdb=" O   PHE C  15 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   VAL C  17 " --> pdb=" O   HIS E  18 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   PHE E  15 " --> pdb=" O   LEU G  16 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   HIS G  18 " --> pdb=" O   PHE E  15 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL E  17 " --> pdb=" O   HIS G  18 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   PHE G  15 " --> pdb=" O   LEU I  16 " (cutoff:3.500A)
      removed outlier: 7.732A  pdb=" N   HIS I  18 " --> pdb=" O   PHE G  15 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   VAL G  17 " --> pdb=" O   HIS I  18 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   PHE I  15 " --> pdb=" O   LEU K  16 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   HIS K  18 " --> pdb=" O   PHE I  15 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   VAL I  17 " --> pdb=" O   HIS K  18 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   PHE K  15 " --> pdb=" O   LEU M  16 " (cutoff:3.500A)
      removed outlier: 7.682A  pdb=" N   HIS M  18 " --> pdb=" O   PHE K  15 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   VAL K  17 " --> pdb=" O   HIS M  18 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   PHE M  15 " --> pdb=" O   LEU O  16 " (cutoff:3.500A)
      removed outlier: 7.508A  pdb=" N   HIS O  18 " --> pdb=" O   PHE M  15 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   VAL M  17 " --> pdb=" O   HIS O  18 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 31
      removed outlier: 6.542A  pdb=" N   ILE A  26 " --> pdb=" O   LEU C  27 " (cutoff:3.500A)
      removed outlier: 8.171A  pdb=" N   SER C  29 " --> pdb=" O   ILE A  26 " (cutoff:3.500A)
      removed outlier: 6.935A  pdb=" N   SER A  28 " --> pdb=" O   SER C  29 " (cutoff:3.500A)
      removed outlier: 8.432A  pdb=" N   ASN C  31 " --> pdb=" O   SER A  28 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   THR A  30 " --> pdb=" O   ASN C  31 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ILE C  26 " --> pdb=" O   LEU E  27 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   SER E  29 " --> pdb=" O   ILE C  26 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   SER C  28 " --> pdb=" O   SER E  29 " (cutoff:3.500A)
      removed outlier: 8.320A  pdb=" N   ASN E  31 " --> pdb=" O   SER C  28 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   THR C  30 " --> pdb=" O   ASN E  31 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ILE E  26 " --> pdb=" O   LEU G  27 " (cutoff:3.500A)
      removed outlier: 8.016A  pdb=" N   SER G  29 " --> pdb=" O   ILE E  26 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   SER E  28 " --> pdb=" O   SER G  29 " (cutoff:3.500A)
      removed outlier: 8.329A  pdb=" N   ASN G  31 " --> pdb=" O   SER E  28 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   THR E  30 " --> pdb=" O   ASN G  31 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   ILE G  26 " --> pdb=" O   LEU I  27 " (cutoff:3.500A)
      removed outlier: 8.002A  pdb=" N   SER I  29 " --> pdb=" O   ILE G  26 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   SER G  28 " --> pdb=" O   SER I  29 " (cutoff:3.500A)
      removed outlier: 8.244A  pdb=" N   ASN I  31 " --> pdb=" O   SER G  28 " (cutoff:3.500A)
      removed outlier: 5.936A  pdb=" N   THR G  30 " --> pdb=" O   ASN I  31 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   ILE I  26 " --> pdb=" O   LEU K  27 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   SER K  29 " --> pdb=" O   ILE I  26 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   SER I  28 " --> pdb=" O   SER K  29 " (cutoff:3.500A)
      removed outlier: 8.293A  pdb=" N   ASN K  31 " --> pdb=" O   SER I  28 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   THR I  30 " --> pdb=" O   ASN K  31 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   ILE K  26 " --> pdb=" O   LEU M  27 " (cutoff:3.500A)
      removed outlier: 7.952A  pdb=" N   SER M  29 " --> pdb=" O   ILE K  26 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   SER K  28 " --> pdb=" O   SER M  29 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   ASN M  31 " --> pdb=" O   SER K  28 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   THR K  30 " --> pdb=" O   ASN M  31 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   ILE M  26 " --> pdb=" O   LEU O  27 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   SER O  29 " --> pdb=" O   ILE M  26 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   SER M  28 " --> pdb=" O   SER O  29 " (cutoff:3.500A)
      removed outlier: 8.412A  pdb=" N   ASN O  31 " --> pdb=" O   SER M  28 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   THR M  30 " --> pdb=" O   ASN O  31 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36
    Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 18
