Starting phenix.real_space_refine
on Mon Jul 28 12:51:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6i3n_4405/07_2025/6i3n_4405.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6i3n_4405/07_2025/6i3n_4405.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6i3n_4405/07_2025/6i3n_4405.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6i3n_4405/07_2025/6i3n_4405.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6i3n_4405/07_2025/6i3n_4405.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6i3n_4405/07_2025/6i3n_4405.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.025
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: 4
    Type Number    sf(0)   Gaussians
     S      39      5.16       5
     C    6721      2.51       5
     N    1898      2.21       5
     O    2002      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10660
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 820
          Classifications: {'peptide': 103}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 98}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, M, L
  Time building chain proxies: 5.46, per 1000 atoms: 0.51
  Number of scatterers: 10660
  At special positions: 0
  Unit cell: (83.74, 83.74, 126.14, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      39     16.00
     O    2002      8.00
     N    1898      7.00
     C    6721      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.58
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2522

  Finding SS restraints...
    Secondary structure from input PDB file:
      104 helices and 0 sheets defined
      79.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'M' and resid 21 through 25
    Processing helix  chain 'M' and resid 26 through 38
      removed outlier: 3.510A  pdb=" N   SER M  34 " --> pdb=" O   ARG M  30 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE M  36 " --> pdb=" O   ARG M  32 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 46 through 54
      removed outlier: 3.531A  pdb=" N   LEU M  50 " --> pdb=" O   ASP M  46 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 57 through 65
    Processing helix  chain 'M' and resid 69 through 78
    Processing helix  chain 'M' and resid 85 through 96
    Processing helix  chain 'M' and resid 99 through 105
      removed outlier: 3.658A  pdb=" N   LEU M 103 " --> pdb=" O   ASP M  99 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   GLU M 104 " --> pdb=" O   ASP M 100 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 105 through 121
      removed outlier: 3.632A  pdb=" N   ILE M 109 " --> pdb=" O   LEU M 105 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU M 110 " --> pdb=" O   GLY M 106 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 21 through 25
    Processing helix  chain 'I' and resid 26 through 38
      removed outlier: 3.511A  pdb=" N   SER I  34 " --> pdb=" O   ARG I  30 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE I  36 " --> pdb=" O   ARG I  32 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 46 through 54
      removed outlier: 3.532A  pdb=" N   LEU I  50 " --> pdb=" O   ASP I  46 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 57 through 65
    Processing helix  chain 'I' and resid 69 through 78
    Processing helix  chain 'I' and resid 85 through 96
    Processing helix  chain 'I' and resid 99 through 105
      removed outlier: 3.658A  pdb=" N   LEU I 103 " --> pdb=" O   ASP I  99 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLU I 104 " --> pdb=" O   ASP I 100 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 105 through 121
      removed outlier: 3.632A  pdb=" N   ILE I 109 " --> pdb=" O   LEU I 105 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLU I 110 " --> pdb=" O   GLY I 106 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 21 through 25
    Processing helix  chain 'J' and resid 26 through 38
      removed outlier: 3.511A  pdb=" N   SER J  34 " --> pdb=" O   ARG J  30 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE J  36 " --> pdb=" O   ARG J  32 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 46 through 54
      removed outlier: 3.531A  pdb=" N   LEU J  50 " --> pdb=" O   ASP J  46 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 57 through 65
    Processing helix  chain 'J' and resid 69 through 78
    Processing helix  chain 'J' and resid 85 through 96
    Processing helix  chain 'J' and resid 99 through 105
      removed outlier: 3.658A  pdb=" N   LEU J 103 " --> pdb=" O   ASP J  99 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   GLU J 104 " --> pdb=" O   ASP J 100 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 105 through 121
      removed outlier: 3.633A  pdb=" N   ILE J 109 " --> pdb=" O   LEU J 105 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU J 110 " --> pdb=" O   GLY J 106 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 21 through 25
    Processing helix  chain 'K' and resid 26 through 38
      removed outlier: 3.511A  pdb=" N   SER K  34 " --> pdb=" O   ARG K  30 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE K  36 " --> pdb=" O   ARG K  32 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 46 through 54
      removed outlier: 3.531A  pdb=" N   LEU K  50 " --> pdb=" O   ASP K  46 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 57 through 65
    Processing helix  chain 'K' and resid 69 through 78
    Processing helix  chain 'K' and resid 85 through 96
    Processing helix  chain 'K' and resid 99 through 105
      removed outlier: 3.658A  pdb=" N   LEU K 103 " --> pdb=" O   ASP K  99 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   GLU K 104 " --> pdb=" O   ASP K 100 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 105 through 121
      removed outlier: 3.632A  pdb=" N   ILE K 109 " --> pdb=" O   LEU K 105 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU K 110 " --> pdb=" O   GLY K 106 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 21 through 25
    Processing helix  chain 'H' and resid 26 through 38
      removed outlier: 3.511A  pdb=" N   SER H  34 " --> pdb=" O   ARG H  30 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE H  36 " --> pdb=" O   ARG H  32 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 46 through 54
      removed outlier: 3.531A  pdb=" N   LEU H  50 " --> pdb=" O   ASP H  46 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 57 through 65
    Processing helix  chain 'H' and resid 69 through 78
    Processing helix  chain 'H' and resid 85 through 96
    Processing helix  chain 'H' and resid 99 through 105
      removed outlier: 3.659A  pdb=" N   LEU H 103 " --> pdb=" O   ASP H  99 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLU H 104 " --> pdb=" O   ASP H 100 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 105 through 121
      removed outlier: 3.633A  pdb=" N   ILE H 109 " --> pdb=" O   LEU H 105 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU H 110 " --> pdb=" O   GLY H 106 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 21 through 25
    Processing helix  chain 'L' and resid 26 through 38
      removed outlier: 3.510A  pdb=" N   SER L  34 " --> pdb=" O   ARG L  30 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE L  36 " --> pdb=" O   ARG L  32 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 46 through 54
      removed outlier: 3.532A  pdb=" N   LEU L  50 " --> pdb=" O   ASP L  46 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 57 through 65
    Processing helix  chain 'L' and resid 69 through 78
    Processing helix  chain 'L' and resid 85 through 96
    Processing helix  chain 'L' and resid 99 through 105
      removed outlier: 3.659A  pdb=" N   LEU L 103 " --> pdb=" O   ASP L  99 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   GLU L 104 " --> pdb=" O   ASP L 100 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 105 through 121
      removed outlier: 3.633A  pdb=" N   ILE L 109 " --> pdb=" O   LEU L 105 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU L 110 " --> pdb=" O   GLY L 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 25
