Starting phenix.real_space_refine
on Tue Jun 17 08:40:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k63_22687/06_2025/7k63_22687.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k63_22687/06_2025/7k63_22687.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k63_22687/06_2025/7k63_22687.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k63_22687/06_2025/7k63_22687.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k63_22687/06_2025/7k63_22687.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k63_22687/06_2025/7k63_22687.cif"
  }
  resolution = 3.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2242 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P     394      5.49       5
     S      32      5.16       5
     C   10288      2.51       5
     N    3355      2.21       5
     O    4261      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 67 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 18330
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 799
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 799
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 4015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 4015
          Classifications: {'DNA': 197}
          Link IDs: {'rna3p': 196}
    Chain: "J"
      Number of atoms: 4062
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 4062
          Classifications: {'DNA': 197}
          Link IDs: {'rna3p': 196}
    Chain: "M"
      Number of atoms: 1777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1777
          Classifications: {'peptide': 227}
          Link IDs: {'PTRANS': 10, 'TRANS': 216}
          Chain breaks: 1
    Chain: "N"
      Number of atoms: 1777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1777
          Classifications: {'peptide': 227}
          Link IDs: {'PTRANS': 10, 'TRANS': 216}
          Chain breaks: 1
    Chain: "U"
      Number of atoms: 607
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 607
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
  Time building chain proxies: 10.11, per 1000 atoms: 0.55
  Number of scatterers: 18330
  At special positions: 0
  Unit cell: (131.62, 123.643, 196.766, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      32     16.00
     P     394     15.00
     O    4261      8.00
     N    3355      7.00
     C   10288      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: 4.27
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2410

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 23 sheets defined
      48.8% alpha, 20.6% beta
      197 base pairs and 334 stacking pairs defined.
    Time for finding SS restraints: 8.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.559A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 124
      removed outlier: 3.950A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 4.156A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.602A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.567A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.255A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.540A  pdb=" N   GLN H  47 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 124
      removed outlier: 3.899A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 98 through 102
    Processing helix  chain 'M' and resid 177 through 179
      No H-bonds generated for 'chain 'M' and resid 177 through 179'
    Processing helix  chain 'M' and resid 211 through 214
      removed outlier: 3.709A  pdb=" N   LYS M 214 " --> pdb=" O   GLU M 211 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'M' and resid 211 through 214'
    Processing helix  chain 'M' and resid 236 through 240
    Processing helix  chain 'N' and resid 98 through 102
      removed outlier: 3.514A  pdb=" N   THR N 102 " --> pdb=" O   SER N  99 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 177 through 179
      No H-bonds generated for 'chain 'N' and resid 177 through 179'
    Processing helix  chain 'N' and resid 211 through 214
      removed outlier: 3.717A  pdb=" N   LYS N 214 " --> pdb=" O   GLU N 211 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 211 through 214'
    Processing helix  chain 'N' and resid 236 through 240
    Processing helix  chain 'U' and resid 45 through 59
      removed outlier: 3.800A  pdb=" N   ARG U  56 " --> pdb=" O   VAL U  52 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 66 through 74
    Processing helix  chain 'U' and resid 83 through 98
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.869A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.067A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.486A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.632A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 6.996A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'M' and resid 23 through 25
      removed outlier: 3.699A  pdb=" N   ASP M  89 " --> pdb=" O   SER M  86 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   SER M  91 " --> pdb=" O   SER M  84 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32
      removed outlier: 3.849A  pdb=" N   GLU M 124 " --> pdb=" O   MET M  30 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ALA M  32 " --> pdb=" O   GLU M 124 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   LEU M  52 " --> pdb=" O   TYR M  68 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   TYR M  68 " --> pdb=" O   LEU M  52 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   TRP M  54 " --> pdb=" O   LEU M  66 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'M' and resid 29 through 32
      removed outlier: 3.849A  pdb=" N   GLU M 124 " --> pdb=" O   MET M  30 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ALA M  32 " --> pdb=" O   GLU M 124 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'M' and resid 152 through 155
    Processing sheet with id=AB6, first strand: chain 'M' and resid 159 through 161
      removed outlier: 6.555A  pdb=" N   ILE M 183 " --> pdb=" O   TYR M 199 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   TYR M 199 " --> pdb=" O   ILE M 183 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   TRP M 185 " --> pdb=" O   ILE M 197 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'M' and resid 159 through 161
      removed outlier: 3.996A  pdb=" N   TYR M 258 " --> pdb=" O   ARG M 247 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'N' and resid 23 through 25
    Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 32
      removed outlier: 6.757A  pdb=" N   LEU N  52 " --> pdb=" O   TYR N  68 " (cutoff:3.500A)
      removed outlier: 4.942A  pdb=" N   TYR N  68 " --> pdb=" O   LEU N  52 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   TRP N  54 " --> pdb=" O   LEU N  66 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'N' and resid 29 through 32
    Processing sheet with id=AC2, first strand: chain 'N' and resid 152 through 155
    Processing sheet with id=AC3, first strand: chain 'N' and resid 159 through 161
      removed outlier: 6.615A  pdb=" N   ILE N 183 " --> pdb=" O   TYR N 199 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   TYR N 199 " --> pdb=" O   ILE N 183 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   TRP N 185 " --> pdb=" O   ILE N 197 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'N' and resid 159 through 161
      removed outlier: 3.944A  pdb=" N   TYR N 258 " --> pdb=" O   ARG N 247 " (cutoff:3.500A)
      removed outlier: 8.168A  pdb=" N   SER N 249 " --> pdb=" O   LEU N 256 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   LEU N 256 " --> pdb=" O   SER N 249 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'U' and resid 64 through 65