      removed outlier: 5.970A  pdb=" N   PHE B  15 " --> pdb=" O   LEU D  16 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   HIS D  18 " --> pdb=" O   PHE B  15 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   VAL B  17 " --> pdb=" O   HIS D  18 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   PHE D  15 " --> pdb=" O   LEU F  16 " (cutoff:3.500A)
      removed outlier: 7.611A  pdb=" N   HIS F  18 " --> pdb=" O   PHE D  15 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   VAL D  17 " --> pdb=" O   HIS F  18 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   PHE F  15 " --> pdb=" O   LEU H  16 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   HIS H  18 " --> pdb=" O   PHE F  15 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   VAL F  17 " --> pdb=" O   HIS H  18 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   PHE H  15 " --> pdb=" O   LEU J  16 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   HIS J  18 " --> pdb=" O   PHE H  15 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   VAL H  17 " --> pdb=" O   HIS J  18 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   PHE J  15 " --> pdb=" O   LEU L  16 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   HIS L  18 " --> pdb=" O   PHE J  15 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   VAL J  17 " --> pdb=" O   HIS L  18 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   PHE L  15 " --> pdb=" O   LEU N  16 " (cutoff:3.500A)
      removed outlier: 7.561A  pdb=" N   HIS N  18 " --> pdb=" O   PHE L  15 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   VAL L  17 " --> pdb=" O   HIS N  18 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   PHE N  15 " --> pdb=" O   LEU P  16 " (cutoff:3.500A)
      removed outlier: 7.559A  pdb=" N   HIS P  18 " --> pdb=" O   PHE N  15 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   VAL N  17 " --> pdb=" O   HIS P  18 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 27
      removed outlier: 6.376A  pdb=" N   ILE B  26 " --> pdb=" O   LEU D  27 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   SER D  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 26 through 27
      removed outlier: 6.376A  pdb=" N   ILE B  26 " --> pdb=" O   LEU D  27 " (cutoff:3.500A)
      removed outlier: 8.036A  pdb=" N   SER D  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   ILE D  26 " --> pdb=" O   LEU F  27 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   SER F  29 " --> pdb=" O   ILE D  26 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   SER D  28 " --> pdb=" O   SER F  29 " (cutoff:3.500A)
      removed outlier: 8.351A  pdb=" N   ASN F  31 " --> pdb=" O   SER D  28 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   THR D  30 " --> pdb=" O   ASN F  31 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   ILE F  26 " --> pdb=" O   LEU H  27 " (cutoff:3.500A)
      removed outlier: 8.013A  pdb=" N   SER H  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   SER F  28 " --> pdb=" O   SER H  29 " (cutoff:3.500A)
      removed outlier: 8.313A  pdb=" N   ASN H  31 " --> pdb=" O   SER F  28 " (cutoff:3.500A)
      removed outlier: 6.011A  pdb=" N   THR F  30 " --> pdb=" O   ASN H  31 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   ILE H  26 " --> pdb=" O   LEU J  27 " (cutoff:3.500A)
      removed outlier: 7.971A  pdb=" N   SER J  29 " --> pdb=" O   ILE H  26 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   SER H  28 " --> pdb=" O   SER J  29 " (cutoff:3.500A)
      removed outlier: 8.297A  pdb=" N   ASN J  31 " --> pdb=" O   SER H  28 " (cutoff:3.500A)
      removed outlier: 5.999A  pdb=" N   THR H  30 " --> pdb=" O   ASN J  31 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ILE J  26 " --> pdb=" O   LEU L  27 " (cutoff:3.500A)
      removed outlier: 8.003A  pdb=" N   SER L  29 " --> pdb=" O   ILE J  26 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   SER J  28 " --> pdb=" O   SER L  29 " (cutoff:3.500A)
      removed outlier: 8.256A  pdb=" N   ASN L  31 " --> pdb=" O   SER J  28 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   THR J  30 " --> pdb=" O   ASN L  31 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   ILE L  26 " --> pdb=" O   LEU N  27 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   SER N  29 " --> pdb=" O   ILE L  26 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   SER L  28 " --> pdb=" O   SER N  29 " (cutoff:3.500A)
      removed outlier: 8.337A  pdb=" N   ASN N  31 " --> pdb=" O   SER L  28 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   THR L  30 " --> pdb=" O   ASN N  31 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ILE N  26 " --> pdb=" O   LEU P  27 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   SER P  29 " --> pdb=" O   ILE N  26 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   SER N  28 " --> pdb=" O   SER P  29 " (cutoff:3.500A)
      removed outlier: 8.383A  pdb=" N   ASN P  31 " --> pdb=" O   SER N  28 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   THR N  30 " --> pdb=" O   ASN P  31 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 36