    Processing helix  chain 'B' and resid 26 through 38
      removed outlier: 3.511A  pdb=" N   SER B  34 " --> pdb=" O   ARG B  30 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE B  36 " --> pdb=" O   ARG B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 54
      removed outlier: 3.531A  pdb=" N   LEU B  50 " --> pdb=" O   ASP B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 65
    Processing helix  chain 'B' and resid 69 through 78
    Processing helix  chain 'B' and resid 85 through 96
    Processing helix  chain 'B' and resid 99 through 105
      removed outlier: 3.657A  pdb=" N   LEU B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLU B 104 " --> pdb=" O   ASP B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 121
      removed outlier: 3.633A  pdb=" N   ILE B 109 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU B 110 " --> pdb=" O   GLY B 106 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 21 through 25
    Processing helix  chain 'F' and resid 26 through 38
      removed outlier: 3.511A  pdb=" N   SER F  34 " --> pdb=" O   ARG F  30 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   PHE F  36 " --> pdb=" O   ARG F  32 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 46 through 54
      removed outlier: 3.531A  pdb=" N   LEU F  50 " --> pdb=" O   ASP F  46 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 57 through 65
    Processing helix  chain 'F' and resid 69 through 78
    Processing helix  chain 'F' and resid 85 through 96
    Processing helix  chain 'F' and resid 99 through 105
      removed outlier: 3.657A  pdb=" N   LEU F 103 " --> pdb=" O   ASP F  99 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLU F 104 " --> pdb=" O   ASP F 100 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 105 through 121
      removed outlier: 3.632A  pdb=" N   ILE F 109 " --> pdb=" O   LEU F 105 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLU F 110 " --> pdb=" O   GLY F 106 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 25
    Processing helix  chain 'C' and resid 26 through 38
      removed outlier: 3.511A  pdb=" N   SER C  34 " --> pdb=" O   ARG C  30 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE C  36 " --> pdb=" O   ARG C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 54
      removed outlier: 3.531A  pdb=" N   LEU C  50 " --> pdb=" O   ASP C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 57 through 65
    Processing helix  chain 'C' and resid 69 through 78
    Processing helix  chain 'C' and resid 85 through 96
    Processing helix  chain 'C' and resid 99 through 105
      removed outlier: 3.657A  pdb=" N   LEU C 103 " --> pdb=" O   ASP C  99 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   GLU C 104 " --> pdb=" O   ASP C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 121
      removed outlier: 3.632A  pdb=" N   ILE C 109 " --> pdb=" O   LEU C 105 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU C 110 " --> pdb=" O   GLY C 106 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 21 through 25
    Processing helix  chain 'D' and resid 26 through 38
      removed outlier: 3.511A  pdb=" N   SER D  34 " --> pdb=" O   ARG D  30 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   PHE D  36 " --> pdb=" O   ARG D  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 46 through 54
      removed outlier: 3.531A  pdb=" N   LEU D  50 " --> pdb=" O   ASP D  46 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 57 through 65
    Processing helix  chain 'D' and resid 69 through 78
    Processing helix  chain 'D' and resid 85 through 96
    Processing helix  chain 'D' and resid 99 through 105
      removed outlier: 3.658A  pdb=" N   LEU D 103 " --> pdb=" O   ASP D  99 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLU D 104 " --> pdb=" O   ASP D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 121
      removed outlier: 3.632A  pdb=" N   ILE D 109 " --> pdb=" O   LEU D 105 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU D 110 " --> pdb=" O   GLY D 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 25
    Processing helix  chain 'A' and resid 26 through 38
      removed outlier: 3.510A  pdb=" N   SER A  34 " --> pdb=" O   ARG A  30 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE A  36 " --> pdb=" O   ARG A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 54
      removed outlier: 3.531A  pdb=" N   LEU A  50 " --> pdb=" O   ASP A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 65
    Processing helix  chain 'A' and resid 69 through 78
    Processing helix  chain 'A' and resid 85 through 96
    Processing helix  chain 'A' and resid 99 through 105
      removed outlier: 3.658A  pdb=" N   LEU A 103 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   GLU A 104 " --> pdb=" O   ASP A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 121
      removed outlier: 3.632A  pdb=" N   ILE A 109 " --> pdb=" O   LEU A 105 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU A 110 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 21 through 25
    Processing helix  chain 'E' and resid 26 through 38
      removed outlier: 3.510A  pdb=" N   SER E  34 " --> pdb=" O   ARG E  30 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE E  36 " --> pdb=" O   ARG E  32 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 54
      removed outlier: 3.531A  pdb=" N   LEU E  50 " --> pdb=" O   ASP E  46 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 57 through 65
    Processing helix  chain 'E' and resid 69 through 78
    Processing helix  chain 'E' and resid 85 through 96
    Processing helix  chain 'E' and resid 99 through 105
      removed outlier: 3.658A  pdb=" N   LEU E 103 " --> pdb=" O   ASP E  99 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   GLU E 104 " --> pdb=" O   ASP E 100 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 105 through 121
      removed outlier: 3.633A  pdb=" N   ILE E 109 " --> pdb=" O   LEU E 105 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLU E 110 " --> pdb=" O   GLY E 106 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 21 through 25
    Processing helix  chain 'G' and resid 26 through 38
      removed outlier: 3.511A  pdb=" N   SER G  34 " --> pdb=" O   ARG G  30 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   PHE G  36 " --> pdb=" O   ARG G  32 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 54
      removed outlier: 3.531A  pdb=" N   LEU G  50 " --> pdb=" O   ASP G  46 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 57 through 65
    Processing helix  chain 'G' and resid 69 through 78
    Processing helix  chain 'G' and resid 85 through 96
    Processing helix  chain 'G' and resid 99 through 105
      removed outlier: 3.658A  pdb=" N   LEU G 103 " --> pdb=" O   ASP G  99 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   GLU G 104 " --> pdb=" O   ASP G 100 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 105 through 121
      removed outlier: 3.633A  pdb=" N   ILE G 109 " --> pdb=" O   LEU G 105 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLU G 110 " --> pdb=" O   GLY G 106 " (cutoff:3.500A)

    572 hydrogen bonds defined for protein.
    1638 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.83

  Time building geometry restraints manager: 5.14 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3653
        1.34 -     1.46: 1579
        1.46 -     1.57: 5506
        1.57 -     1.69: 0
        1.69 -     1.80: 65
  Bond restraints: 10803
  Sorted by residual:
  bond pdb=" SD  MET J  54 "
       pdb=" CE  MET J  54 "
    ideal  model  delta    sigma   weight residual
    1.791  1.755  0.036 2.50e-02 1.60e+03 2.10e+00
  bond pdb=" SD  MET A  54 "
       pdb=" CE  MET A  54 "
    ideal  model  delta    sigma   weight residual
    1.791  1.755  0.036 2.50e-02 1.60e+03 2.07e+00
  bond pdb=" SD  MET I  54 "
       pdb=" CE  MET I  54 "
    ideal  model  delta    sigma   weight residual
    1.791  1.755  0.036 2.50e-02 1.60e+03 2.07e+00
  bond pdb=" SD  MET H  54 "
       pdb=" CE  MET H  54 "
    ideal  model  delta    sigma   weight residual
    1.791  1.755  0.036 2.50e-02 1.60e+03 2.06e+00
  bond pdb=" SD  MET E  54 "
       pdb=" CE  MET E  54 "
    ideal  model  delta    sigma   weight residual
    1.791  1.755  0.036 2.50e-02 1.60e+03 2.06e+00
  ... (remaining 10798 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 12889
        1.42 -     2.84: 1369
        2.84 -     4.27: 231
        4.27 -     5.69: 97
        5.69 -     7.11: 26
  Bond angle restraints: 14612
  Sorted by residual:
  angle pdb=" C   LEU A  37 "
        pdb=" N   ASN A  38 "
        pdb=" CA  ASN A  38 "
      ideal   model   delta    sigma   weight residual
     122.65  117.65    5.00 1.60e+00 3.91e-01 9.75e+00
  angle pdb=" C   LEU I  37 "
        pdb=" N   ASN I  38 "
        pdb=" CA  ASN I  38 "
      ideal   model   delta    sigma   weight residual
     122.65  117.65    5.00 1.60e+00 3.91e-01 9.75e+00
  angle pdb=" C   LEU J  37 "
        pdb=" N   ASN J  38 "
        pdb=" CA  ASN J  38 "
      ideal   model   delta    sigma   weight residual
     122.65  117.66    4.99 1.60e+00 3.91e-01 9.74e+00
  angle pdb=" C   LEU C  37 "
        pdb=" N   ASN C  38 "
        pdb=" CA  ASN C  38 "
      ideal   model   delta    sigma   weight residual
     122.65  117.67    4.98 1.60e+00 3.91e-01 9.70e+00
  angle pdb=" C   LEU B  37 "
        pdb=" N   ASN B  38 "
        pdb=" CA  ASN B  38 "
      ideal   model   delta    sigma   weight residual
     122.65  117.68    4.97 1.60e+00 3.91e-01 9.65e+00
  ... (remaining 14607 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.43: 6215
       14.43 -    28.86: 301
       28.86 -    43.29: 140
       43.29 -    57.72: 0
       57.72 -    72.14: 26
  Dihedral angle restraints: 6682
    sinusoidal: 2808
      harmonic: 3874
  Sorted by residual:
  dihedral pdb=" CA  PHE E  36 "
           pdb=" C   PHE E  36 "
           pdb=" N   LEU E  37 "
           pdb=" CA  LEU E  37 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.35  -17.65     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  PHE L  36 "
           pdb=" C   PHE L  36 "
           pdb=" N   LEU L  37 "
           pdb=" CA  LEU L  37 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.36  -17.64     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  PHE H  36 "
           pdb=" C   PHE H  36 "
           pdb=" N   LEU H  37 "
           pdb=" CA  LEU H  37 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.36  -17.64     0      5.00e+00 4.00e-02 1.24e+01
  ... (remaining 6679 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 945
       0.039 -    0.078: 561
       0.078 -    0.118: 138
       0.118 -    0.157: 33
       0.157 -    0.196: 13
  Chirality restraints: 1690
  Sorted by residual:
  chirality pdb=" CA  ASN M  38 "
            pdb=" N   ASN M  38 "
            pdb=" C   ASN M  38 "
            pdb=" CB  ASN M  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.59e-01
  chirality pdb=" CA  ASN H  38 "
            pdb=" N   ASN H  38 "
            pdb=" C   ASN H  38 "
            pdb=" CB  ASN H  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.58e-01
  chirality pdb=" CA  ASN F  38 "
            pdb=" N   ASN F  38 "
            pdb=" C   ASN F  38 "
            pdb=" CB  ASN F  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.56e-01
  ... (remaining 1687 not shown)

  Planarity restraints: 1898
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG G  81 "    0.032 5.00e-02 4.00e+02   4.90e-02 3.84e+00
        pdb=" N   PRO G  82 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO G  82 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO G  82 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG H  81 "    0.032 5.00e-02 4.00e+02   4.89e-02 3.83e+00
        pdb=" N   PRO H  82 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO H  82 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO H  82 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG M  81 "    0.032 5.00e-02 4.00e+02   4.89e-02 3.82e+00
        pdb=" N   PRO M  82 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO M  82 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO M  82 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1895 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 3976
        2.91 -     3.41: 11047
        3.41 -     3.90: 16996
        3.90 -     4.40: 20180
        4.40 -     4.90: 33209
  Nonbonded interactions: 85408
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  58 "
            pdb=" OD1 ASP E  76 "
     model   vdw
     2.410 3.040
  nonbonded pdb=" OD1 ASP D  76 "
            pdb=" OH  TYR A  58 "
     model   vdw
     2.411 3.040
  nonbonded pdb=" ND2 ASN K  26 "
            pdb=" OE2 GLU H  52 "
     model   vdw
     2.419 3.120
  nonbonded pdb=" OH  TYR I  58 "
            pdb=" OD1 ASP L  76 "
     model   vdw
     2.428 3.040
  nonbonded pdb=" OD1 ASP K  76 "
            pdb=" OH  TYR H  58 "
     model   vdw
     2.432 3.040
  ... (remaining 85403 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: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             25.640
  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:             0.060
  Extract box with map and model:          0.750
  Check model and map are aligned:         0.160
  Set scattering table:                    0.210
  Process input model:                     32.280
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   63.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
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      :  0.007   0.037  10803  Z= 0.315
  Angle     :  1.055   7.112  14612  Z= 0.577
  Chirality :  0.052   0.196   1690
  Planarity :  0.006   0.049   1898
  Dihedral  : 11.331  72.145   4160
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.92 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  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: -5.28 (0.16), residues: 1313
  helix: -3.60 (0.10), residues: 1027
  sheet:  None (None), residues: 0
  loop : -1.86 (0.31), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.003   TRP B  78 
 PHE   0.010   0.002   PHE H  36 
 TYR   0.010   0.003   TYR I 116 
 ARG   0.012   0.002   ARG K  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22172 (  572)
  hydrogen bonds       : angle       7.69490 ( 1638)
  covalent geometry    : bond        0.00714 (10803)
  covalent geometry    : angle       1.05466 (14612)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  421 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 421
  time to evaluate  : 1.304 
Fit side-chains
   revert: symmetry clash
REVERT: I  119 LYS cc_start: 0.7860 (tttt) cc_final: 0.7576 (ttpp)
REVERT: J   27 MET cc_start: 0.9075 (mmm) cc_final: 0.8746 (mmt)
REVERT: K   27 MET cc_start: 0.9106 (mmm) cc_final: 0.8778 (mmm)
REVERT: K   60 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6956 (mm-30)
REVERT: H  103 LEU cc_start: 0.8592 (tt) cc_final: 0.8317 (mt)
REVERT: L   39 VAL cc_start: 0.9145 (t) cc_final: 0.8942 (p)
REVERT: B   27 MET cc_start: 0.8838 (mmm) cc_final: 0.8622 (mmp)
REVERT: F   99 ASP cc_start: 0.8211 (m-30) cc_final: 0.7960 (m-30)
REVERT: F  119 LYS cc_start: 0.8336 (tttt) cc_final: 0.7952 (ttpp)
REVERT: C   27 MET cc_start: 0.8640 (mmm) cc_final: 0.8127 (mmp)
REVERT: C  119 LYS cc_start: 0.7846 (tttt) cc_final: 0.7554 (ttpp)
REVERT: A   27 MET cc_start: 0.8912 (mmm) cc_final: 0.8645 (mmp)
REVERT: A   73 ARG cc_start: 0.8796 (mmp80) cc_final: 0.8401 (mmp-170)
REVERT: A   76 ASP cc_start: 0.8210 (m-30) cc_final: 0.7642 (m-30)
REVERT: G   53 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6974 (mm-30)
REVERT: G  119 LYS cc_start: 0.8197 (tttt) cc_final: 0.7796 (tttm)
  outliers start: 0
  outliers final: 0
  residues processed: 421
  average time/residue: 0.3962
  time to fit residues: 205.7762
Evaluate side-chains