    16 hydrogen bonds defined for protein.
    45 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.69

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 480
        1.29 -     1.36: 512
        1.36 -     1.42: 416
        1.42 -     1.48: 416
        1.48 -     1.55: 1168
  Bond restraints: 2992
  Sorted by residual:
  bond pdb=" N   ALA M  13 "
       pdb=" CA  ALA M  13 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.02e+00
  bond pdb=" N   ALA B  13 "
       pdb=" CA  ALA B  13 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.01e+00
  bond pdb=" N   ALA E  13 "
       pdb=" CA  ALA E  13 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.00e+00
  bond pdb=" N   ALA N  13 "
       pdb=" CA  ALA N  13 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.94e+00
  bond pdb=" N   ALA J  13 "
       pdb=" CA  ALA J  13 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.94e+00
  ... (remaining 2987 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.95: 3093
        0.95 -     1.90: 622
        1.90 -     2.85: 168
        2.85 -     3.80: 116
        3.80 -     4.75: 65
  Bond angle restraints: 4064
  Sorted by residual:
  angle pdb=" N   THR D  36 "
        pdb=" CA  THR D  36 "
        pdb=" C   THR D  36 "
      ideal   model   delta    sigma   weight residual
     109.24  113.99   -4.75 1.67e+00 3.59e-01 8.10e+00
  angle pdb=" N   THR C  36 "
        pdb=" CA  THR C  36 "
        pdb=" C   THR C  36 "
      ideal   model   delta    sigma   weight residual
     109.24  113.97   -4.73 1.67e+00 3.59e-01 8.02e+00
  angle pdb=" N   THR E  36 "
        pdb=" CA  THR E  36 "
        pdb=" C   THR E  36 "
      ideal   model   delta    sigma   weight residual
     109.24  113.96   -4.72 1.67e+00 3.59e-01 8.00e+00
  angle pdb=" N   THR L  36 "
        pdb=" CA  THR L  36 "
        pdb=" C   THR L  36 "
      ideal   model   delta    sigma   weight residual
     109.24  113.95   -4.71 1.67e+00 3.59e-01 7.95e+00
  angle pdb=" N   THR I  36 "
        pdb=" CA  THR I  36 "
        pdb=" C   THR I  36 "
      ideal   model   delta    sigma   weight residual
     109.24  113.92   -4.68 1.67e+00 3.59e-01 7.87e+00
  ... (remaining 4059 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     6.00: 1472
        6.00 -    12.00: 50
       12.00 -    18.00: 46
       18.00 -    23.99: 26
       23.99 -    29.99: 70
  Dihedral angle restraints: 1664
    sinusoidal: 528
      harmonic: 1136
  Sorted by residual:
  dihedral pdb=" CA  ASN L  31 "
           pdb=" CB  ASN L  31 "
           pdb=" CG  ASN L  31 "
           pdb=" OD1 ASN L  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -59.99   29.99     2      2.00e+01 2.50e-03 3.00e+00
  dihedral pdb=" CA  ASN O  31 "
           pdb=" CB  ASN O  31 "
           pdb=" CG  ASN O  31 "
           pdb=" OD1 ASN O  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -60.02  -29.98     2      2.00e+01 2.50e-03 3.00e+00
  dihedral pdb=" CA  ASN I  31 "
           pdb=" CB  ASN I  31 "
           pdb=" CG  ASN I  31 "
           pdb=" OD1 ASN I  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -59.98   29.98     2      2.00e+01 2.50e-03 3.00e+00
  ... (remaining 1661 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 171
       0.035 -    0.069: 167
       0.069 -    0.103: 87
       0.103 -    0.138: 39
       0.138 -    0.172: 16
  Chirality restraints: 480
  Sorted by residual:
  chirality pdb=" CA  VAL G  32 "
            pdb=" N   VAL G  32 "
            pdb=" C   VAL G  32 "
            pdb=" CB  VAL G  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.43e-01
  chirality pdb=" CA  VAL A  32 "
            pdb=" N   VAL A  32 "
            pdb=" C   VAL A  32 "
            pdb=" CB  VAL A  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.36e-01
  chirality pdb=" CA  VAL E  32 "
            pdb=" N   VAL E  32 "
            pdb=" C   VAL E  32 "
            pdb=" CB  VAL E  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.31e-01
  ... (remaining 477 not shown)