  328 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 328
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    6.9990
   chunk 98 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0870
   chunk 33 optimal weight:    0.0070
   chunk 66 optimal weight:    6.9990
   chunk 52 optimal weight:    8.9990
   chunk 101 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 118 optimal weight:    0.9990
   overall best weight:    0.5376

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

Flipped N/Q/H residues before XYZ refinement:
I  79 GLN
J  42 GLN
K  79 GLN
B  42 GLN
B  63 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.131583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.118025 restraints weight = 12279.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 1.61
r_work: 0.3171 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3023 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019  10803  Z= 0.105
  Angle     :  0.551   5.770  14612  Z= 0.282
  Chirality :  0.037   0.123   1690
  Planarity :  0.004   0.038   1898
  Dihedral  :  5.192  16.711   1482
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  :  8.22 %
    Favored  : 89.92 %
  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: -2.07 (0.20), residues: 1313
  helix: -1.20 (0.14), residues: 975
  sheet:  None (None), residues: 0
  loop : -1.34 (0.29), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  78 
 PHE   0.005   0.001   PHE I  56 
 TYR   0.009   0.001   TYR F 116 
 ARG   0.007   0.001   ARG L  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03486 (  572)
  hydrogen bonds       : angle       4.26846 ( 1638)
  covalent geometry    : bond        0.00222 (10803)
  covalent geometry    : angle       0.55086 (14612)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  352 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 331
  time to evaluate  : 1.250 
Fit side-chains
   revert: symmetry clash
REVERT: J   27 MET cc_start: 0.9158 (mmm) cc_final: 0.8943 (mmt)
REVERT: J   32 ARG cc_start: 0.8564 (tpt90) cc_final: 0.8298 (tpt170)
REVERT: K   27 MET cc_start: 0.9187 (mmm) cc_final: 0.8983 (mmt)
REVERT: K   62 ARG cc_start: 0.9341 (mmm160) cc_final: 0.9114 (mmm-85)
REVERT: K   63 GLN cc_start: 0.8986 (tm-30) cc_final: 0.8728 (tm-30)
REVERT: K   67 GLN cc_start: 0.8155 (pt0) cc_final: 0.7830 (pt0)
REVERT: H  103 LEU cc_start: 0.8879 (tt) cc_final: 0.8553 (mt)
REVERT: L  110 GLU cc_start: 0.7655 (pp20) cc_final: 0.7444 (pp20)
REVERT: L  119 LYS cc_start: 0.7798 (tttt) cc_final: 0.7136 (tttm)
REVERT: B   27 MET cc_start: 0.9038 (mmm) cc_final: 0.8700 (mmp)
REVERT: B   31 ARG cc_start: 0.8394 (mtm110) cc_final: 0.7425 (ttt-90)
REVERT: B   76 ASP cc_start: 0.8532 (m-30) cc_final: 0.7651 (m-30)
REVERT: B   99 ASP cc_start: 0.8380 (m-30) cc_final: 0.8065 (m-30)
REVERT: F   31 ARG cc_start: 0.8402 (mtt180) cc_final: 0.8103 (mtm-85)
REVERT: F   38 ASN cc_start: 0.7933 (p0) cc_final: 0.7699 (p0)
REVERT: F   60 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7876 (mm-30)
REVERT: F   76 ASP cc_start: 0.8420 (m-30) cc_final: 0.8121 (m-30)
REVERT: F   95 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8597 (tttp)
REVERT: F   99 ASP cc_start: 0.8589 (m-30) cc_final: 0.8368 (m-30)
REVERT: F  119 LYS cc_start: 0.8277 (tttt) cc_final: 0.7794 (ttpp)
REVERT: C   27 MET cc_start: 0.8630 (mmm) cc_final: 0.8207 (mmp)
REVERT: C   62 ARG cc_start: 0.9041 (mmm160) cc_final: 0.8686 (mmm160)
REVERT: C  119 LYS cc_start: 0.7876 (tttt) cc_final: 0.7408 (ttpp)
REVERT: D   38 ASN cc_start: 0.8121 (p0) cc_final: 0.7874 (p0)
REVERT: D   42 GLN cc_start: 0.8477 (tp-100) cc_final: 0.8222 (mm-40)
REVERT: D  103 LEU cc_start: 0.8923 (tp) cc_final: 0.8565 (mp)
REVERT: A   27 MET cc_start: 0.8844 (mmm) cc_final: 0.8483 (mmp)
REVERT: A   52 GLU cc_start: 0.8524 (tt0) cc_final: 0.8309 (tt0)
REVERT: E   42 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7646 (tm-30)
REVERT: E   53 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7729 (mm-30)
REVERT: G   53 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7954 (mm-30)
REVERT: G  112 ASP cc_start: 0.8429 (m-30) cc_final: 0.8102 (m-30)
REVERT: G  119 LYS cc_start: 0.8270 (tttt) cc_final: 0.7648 (tttm)
  outliers start: 21
  outliers final: 12
  residues processed: 338
  average time/residue: 0.4082
  time to fit residues: 177.3143
Evaluate side-chains
  322 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 309
  time to evaluate  : 1.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   42 GLN
Chi-restraints excluded: chain I residue  103 LEU
Chi-restraints excluded: chain I residue  118 LEU
Chi-restraints excluded: chain J residue   26 ASN
Chi-restraints excluded: chain J residue  103 LEU
Chi-restraints excluded: chain J residue  118 LEU
Chi-restraints excluded: chain K residue   79 GLN
Chi-restraints excluded: chain K residue   94 THR
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain E residue   42 GLN
Chi-restraints excluded: chain E residue   91 GLU
Chi-restraints excluded: chain G residue   85 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 71 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 101 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
M  67 GLN
J  79 GLN
K  79 GLN
F  67 GLN
** F  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  67 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.123324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.109473 restraints weight = 12581.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 1.61
r_work: 0.3074 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.3301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10803  Z= 0.184
  Angle     :  0.607   5.501  14612  Z= 0.306
  Chirality :  0.041   0.132   1690
  Planarity :  0.005   0.054   1898
  Dihedral  :  5.069  17.353   1482
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.58 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.22), residues: 1313
  helix:  0.12 (0.16), residues: 975
  sheet:  None (None), residues: 0
  loop : -1.00 (0.28), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  78 
 PHE   0.011   0.001   PHE G  36 
 TYR   0.012   0.003   TYR A  58 
 ARG   0.005   0.001   ARG H  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03439 (  572)
  hydrogen bonds       : angle       3.99853 ( 1638)
  covalent geometry    : bond        0.00438 (10803)
  covalent geometry    : angle       0.60743 (14612)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  346 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 325
  time to evaluate  : 1.130 
Fit side-chains
REVERT: J   27 MET cc_start: 0.9174 (mmm) cc_final: 0.8880 (mmt)
REVERT: K   27 MET cc_start: 0.9199 (mmm) cc_final: 0.8982 (mmt)
REVERT: H  103 LEU cc_start: 0.8963 (tt) cc_final: 0.8701 (mt)
REVERT: L   27 MET cc_start: 0.8972 (mmt) cc_final: 0.8763 (mmm)
REVERT: B   42 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.6936 (tm-30)
REVERT: B   99 ASP cc_start: 0.8287 (m-30) cc_final: 0.7957 (m-30)
REVERT: F   31 ARG cc_start: 0.8567 (mtt180) cc_final: 0.8308 (mtm110)
REVERT: F   79 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7895 (tp40)
REVERT: F   95 LYS cc_start: 0.8904 (ttmt) cc_final: 0.8688 (tttt)
REVERT: F  119 LYS cc_start: 0.8442 (tttt) cc_final: 0.7856 (ttpp)
REVERT: C   27 MET cc_start: 0.8831 (mmm) cc_final: 0.8352 (mmp)
REVERT: C  119 LYS cc_start: 0.8155 (tttt) cc_final: 0.7649 (tmmt)
REVERT: D   42 GLN cc_start: 0.8472 (tp-100) cc_final: 0.8222 (mm-40)
REVERT: D  103 LEU cc_start: 0.9098 (tp) cc_final: 0.8897 (tp)
REVERT: A   27 MET cc_start: 0.8924 (mmm) cc_final: 0.8526 (mmp)
REVERT: A   76 ASP cc_start: 0.8600 (m-30) cc_final: 0.8180 (m-30)
REVERT: E   32 ARG cc_start: 0.8450 (tpp-160) cc_final: 0.8119 (tpt170)
REVERT: E   42 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.7607 (tm-30)
REVERT: E   53 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7915 (mm-30)
REVERT: G  119 LYS cc_start: 0.8442 (tttt) cc_final: 0.7972 (ttpt)
  outliers start: 21
  outliers final: 13
  residues processed: 334
  average time/residue: 0.3362
  time to fit residues: 145.1101
Evaluate side-chains
  327 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 312
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   67 GLN
Chi-restraints excluded: chain M residue   85 SER
Chi-restraints excluded: chain J residue   26 ASN
Chi-restraints excluded: chain J residue   94 THR
Chi-restraints excluded: chain J residue  103 LEU
Chi-restraints excluded: chain K residue   94 THR
Chi-restraints excluded: chain H residue   94 THR
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain E residue   42 GLN
Chi-restraints excluded: chain E residue   67 GLN
Chi-restraints excluded: chain E residue   91 GLU
Chi-restraints excluded: chain G residue   85 SER
Chi-restraints excluded: chain G residue  103 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 117 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 14 optimal weight:    0.2980
   chunk 60 optimal weight:    8.9990
   chunk 96 optimal weight:    0.2980
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
M  67 GLN
J  79 GLN
K  79 GLN
L  79 GLN
F  79 GLN
A  63 GLN
A 114 GLN
E  67 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.125837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.112054 restraints weight = 12327.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.60
r_work: 0.3097 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.3615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10803  Z= 0.106
  Angle     :  0.518   5.772  14612  Z= 0.260
  Chirality :  0.038   0.118   1690
  Planarity :  0.003   0.031   1898
  Dihedral  :  4.671  17.395   1482
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 13.44 %
    Favored  : 84.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.22), residues: 1313
  helix:  1.51 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.10 (0.25), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  78 
 PHE   0.006   0.001   PHE M  36 
 TYR   0.008   0.001   TYR E 116 
 ARG   0.004   0.000   ARG H  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02731 (  572)
  hydrogen bonds       : angle       3.72571 ( 1638)
  covalent geometry    : bond        0.00242 (10803)
  covalent geometry    : angle       0.51805 (14612)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 313
  time to evaluate  : 1.312 
Fit side-chains
REVERT: I   31 ARG cc_start: 0.8411 (mtm110) cc_final: 0.8155 (mtm-85)
REVERT: I   60 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8484 (mt-10)
REVERT: J   27 MET cc_start: 0.9194 (mmm) cc_final: 0.8850 (mmt)
REVERT: K   27 MET cc_start: 0.9174 (mmm) cc_final: 0.8950 (mmt)
REVERT: H   42 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7698 (tm-30)
REVERT: H  103 LEU cc_start: 0.8925 (tt) cc_final: 0.8657 (mt)
REVERT: B   31 ARG cc_start: 0.8468 (mtm110) cc_final: 0.7629 (ttt-90)
REVERT: B   99 ASP cc_start: 0.8221 (m-30) cc_final: 0.7902 (m-30)
REVERT: B  119 LYS cc_start: 0.8313 (tttt) cc_final: 0.8058 (tmmt)
REVERT: F   31 ARG cc_start: 0.8533 (mtt180) cc_final: 0.8281 (mtm110)
REVERT: F  119 LYS cc_start: 0.8443 (tttt) cc_final: 0.7889 (ttpp)
REVERT: C   27 MET cc_start: 0.8836 (mmm) cc_final: 0.8353 (mmp)
REVERT: C  119 LYS cc_start: 0.8135 (tttt) cc_final: 0.7657 (tmmt)
REVERT: D   42 GLN cc_start: 0.8408 (tp-100) cc_final: 0.8129 (mm-40)
REVERT: A   27 MET cc_start: 0.8913 (mmm) cc_final: 0.8545 (mmp)
REVERT: A   42 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8106 (mm-40)
REVERT: A   52 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8159 (tt0)
REVERT: A   76 ASP cc_start: 0.8532 (m-30) cc_final: 0.8087 (m-30)
REVERT: E   32 ARG cc_start: 0.8410 (tpp-160) cc_final: 0.8080 (tpt170)
REVERT: E   42 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.7561 (tm-30)
REVERT: G  119 LYS cc_start: 0.8420 (tttt) cc_final: 0.7992 (ttpt)
  outliers start: 25
  outliers final: 15
  residues processed: 319
  average time/residue: 0.3849
  time to fit residues: 157.8792
Evaluate side-chains
  323 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 304
  time to evaluate  : 1.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   85 SER
Chi-restraints excluded: chain J residue   26 ASN
Chi-restraints excluded: chain J residue   94 THR
Chi-restraints excluded: chain J residue  103 LEU
Chi-restraints excluded: chain J residue  118 LEU
Chi-restraints excluded: chain K residue   94 THR
Chi-restraints excluded: chain H residue   42 GLN
Chi-restraints excluded: chain L residue  102 LEU
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain E residue   42 GLN
Chi-restraints excluded: chain E residue   52 GLU
Chi-restraints excluded: chain E residue   67 GLN
Chi-restraints excluded: chain E residue   91 GLU
Chi-restraints excluded: chain G residue   85 SER
Chi-restraints excluded: chain G residue   94 THR
Chi-restraints excluded: chain G residue  103 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 74 optimal weight:    0.0980
   chunk 26 optimal weight:    7.9990
   chunk 83 optimal weight:    4.9990
   chunk 88 optimal weight:    0.0170
   chunk 118 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0040
   chunk 46 optimal weight:    6.9990
   chunk 55 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.6234

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

Flipped N/Q/H residues before XYZ refinement:
I  79 GLN
J  79 GLN
K  79 GLN
L 114 GLN
E  67 GLN
** G  38 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 = 0.3435 r_free = 0.3435 target = 0.128034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.114529 restraints weight = 12272.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 1.59
r_work: 0.3127 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.3796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10803  Z= 0.087
  Angle     :  0.491   6.833  14612  Z= 0.245
  Chirality :  0.037   0.116   1690
  Planarity :  0.003   0.025   1898
  Dihedral  :  4.381  16.568   1482
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 14.41 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.23), residues: 1313
  helix:  2.03 (0.17), residues: 910
  sheet:  None (None), residues: 0
  loop : -1.10 (0.24), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F  78 
 PHE   0.005   0.001   PHE G  36 
 TYR   0.006   0.001   TYR E  58 
 ARG   0.004   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02451 (  572)
  hydrogen bonds       : angle       3.58945 ( 1638)
  covalent geometry    : bond        0.00194 (10803)
  covalent geometry    : angle       0.49099 (14612)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 309
  time to evaluate  : 1.222 
Fit side-chains
REVERT: I   31 ARG cc_start: 0.8430 (mtm110) cc_final: 0.8175 (mtm-85)
REVERT: K   27 MET cc_start: 0.9122 (mmm) cc_final: 0.8873 (mmt)
REVERT: K   67 GLN cc_start: 0.8097 (pt0) cc_final: 0.7761 (pt0)
REVERT: H   28 ARG cc_start: 0.8486 (ttm170) cc_final: 0.8125 (mtm-85)
REVERT: H   42 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7670 (tm-30)
REVERT: H  103 LEU cc_start: 0.8924 (tt) cc_final: 0.8646 (mt)
REVERT: L  119 LYS cc_start: 0.7908 (tttt) cc_final: 0.7425 (tmtt)
REVERT: B   31 ARG cc_start: 0.8432 (mtm110) cc_final: 0.7572 (ttt-90)
REVERT: B   67 GLN cc_start: 0.8261 (pt0) cc_final: 0.8056 (pt0)
REVERT: B   76 ASP cc_start: 0.8554 (m-30) cc_final: 0.7697 (m-30)
REVERT: B   99 ASP cc_start: 0.8179 (m-30) cc_final: 0.7843 (m-30)
REVERT: F   31 ARG cc_start: 0.8519 (mtt180) cc_final: 0.8270 (mtm110)
REVERT: F  119 LYS cc_start: 0.8387 (tttt) cc_final: 0.7816 (ttpp)
REVERT: C   27 MET cc_start: 0.8770 (mmm) cc_final: 0.8306 (mmp)
REVERT: C  119 LYS cc_start: 0.8046 (tttt) cc_final: 0.7598 (tmmt)
REVERT: D   42 GLN cc_start: 0.8388 (tp-100) cc_final: 0.8098 (mm-40)
REVERT: D   63 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8446 (tm-30)
REVERT: A   27 MET cc_start: 0.8913 (mmm) cc_final: 0.8505 (mmp)
REVERT: A   42 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8080 (mm-40)
REVERT: A   52 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8237 (tt0)