  Planarity restraints: 528
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR K  36 "    0.002 2.00e-02 2.50e+03   4.08e-03 1.67e-01
        pdb=" C   THR K  36 "   -0.007 2.00e-02 2.50e+03
        pdb=" O   THR K  36 "    0.003 2.00e-02 2.50e+03
        pdb=" N   TYR K  37 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR P  36 "   -0.002 2.00e-02 2.50e+03   4.08e-03 1.66e-01
        pdb=" C   THR P  36 "    0.007 2.00e-02 2.50e+03
        pdb=" O   THR P  36 "   -0.003 2.00e-02 2.50e+03
        pdb=" N   TYR P  37 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR H  36 "   -0.002 2.00e-02 2.50e+03   3.92e-03 1.53e-01
        pdb=" C   THR H  36 "    0.007 2.00e-02 2.50e+03
        pdb=" O   THR H  36 "   -0.003 2.00e-02 2.50e+03
        pdb=" N   TYR H  37 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 525 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 1676
        2.99 -     3.47: 2760
        3.47 -     3.94: 5099
        3.94 -     4.42: 5452
        4.42 -     4.90: 10567
  Nonbonded interactions: 25554
  Sorted by model distance:
  nonbonded pdb=" OG  SER G  19 "
            pdb=" OD1 ASN G  22 "
     model   vdw
     2.509 3.040
  nonbonded pdb=" OG  SER D  19 "
            pdb=" OD1 ASN D  22 "
     model   vdw
     2.510 3.040
  nonbonded pdb=" OG  SER H  19 "
            pdb=" OD1 ASN H  22 "
     model   vdw
     2.510 3.040
  nonbonded pdb=" OG  SER K  19 "
            pdb=" OD1 ASN K  22 "
     model   vdw
     2.510 3.040
  nonbonded pdb=" OG  SER J  19 "
            pdb=" OD1 ASN J  22 "
     model   vdw
     2.510 3.040
  ... (remaining 25549 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'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.570
  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:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.600
  Find NCS groups from input model:        0.220
  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:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6387
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      :  0.009   0.101   3008  Z= 0.775
  Angle     :  1.094   4.752   4064  Z= 0.710
  Chirality :  0.067   0.172    480
  Planarity :  0.001   0.004    528
  Dihedral  :  9.418  29.993    928
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 15.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  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: -4.99 (0.21), residues: 368
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.80 (0.16), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS N  18 
 PHE   0.004   0.001   PHE O  23 
 TYR   0.004   0.001   TYR P  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.34558 (   16)
  hydrogen bonds       : angle      11.42292 (   45)
  covalent geometry    : bond        0.00483 ( 2992)
  covalent geometry    : angle       1.09407 ( 4064)
  Misc. bond           : bond        0.09912 (   16)