REVERT: E   32 ARG cc_start: 0.8403 (tpp-160) cc_final: 0.8071 (tpt170)
REVERT: E   42 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7517 (tm-30)
REVERT: G  119 LYS cc_start: 0.8305 (tttt) cc_final: 0.7873 (ttpt)
  outliers start: 21
  outliers final: 13
  residues processed: 316
  average time/residue: 0.3405
  time to fit residues: 138.9869
Evaluate side-chains
  320 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 303
  time to evaluate  : 2.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   85 SER
Chi-restraints excluded: chain J residue   26 ASN
Chi-restraints excluded: chain J residue   94 THR
Chi-restraints excluded: chain J residue  103 LEU
Chi-restraints excluded: chain J residue  118 LEU
Chi-restraints excluded: chain K residue   79 GLN
Chi-restraints excluded: chain K residue  102 LEU
Chi-restraints excluded: chain H residue   42 GLN
Chi-restraints excluded: chain H residue   91 GLU
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue   52 GLU
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain E residue   42 GLN
Chi-restraints excluded: chain E residue   52 GLU
Chi-restraints excluded: chain E residue   67 GLN
Chi-restraints excluded: chain E residue   91 GLU
Chi-restraints excluded: chain G residue   85 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 30 optimal weight:   10.0000
   chunk 41 optimal weight:    1.9990
   chunk 62 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9990
   chunk 78 optimal weight:    6.9990
   chunk 35 optimal weight:    0.7980
   chunk 109 optimal weight:    5.9990
   chunk 125 optimal weight:    0.9990
   overall best weight:    1.1588

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

Flipped N/Q/H residues before XYZ refinement:
J  79 GLN
K  79 GLN
F  67 GLN
F 120 GLN
A 114 GLN
G  38 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.126583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.112980 restraints weight = 12513.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 1.60
r_work: 0.3106 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.3891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10803  Z= 0.104
  Angle     :  0.505   6.962  14612  Z= 0.251
  Chirality :  0.038   0.124   1690
  Planarity :  0.003   0.030   1898
  Dihedral  :  4.331  16.505   1482
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 16.09 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.23), residues: 1313
  helix:  2.20 (0.18), residues: 910
  sheet:  None (None), residues: 0
  loop : -0.99 (0.24), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K  78 
 PHE   0.006   0.001   PHE G  36 
 TYR   0.008   0.002   TYR A  58 
 ARG   0.003   0.000   ARG D  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02541 (  572)
  hydrogen bonds       : angle       3.60830 ( 1638)
  covalent geometry    : bond        0.00245 (10803)
  covalent geometry    : angle       0.50513 (14612)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 307
  time to evaluate  : 1.170 
Fit side-chains
REVERT: I   31 ARG cc_start: 0.8444 (mtm110) cc_final: 0.8180 (mtm-85)
REVERT: I   60 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8519 (mt-10)
REVERT: K   27 MET cc_start: 0.9139 (mmm) cc_final: 0.8889 (mmt)
REVERT: H   42 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7686 (tm-30)
REVERT: H  103 LEU cc_start: 0.8962 (tt) cc_final: 0.8661 (mt)
REVERT: L  119 LYS cc_start: 0.7956 (tttt) cc_final: 0.7388 (tmtt)
REVERT: B   31 ARG cc_start: 0.8441 (mtm110) cc_final: 0.7590 (ttt-90)
REVERT: B   67 GLN cc_start: 0.8247 (pt0) cc_final: 0.8020 (pt0)
REVERT: B   99 ASP cc_start: 0.8108 (m-30) cc_final: 0.7745 (m-30)
REVERT: F   31 ARG cc_start: 0.8511 (mtt180) cc_final: 0.8270 (mtm110)
REVERT: F  119 LYS cc_start: 0.8487 (tttt) cc_final: 0.7988 (ttpp)
REVERT: C   27 MET cc_start: 0.8788 (mmm) cc_final: 0.8336 (mmp)
REVERT: C   32 ARG cc_start: 0.8720 (tpt170) cc_final: 0.8486 (tpt170)
REVERT: C  119 LYS cc_start: 0.8055 (tttt) cc_final: 0.7598 (tmmt)
REVERT: D   27 MET cc_start: 0.8365 (mmt) cc_final: 0.8113 (mmp)
REVERT: D   42 GLN cc_start: 0.8405 (tp-100) cc_final: 0.8113 (mm-40)
REVERT: D   63 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8447 (tm-30)
REVERT: A   27 MET cc_start: 0.8947 (mmm) cc_final: 0.8531 (mmp)
REVERT: E   32 ARG cc_start: 0.8412 (tpp-160) cc_final: 0.7972 (tpt170)
REVERT: E   42 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7453 (tm-30)
REVERT: G  119 LYS cc_start: 0.8395 (tttt) cc_final: 0.7998 (ttpt)
  outliers start: 20
  outliers final: 15
  residues processed: 313
  average time/residue: 0.2997
  time to fit residues: 122.2090
Evaluate side-chains
  315 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 298
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   85 SER
Chi-restraints excluded: chain J residue   26 ASN
Chi-restraints excluded: chain J residue   94 THR
Chi-restraints excluded: chain J residue  103 LEU
Chi-restraints excluded: chain J residue  118 LEU
Chi-restraints excluded: chain K residue  102 LEU
Chi-restraints excluded: chain H residue   42 GLN
Chi-restraints excluded: chain H residue   91 GLU
Chi-restraints excluded: chain L residue  102 LEU
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain E residue   42 GLN
Chi-restraints excluded: chain E residue   52 GLU
Chi-restraints excluded: chain E residue   91 GLU
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   85 SER
Chi-restraints excluded: chain G residue  103 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 114 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   chunk 72 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 42 optimal weight:    0.2980
   chunk 36 optimal weight:   10.0000
   chunk 58 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
I  79 GLN
J  79 GLN
K  79 GLN
L  79 GLN
F 120 GLN
D 114 GLN
A 114 GLN
E  67 GLN
** G  38 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 = 0.3386 r_free = 0.3386 target = 0.124033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.110308 restraints weight = 12636.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 1.61
r_work: 0.3073 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2922 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.3914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10803  Z= 0.139
  Angle     :  0.540   7.108  14612  Z= 0.266
  Chirality :  0.039   0.127   1690
  Planarity :  0.004   0.038   1898
  Dihedral  :  4.412  17.041   1482
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 16.36 %
    Favored  : 81.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.23), residues: 1313
  helix:  2.17 (0.18), residues: 910
  sheet:  None (None), residues: 0
  loop : -0.86 (0.25), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP H  78 
 PHE   0.012   0.001   PHE G  36 
 TYR   0.011   0.002   TYR A  58 
 ARG   0.003   0.000   ARG C  98 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02779 (  572)
  hydrogen bonds       : angle       3.65417 ( 1638)
  covalent geometry    : bond        0.00333 (10803)
  covalent geometry    : angle       0.53974 (14612)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  340 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 319
  time to evaluate  : 1.888 
Fit side-chains
REVERT: I   31 ARG cc_start: 0.8459 (mtm110) cc_final: 0.8198 (mtm-85)
REVERT: I   60 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8563 (mt-10)
REVERT: J   52 GLU cc_start: 0.8400 (tt0) cc_final: 0.8098 (tt0)
REVERT: K   27 MET cc_start: 0.9159 (mmm) cc_final: 0.8909 (mmt)
REVERT: H   42 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7663 (tm-30)
REVERT: H  103 LEU cc_start: 0.8972 (tt) cc_final: 0.8561 (mt)
REVERT: L  119 LYS cc_start: 0.8057 (tttt) cc_final: 0.7428 (tmtt)
REVERT: B   31 ARG cc_start: 0.8495 (mtm110) cc_final: 0.7646 (ttt-90)
REVERT: B   99 ASP cc_start: 0.8135 (m-30) cc_final: 0.7720 (m-30)
REVERT: B  119 LYS cc_start: 0.8366 (tttt) cc_final: 0.8017 (ttpp)
REVERT: F   31 ARG cc_start: 0.8561 (mtt180) cc_final: 0.8271 (mtm-85)
REVERT: F  119 LYS cc_start: 0.8559 (tttt) cc_final: 0.8188 (ttpp)
REVERT: C   27 MET cc_start: 0.8853 (mmm) cc_final: 0.8360 (mmp)
REVERT: C  119 LYS cc_start: 0.8112 (tttt) cc_final: 0.7590 (tmmt)
REVERT: D   42 GLN cc_start: 0.8424 (tp-100) cc_final: 0.8143 (mm-40)
REVERT: D   63 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8418 (tm-30)
REVERT: A   27 MET cc_start: 0.8964 (mmm) cc_final: 0.8563 (mmp)
REVERT: E   32 ARG cc_start: 0.8394 (tpp-160) cc_final: 0.7970 (tpt170)
REVERT: E   42 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7428 (tm-30)
REVERT: G  119 LYS cc_start: 0.8464 (tttt) cc_final: 0.7985 (ttpt)
  outliers start: 21
  outliers final: 17
  residues processed: 327
  average time/residue: 0.3822
  time to fit residues: 162.1078
Evaluate side-chains
  331 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 312
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   85 SER
Chi-restraints excluded: chain I residue  118 LEU
Chi-restraints excluded: chain J residue   26 ASN
Chi-restraints excluded: chain J residue   94 THR
Chi-restraints excluded: chain J residue  103 LEU
Chi-restraints excluded: chain J residue  118 LEU
Chi-restraints excluded: chain K residue   79 GLN
Chi-restraints excluded: chain K residue  102 LEU
Chi-restraints excluded: chain H residue   42 GLN
Chi-restraints excluded: chain H residue   91 GLU
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain E residue   42 GLN
Chi-restraints excluded: chain E residue   52 GLU
Chi-restraints excluded: chain E residue   67 GLN
Chi-restraints excluded: chain E residue   91 GLU
Chi-restraints excluded: chain G residue   85 SER
Chi-restraints excluded: chain G residue   94 THR
Chi-restraints excluded: chain G residue  103 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 62 optimal weight:    8.9990
   chunk 125 optimal weight:    0.6980
   chunk 99 optimal weight:    4.9990
   chunk 67 optimal weight:    0.7980
   chunk 89 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0980
   chunk 14 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 102 optimal weight:    4.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
I  79 GLN
J  79 GLN
L  79 GLN
C  38 ASN
E  67 GLN
G  38 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.126771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.113214 restraints weight = 12473.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 1.62
r_work: 0.3114 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.4067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10803  Z= 0.088
  Angle     :  0.495   7.205  14612  Z= 0.245
  Chirality :  0.037   0.119   1690
  Planarity :  0.003   0.027   1898
  Dihedral  :  4.191  17.120   1482
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 16.62 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.23), residues: 1313
  helix:  2.41 (0.18), residues: 910
  sheet:  None (None), residues: 0
  loop : -0.84 (0.25), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP K  78 
 PHE   0.004   0.001   PHE M  36 
 TYR   0.006   0.001   TYR E  58 
 ARG   0.003   0.000   ARG H  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02399 (  572)
  hydrogen bonds       : angle       3.54892 ( 1638)
  covalent geometry    : bond        0.00199 (10803)
  covalent geometry    : angle       0.49519 (14612)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 321
  time to evaluate  : 2.302 
Fit side-chains
   revert: symmetry clash
REVERT: I   31 ARG cc_start: 0.8427 (mtm110) cc_final: 0.8166 (mtm-85)
REVERT: J   52 GLU cc_start: 0.8438 (tt0) cc_final: 0.8153 (tt0)
REVERT: K   27 MET cc_start: 0.9116 (mmm) cc_final: 0.8866 (mmt)
REVERT: H   28 ARG cc_start: 0.8389 (mtm-85) cc_final: 0.8044 (mtm-85)
REVERT: H   42 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7597 (tm-30)
REVERT: H  103 LEU cc_start: 0.8931 (tt) cc_final: 0.8537 (mt)
REVERT: L  119 LYS cc_start: 0.7898 (tttt) cc_final: 0.7434 (tmtt)
REVERT: B   31 ARG cc_start: 0.8416 (mtm110) cc_final: 0.7568 (ttt-90)
REVERT: B   67 GLN cc_start: 0.8276 (pt0) cc_final: 0.8021 (pt0)
REVERT: B   99 ASP cc_start: 0.7961 (m-30) cc_final: 0.7585 (m-30)
REVERT: F   31 ARG cc_start: 0.8426 (mtt180) cc_final: 0.8220 (mtm-85)
REVERT: F  119 LYS cc_start: 0.8499 (tttt) cc_final: 0.8161 (ttpp)
REVERT: C   27 MET cc_start: 0.8770 (mmm) cc_final: 0.8299 (mmp)
REVERT: C  119 LYS cc_start: 0.8091 (tttt) cc_final: 0.7611 (tmmt)
REVERT: D   31 ARG cc_start: 0.8558 (mtm180) cc_final: 0.8356 (mtm-85)
REVERT: D   42 GLN cc_start: 0.8479 (tp-100) cc_final: 0.8076 (mm-40)
REVERT: D   63 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8402 (tm-30)
REVERT: A   27 MET cc_start: 0.8991 (mmm) cc_final: 0.8585 (mmp)
REVERT: A   67 GLN cc_start: 0.8502 (pt0) cc_final: 0.8266 (pt0)
REVERT: E   32 ARG cc_start: 0.8384 (tpp-160) cc_final: 0.7957 (tpt170)
REVERT: E   42 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7375 (tm-30)
REVERT: G  119 LYS cc_start: 0.8416 (tttt) cc_final: 0.7779 (tttm)
  outliers start: 23
  outliers final: 15
  residues processed: 329
  average time/residue: 0.3741
  time to fit residues: 160.7653
Evaluate side-chains
  326 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 309
  time to evaluate  : 2.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   85 SER
Chi-restraints excluded: chain J residue   26 ASN
Chi-restraints excluded: chain J residue  103 LEU
Chi-restraints excluded: chain J residue  118 LEU
Chi-restraints excluded: chain H residue   42 GLN
Chi-restraints excluded: chain H residue  104 GLU
Chi-restraints excluded: chain H residue  117 ILE
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain E residue   42 GLN
Chi-restraints excluded: chain E residue   52 GLU
Chi-restraints excluded: chain E residue   67 GLN
Chi-restraints excluded: chain E residue   91 GLU
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue   85 SER
Chi-restraints excluded: chain G residue   94 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 51 optimal weight:    7.9990
   chunk 126 optimal weight:    6.9990
   chunk 86 optimal weight:    0.2980
   chunk 111 optimal weight:    2.9990
   chunk 60 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 106 optimal weight:    6.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
I  67 GLN
I  79 GLN
** J  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  79 GLN
K  79 GLN
L 114 GLN
C  38 ASN
** D  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 114 GLN
E  67 GLN
G  38 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.126391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.112998 restraints weight = 12565.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 1.61
r_work: 0.3102 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.4124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10803  Z= 0.102
  Angle     :  0.512   7.310  14612  Z= 0.252
  Chirality :  0.037   0.123   1690
  Planarity :  0.003   0.037   1898
  Dihedral  :  4.156  17.421   1482
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 16.89 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.23), residues: 1313
  helix:  2.41 (0.18), residues: 910
  sheet:  None (None), residues: 0
  loop : -0.79 (0.25), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  78 
 PHE   0.005   0.001   PHE M  36 
 TYR   0.007   0.001   TYR A  58 
 ARG   0.008   0.000   ARG H  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02477 (  572)
  hydrogen bonds       : angle       3.55237 ( 1638)
  covalent geometry    : bond        0.00239 (10803)
  covalent geometry    : angle       0.51250 (14612)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 309
  time to evaluate  : 1.978 
Fit side-chains
   revert: symmetry clash
REVERT: I   31 ARG cc_start: 0.8452 (mtm110) cc_final: 0.8194 (mtm-85)
REVERT: J   52 GLU cc_start: 0.8396 (tt0) cc_final: 0.8076 (tt0)
REVERT: K   27 MET cc_start: 0.9136 (mmm) cc_final: 0.8905 (mmt)
REVERT: H   28 ARG cc_start: 0.8369 (mtm-85) cc_final: 0.8024 (mtm-85)
REVERT: H   42 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7591 (tm-30)