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

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

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   37 TYR cc_start: 0.5198 (m-80) cc_final: 0.4194 (p90)
REVERT: B   23 PHE cc_start: 0.5808 (m-80) cc_final: 0.4598 (p90)
REVERT: B   37 TYR cc_start: 0.5717 (m-80) cc_final: 0.4405 (p90)
REVERT: C   34 SER cc_start: 0.7377 (m) cc_final: 0.7124 (p)
REVERT: N   27 LEU cc_start: 0.8572 (tp) cc_final: 0.8105 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.0706
  time to fit residues: 11.6739
Evaluate side-chains
  48 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 24 optimal weight:    8.9990
   chunk 13 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 9 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  31 ASN
B  31 ASN
C  31 ASN
** D  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  31 ASN
** E  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  31 ASN
F  31 ASN
G  31 ASN
** H  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN
I  31 ASN
K  31 ASN
** L  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  31 ASN
** M  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  31 ASN
N  31 ASN
P  31 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.088333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.075668 restraints weight = 8832.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.077760 restraints weight = 4566.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.079291 restraints weight = 3023.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.5003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   3008  Z= 0.209
  Angle     :  0.597   4.799   4064  Z= 0.332
  Chirality :  0.040   0.129    480
  Planarity :  0.002   0.010    528
  Dihedral  :  5.038  17.159    400
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 17.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  3.57 %
    Favored  : 96.13 %
  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: -4.92 (0.27), residues: 368
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.74 (0.21), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.002   HIS J  18 
 PHE   0.024   0.003   PHE L  23 
 TYR   0.005   0.001   TYR A  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03801 (   16)
  hydrogen bonds       : angle       5.50023 (   45)
  covalent geometry    : bond        0.00466 ( 2992)
  covalent geometry    : angle       0.59722 ( 4064)
  Misc. bond           : bond        0.00070 (   16)

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

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

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.335 
Fit side-chains
REVERT: C   20 SER cc_start: 0.9080 (p) cc_final: 0.8816 (m)
REVERT: C   21 ASN cc_start: 0.7419 (m-40) cc_final: 0.6991 (m-40)
REVERT: E   21 ASN cc_start: 0.7675 (m-40) cc_final: 0.7427 (m-40)
REVERT: G   36 THR cc_start: 0.9142 (m) cc_final: 0.8906 (p)
REVERT: K   36 THR cc_start: 0.9167 (m) cc_final: 0.8886 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0686
  time to fit residues: 5.6572
Evaluate side-chains
  22 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 29 optimal weight:    0.6980
   chunk 16 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 24 optimal weight:   30.0000
   chunk 30 optimal weight:    0.1980
   chunk 2 optimal weight:   20.0000
   chunk 25 optimal weight:    5.9990
   chunk 22 optimal weight:    9.9990
   chunk 15 optimal weight:   20.0000
   overall best weight:    3.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  31 ASN
B  14 ASN
B  31 ASN
C  31 ASN
** D  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  31 ASN
** F  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  31 ASN
K  31 ASN
** L  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  31 ASN
** N  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.084983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.073041 restraints weight = 9180.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.075186 restraints weight = 4406.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.076465 restraints weight = 2758.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7361
moved from start:          0.5586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3008  Z= 0.138
  Angle     :  0.475   4.297   4064  Z= 0.255
  Chirality :  0.036   0.110    480
  Planarity :  0.002   0.008    528
  Dihedral  :  4.053  11.907    400
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  1.79 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.76 (0.27), residues: 368
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.62 (0.21), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.002   HIS L  18 
 PHE   0.017   0.002   PHE L  23 
 TYR   0.004   0.001   TYR O  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05146 (   16)
  hydrogen bonds       : angle       5.66124 (   45)
  covalent geometry    : bond        0.00308 ( 2992)
  covalent geometry    : angle       0.47522 ( 4064)
  Misc. bond           : bond        0.00058 (   16)