REVERT: H  103 LEU cc_start: 0.8946 (tt) cc_final: 0.8558 (mt)
REVERT: L  119 LYS cc_start: 0.7984 (tttt) cc_final: 0.7307 (tmtt)
REVERT: B   31 ARG cc_start: 0.8422 (mtm110) cc_final: 0.7572 (ttt-90)
REVERT: B   67 GLN cc_start: 0.8269 (pt0) cc_final: 0.8010 (pt0)
REVERT: B   99 ASP cc_start: 0.7966 (m-30) cc_final: 0.7550 (m-30)
REVERT: F   27 MET cc_start: 0.8914 (mmt) cc_final: 0.8295 (mmt)
REVERT: C   27 MET cc_start: 0.8813 (mmm) cc_final: 0.8335 (mmp)
REVERT: C  119 LYS cc_start: 0.8130 (tttt) cc_final: 0.7630 (ttpt)
REVERT: D   42 GLN cc_start: 0.8481 (tp-100) cc_final: 0.8074 (mm-40)
REVERT: D   63 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8399 (tm-30)
REVERT: D  114 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8194 (mm110)
REVERT: A   27 MET cc_start: 0.8980 (mmm) cc_final: 0.8579 (mmp)
REVERT: E   32 ARG cc_start: 0.8410 (tpp-160) cc_final: 0.8024 (tpt170)
REVERT: E   42 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.7420 (tm-30)
REVERT: G  119 LYS cc_start: 0.8459 (tttt) cc_final: 0.7831 (tttm)
  outliers start: 20
  outliers final: 16
  residues processed: 315
  average time/residue: 0.3000
  time to fit residues: 123.5694
Evaluate side-chains
  326 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 308
  time to evaluate  : 1.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   85 SER
Chi-restraints excluded: chain J residue   26 ASN
Chi-restraints excluded: chain J residue  103 LEU
Chi-restraints excluded: chain J residue  118 LEU
Chi-restraints excluded: chain K residue   79 GLN
Chi-restraints excluded: chain H residue   42 GLN
Chi-restraints excluded: chain H residue  104 GLU
Chi-restraints excluded: chain H residue  117 ILE
Chi-restraints excluded: chain L residue   54 MET
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain E residue   42 GLN
Chi-restraints excluded: chain E residue   52 GLU
Chi-restraints excluded: chain E residue   67 GLN
Chi-restraints excluded: chain E residue   91 GLU
Chi-restraints excluded: chain G residue   85 SER
Chi-restraints excluded: chain G residue   94 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 62 optimal weight:    7.9990
   chunk 58 optimal weight:    9.9990
   chunk 99 optimal weight:    0.9990
   chunk 111 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 41 optimal weight:    4.9990
   chunk 122 optimal weight:    4.9990
   chunk 106 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
I  67 GLN
J  63 GLN
J  67 GLN
K  79 GLN
C  38 ASN
** D  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  67 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.124246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.110260 restraints weight = 12540.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 1.61
r_work: 0.3069 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.4108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10803  Z= 0.159
  Angle     :  0.566   7.051  14612  Z= 0.279
  Chirality :  0.040   0.135   1690
  Planarity :  0.004   0.037   1898
  Dihedral  :  4.318  15.333   1482
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 17.24 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.23), residues: 1313
  helix:  2.21 (0.18), residues: 910
  sheet:  None (None), residues: 0
  loop : -0.71 (0.26), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K  78 
 PHE   0.030   0.001   PHE C  36 
 TYR   0.012   0.002   TYR A  58 
 ARG   0.009   0.001   ARG E  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02865 (  572)
  hydrogen bonds       : angle       3.65431 ( 1638)
  covalent geometry    : bond        0.00382 (10803)
  covalent geometry    : angle       0.56558 (14612)

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

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

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2626 Ramachandran restraints generated.
    1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 318
  time to evaluate  : 1.297 
Fit side-chains
REVERT: I   31 ARG cc_start: 0.8453 (mtm110) cc_final: 0.8189 (mtm-85)
REVERT: J   88 ARG cc_start: 0.8866 (tpt170) cc_final: 0.8631 (tpt170)
REVERT: K   27 MET cc_start: 0.9126 (mmm) cc_final: 0.8884 (mmt)
REVERT: K  120 GLN cc_start: 0.6967 (mm-40) cc_final: 0.6693 (mm-40)
REVERT: H   28 ARG cc_start: 0.8429 (mtm-85) cc_final: 0.8099 (mtm-85)
REVERT: H   42 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7675 (tm-30)
REVERT: H  103 LEU cc_start: 0.8976 (tt) cc_final: 0.8587 (mt)
REVERT: L  119 LYS cc_start: 0.7964 (tttt) cc_final: 0.7337 (tmtt)
REVERT: B   31 ARG cc_start: 0.8467 (mtm110) cc_final: 0.7650 (ttt-90)
REVERT: B   99 ASP cc_start: 0.8012 (m-30) cc_final: 0.7562 (m-30)
REVERT: B  119 LYS cc_start: 0.8391 (tttt) cc_final: 0.8069 (ttmt)
REVERT: C   27 MET cc_start: 0.8823 (mmm) cc_final: 0.8348 (mmp)
REVERT: C  119 LYS cc_start: 0.8212 (tttt) cc_final: 0.7682 (ttpt)
REVERT: D   42 GLN cc_start: 0.8468 (tp-100) cc_final: 0.8068 (mm-40)
REVERT: D   63 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8482 (tm-30)
REVERT: D  114 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8197 (mm-40)
REVERT: A   27 MET cc_start: 0.8965 (mmm) cc_final: 0.8571 (mmp)
REVERT: E   32 ARG cc_start: 0.8467 (tpp-160) cc_final: 0.8092 (tpt170)
REVERT: E   42 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.7450 (tm-30)
REVERT: G  119 LYS cc_start: 0.8495 (tttt) cc_final: 0.7919 (tttm)
  outliers start: 18
  outliers final: 15
  residues processed: 323
  average time/residue: 0.3248
  time to fit residues: 135.6282
Evaluate side-chains
  334 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 317
  time to evaluate  : 1.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue   85 SER
Chi-restraints excluded: chain J residue   26 ASN
Chi-restraints excluded: chain J residue   94 THR
Chi-restraints excluded: chain J residue  103 LEU
Chi-restraints excluded: chain J residue  118 LEU
Chi-restraints excluded: chain H residue   42 GLN
Chi-restraints excluded: chain H residue  117 ILE
Chi-restraints excluded: chain L residue   54 MET
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain C residue   38 ASN
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain E residue   42 GLN
Chi-restraints excluded: chain E residue   52 GLU
Chi-restraints excluded: chain E residue   67 GLN
Chi-restraints excluded: chain E residue   91 GLU
Chi-restraints excluded: chain G residue   85 SER
Chi-restraints excluded: chain G residue   94 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 107 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 78 optimal weight:    0.0670
   chunk 9 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
I  67 GLN
I  79 GLN
J  63 GLN
K  79 GLN
C  38 ASN
** D  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  67 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.127333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.114003 restraints weight = 12357.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 1.58
r_work: 0.3126 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.4218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10803  Z= 0.097
  Angle     :  0.517   7.228  14612  Z= 0.255
  Chirality :  0.037   0.133   1690
  Planarity :  0.003   0.037   1898
  Dihedral  :  4.174  15.657   1482
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 16.98 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.23), residues: 1313
  helix:  2.37 (0.18), residues: 910
  sheet:  None (None), residues: 0
  loop : -0.70 (0.26), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F  78 
 PHE   0.019   0.001   PHE C  36 
 TYR   0.006   0.001   TYR E  58 
 ARG   0.008   0.000   ARG E  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02496 (  572)
  hydrogen bonds       : angle       3.58152 ( 1638)
  covalent geometry    : bond        0.00224 (10803)
  covalent geometry    : angle       0.51730 (14612)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6346.14 seconds
wall clock time: 113 minutes 54.58 seconds (6834.58 seconds total)