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

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

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.349 
Fit side-chains
REVERT: F   21 ASN cc_start: 0.7299 (m-40) cc_final: 0.6578 (m-40)
REVERT: I   36 THR cc_start: 0.9142 (m) cc_final: 0.8906 (p)
REVERT: L   36 THR cc_start: 0.9134 (m) cc_final: 0.8893 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0691
  time to fit residues: 5.0042
Evaluate side-chains
  25 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 8 optimal weight:   30.0000
   chunk 20 optimal weight:   20.0000
   chunk 4 optimal weight:    5.9990
   chunk 9 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 11 optimal weight:    4.9990
   chunk 30 optimal weight:   20.0000
   chunk 14 optimal weight:    9.9990
   chunk 1 optimal weight:   20.0000
   chunk 15 optimal weight:    3.9990
   chunk 7 optimal weight:    7.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  14 ASN
** D  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  31 ASN
D  35 ASN
** H  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  35 ASN
M  31 ASN
** N  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.078787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.067840 restraints weight = 12517.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.069833 restraints weight = 5566.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.071107 restraints weight = 3357.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.6660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   3008  Z= 0.246
  Angle     :  0.533   4.497   4064  Z= 0.301
  Chirality :  0.039   0.146    480
  Planarity :  0.002   0.010    528
  Dihedral  :  5.069  17.799    400
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 16.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.79 (0.29), residues: 368
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.65 (0.22), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS J  18 
 PHE   0.022   0.002   PHE G  23 
 TYR   0.008   0.001   TYR D  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05698 (   16)
  hydrogen bonds       : angle       6.47702 (   45)
  covalent geometry    : bond        0.00544 ( 2992)
  covalent geometry    : angle       0.53296 ( 4064)
  Misc. bond           : bond        0.00017 (   16)

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

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

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.333 
Fit side-chains
REVERT: C   27 LEU cc_start: 0.8838 (mt) cc_final: 0.8528 (tt)
REVERT: D   31 ASN cc_start: 0.8459 (m-40) cc_final: 0.7985 (m-40)
REVERT: G   27 LEU cc_start: 0.8935 (mt) cc_final: 0.8654 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 32
  average time/residue: 0.0701
  time to fit residues: 3.5386
Evaluate side-chains
  19 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 19 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 15 optimal weight:    8.9990
   chunk 24 optimal weight:   20.0000
   chunk 20 optimal weight:   10.0000
   chunk 18 optimal weight:    5.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  31 ASN
B  14 ASN
C  31 ASN
D  18 HIS
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  31 ASN
F  31 ASN
H  18 HIS
** H  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  31 ASN
K  31 ASN
** L  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.079425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.068710 restraints weight = 11873.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.070650 restraints weight = 5553.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.071968 restraints weight = 3398.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.7116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3008  Z= 0.219
  Angle     :  0.552   6.935   4064  Z= 0.297
  Chirality :  0.038   0.120    480
  Planarity :  0.002   0.008    528
  Dihedral  :  4.903  18.939    400
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 15.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  2.08 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.66 (0.29), residues: 368
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.54 (0.22), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS L  18 
 PHE   0.015   0.002   PHE H  23 
 TYR   0.006   0.001   TYR D  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06179 (   16)
  hydrogen bonds       : angle       6.64061 (   45)
  covalent geometry    : bond        0.00476 ( 2992)
  covalent geometry    : angle       0.55158 ( 4064)
  Misc. bond           : bond        0.00018 (   16)

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

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

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.342 
Fit side-chains
REVERT: C   27 LEU cc_start: 0.8879 (mt) cc_final: 0.8537 (tt)
REVERT: D   31 ASN cc_start: 0.8025 (m-40) cc_final: 0.6977 (t0)
REVERT: L   36 THR cc_start: 0.9249 (m) cc_final: 0.8887 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0695
  time to fit residues: 2.8628
Evaluate side-chains
  17 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 4 optimal weight:   10.0000
   chunk 17 optimal weight:   20.0000
   chunk 30 optimal weight:   20.0000
   chunk 31 optimal weight:   30.0000
   chunk 23 optimal weight:    8.9990
   chunk 12 optimal weight:    8.9990
   chunk 20 optimal weight:   20.0000
   chunk 14 optimal weight:   20.0000
   chunk 16 optimal weight:    9.9990
   overall best weight:    8.7992

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

Flipped N/Q/H residues before XYZ refinement:
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  31 ASN
** H  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.075435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.065447 restraints weight = 10498.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.067128 restraints weight = 5167.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.068263 restraints weight = 3300.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.7761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   3008  Z= 0.302
  Angle     :  0.611   7.309   4064  Z= 0.342
  Chirality :  0.040   0.141    480
  Planarity :  0.003   0.023    528
  Dihedral  :  5.727  21.743    400
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 19.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  3.87 %
    Favored  : 95.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.81 (0.28), residues: 368
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.66 (0.21), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.003   HIS L  18 
 PHE   0.018   0.002   PHE F  23 
 TYR   0.009   0.002   TYR D  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07024 (   16)
  hydrogen bonds       : angle       6.68670 (   45)
  covalent geometry    : bond        0.00648 ( 2992)
  covalent geometry    : angle       0.61050 ( 4064)
  Misc. bond           : bond        0.00056 (   16)

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

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

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.347 
Fit side-chains
REVERT: C   27 LEU cc_start: 0.8860 (mt) cc_final: 0.8532 (tp)
REVERT: D   31 ASN cc_start: 0.8223 (m-40) cc_final: 0.7099 (t0)
REVERT: K   27 LEU cc_start: 0.9062 (mt) cc_final: 0.8644 (tt)
  outliers start: 1
  outliers final: 1
  residues processed: 25
  average time/residue: 0.0709
  time to fit residues: 2.8780
Evaluate side-chains
  20 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 19
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 8 optimal weight:   20.0000
   chunk 19 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 30 optimal weight:   20.0000
   chunk 15 optimal weight:    6.9990
   chunk 26 optimal weight:   20.0000
   chunk 31 optimal weight:    9.9990
   chunk 16 optimal weight:    0.6980
   chunk 5 optimal weight:    9.9990
   overall best weight:    4.9388

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

Flipped N/Q/H residues before XYZ refinement:
G  18 HIS
** H  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  18 HIS
** L  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  18 HIS
M  31 ASN
** N  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.078039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.067871 restraints weight = 10546.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.069598 restraints weight = 5300.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.070713 restraints weight = 3402.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.7784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3008  Z= 0.184
  Angle     :  0.534   7.262   4064  Z= 0.287
  Chirality :  0.038   0.147    480
  Planarity :  0.002   0.015    528
  Dihedral  :  4.813  18.566    400
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 15.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.66 (0.28), residues: 368
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.54 (0.21), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS F  18 
 PHE   0.012   0.002   PHE H  23 
 TYR   0.005   0.001   TYR D  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06284 (   16)
  hydrogen bonds       : angle       6.26331 (   45)
  covalent geometry    : bond        0.00414 ( 2992)
  covalent geometry    : angle       0.53368 ( 4064)
  Misc. bond           : bond        0.00016 (   16)

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

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

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.384 
Fit side-chains
REVERT: C   27 LEU cc_start: 0.8863 (mt) cc_final: 0.8548 (tt)
REVERT: L   31 ASN cc_start: 0.8269 (m110) cc_final: 0.6363 (p0)
REVERT: N   26 ILE cc_start: 0.9213 (mm) cc_final: 0.8988 (mm)
REVERT: N   31 ASN cc_start: 0.7830 (m110) cc_final: 0.7610 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 30
  average time/residue: 0.0701
  time to fit residues: 3.3399
Evaluate side-chains
  23 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   chunk 25 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 26 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** D  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  31 ASN
** H  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  18 HIS
** L  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.077014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.066625 restraints weight = 10727.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.068364 restraints weight = 5386.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.069537 restraints weight = 3453.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.7984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3008  Z= 0.190
  Angle     :  0.552   7.021   4064  Z= 0.291
  Chirality :  0.039   0.129    480
  Planarity :  0.002   0.012    528
  Dihedral  :  4.903  18.138    400
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  0.30 %
    Favored  : 99.40 %
  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: -4.57 (0.28), residues: 368
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.48 (0.22), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS J  18 
 PHE   0.012   0.002   PHE F  23 
 TYR   0.005   0.001   TYR D  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06322 (   16)
  hydrogen bonds       : angle       6.32497 (   45)
  covalent geometry    : bond        0.00428 ( 2992)
  covalent geometry    : angle       0.55223 ( 4064)
  Misc. bond           : bond        0.00026 (   16)

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

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

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.325 
Fit side-chains
REVERT: C   27 LEU cc_start: 0.8900 (mt) cc_final: 0.8531 (tp)
REVERT: N   26 ILE cc_start: 0.9200 (mm) cc_final: 0.8959 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 27
  average time/residue: 0.0695
  time to fit residues: 2.9823
Evaluate side-chains
  22 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 16 optimal weight:   30.0000
   chunk 18 optimal weight:   20.0000
   chunk 28 optimal weight:   20.0000
   chunk 29 optimal weight:   20.0000
   chunk 3 optimal weight:    0.0870
   chunk 26 optimal weight:   20.0000
   chunk 5 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    2.3364

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

Flipped N/Q/H residues before XYZ refinement:
** B  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN
** L  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.080791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.070209 restraints weight = 9984.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.072036 restraints weight = 4907.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.073278 restraints weight = 3113.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.7881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3008  Z= 0.104
  Angle     :  0.512   7.298   4064  Z= 0.259
  Chirality :  0.037   0.123    480
  Planarity :  0.001   0.009    528
  Dihedral  :  4.194  12.507    400
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  0.30 %
    Favored  : 99.40 %
  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: -4.48 (0.28), residues: 368
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.41 (0.22), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS J  18 
 PHE   0.008   0.001   PHE F  23 
 TYR   0.004   0.001   TYR P  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05527 (   16)
  hydrogen bonds       : angle       5.72663 (   45)
  covalent geometry    : bond        0.00233 ( 2992)
  covalent geometry    : angle       0.51202 ( 4064)
  Misc. bond           : bond        0.00010 (   16)

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

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

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.319 
Fit side-chains
REVERT: C   27 LEU cc_start: 0.8881 (mt) cc_final: 0.8516 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 27
  average time/residue: 0.0774
  time to fit residues: 3.3207
Evaluate side-chains
  21 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 1 optimal weight:    0.4980
   chunk 23 optimal weight:   20.0000
   chunk 12 optimal weight:    1.9990
   chunk 20 optimal weight:   20.0000
   chunk 16 optimal weight:    6.9990
   chunk 28 optimal weight:   20.0000
   chunk 5 optimal weight:    3.9990
   chunk 6 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   chunk 2 optimal weight:    8.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    3.8988

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

Flipped N/Q/H residues before XYZ refinement:
** B  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  31 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.079319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.068757 restraints weight = 11146.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.070555 restraints weight = 5416.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.071796 restraints weight = 3427.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.8035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3008  Z= 0.149
  Angle     :  0.533   7.170   4064  Z= 0.274
  Chirality :  0.039   0.141    480
  Planarity :  0.002   0.011    528
  Dihedral  :  4.507  13.573    400
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  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: -4.47 (0.29), residues: 368
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.40 (0.22), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS J  18 
 PHE   0.010   0.002   PHE H  23 
 TYR   0.004   0.001   TYR D  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05806 (   16)
  hydrogen bonds       : angle       5.97429 (   45)
  covalent geometry    : bond        0.00339 ( 2992)
  covalent geometry    : angle       0.53312 ( 4064)
  Misc. bond           : bond        0.00018 (   16)

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

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

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  736 Ramachandran restraints generated.
    368 Oldfield, 0 Emsley, 368 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.365 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.0776
  time to fit residues: 3.1168
Evaluate side-chains
  19 residues out of total 336 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 4 optimal weight:   20.0000
   chunk 22 optimal weight:    9.9990
   chunk 28 optimal weight:   20.0000
   chunk 11 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 3 optimal weight:    8.9990
   chunk 31 optimal weight:   30.0000
   chunk 24 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.077780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.067019 restraints weight = 11542.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.068871 restraints weight = 5579.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.070074 restraints weight = 3459.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.8186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   3008  Z= 0.219
  Angle     :  0.577   7.166   4064  Z= 0.306
  Chirality :  0.040   0.153    480
  Planarity :  0.002   0.012    528
  Dihedral  :  5.090  16.430    400
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 17.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.88 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -4.28 (0.29), residues: 368
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.26 (0.22), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS F  18 
 PHE   0.012   0.002   PHE F  23 
 TYR   0.007   0.001   TYR D  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06341 (   16)
  hydrogen bonds       : angle       6.31886 (   45)
  covalent geometry    : bond        0.00488 ( 2992)
  covalent geometry    : angle       0.57743 ( 4064)
  Misc. bond           : bond        0.00033 (   16)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1101.08 seconds
wall clock time: 20 minutes 32.98 seconds (1232.98 seconds total)