    617 hydrogen bonds defined for protein.
    1692 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      510 hydrogen bonds
      1020 hydrogen bond angles
      0 basepair planarities
      197 basepair parallelities
      334 stacking parallelities
  Total time for adding SS restraints: 7.72

  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:
        1.21 -     1.33: 3676
        1.33 -     1.45: 6202
        1.45 -     1.57: 8770
        1.57 -     1.69: 786
        1.69 -     1.81: 52
  Bond restraints: 19486
  Sorted by residual:
  bond pdb=" C3'  DT J 153 "
       pdb=" O3'  DT J 153 "
    ideal  model  delta    sigma   weight residual
    1.422  1.459 -0.037 3.00e-02 1.11e+03 1.51e+00
  bond pdb=" CA  GLY U  59 "
       pdb=" C   GLY U  59 "
    ideal  model  delta    sigma   weight residual
    1.514  1.531 -0.017 1.41e-02 5.03e+03 1.48e+00
  bond pdb=" N   GLY D  53 "
       pdb=" CA  GLY D  53 "
    ideal  model  delta    sigma   weight residual
    1.442  1.450 -0.009 7.70e-03 1.69e+04 1.26e+00
  bond pdb=" C3'  DG J 119 "
       pdb=" O3'  DG J 119 "
    ideal  model  delta    sigma   weight residual
    1.422  1.455 -0.033 3.00e-02 1.11e+03 1.22e+00
  bond pdb=" CA  GLU U  60 "
       pdb=" C   GLU U  60 "
    ideal  model  delta    sigma   weight residual
    1.532  1.522  0.010 9.60e-03 1.09e+04 1.19e+00
  ... (remaining 19481 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 26867
        1.42 -     2.85: 1060
        2.85 -     4.27: 73
        4.27 -     5.69: 18
        5.69 -     7.12: 5
  Bond angle restraints: 28023
  Sorted by residual:
  angle pdb=" CA  GLY D  53 "
        pdb=" C   GLY D  53 "
        pdb=" N   ILE D  54 "
      ideal   model   delta    sigma   weight residual
     114.65  118.04   -3.39 9.20e-01 1.18e+00 1.36e+01
  angle pdb=" CB  LYS C  74 "
        pdb=" CG  LYS C  74 "
        pdb=" CD  LYS C  74 "
      ideal   model   delta    sigma   weight residual
     111.30  118.42   -7.12 2.30e+00 1.89e-01 9.57e+00
  angle pdb=" C3'  DC I  72 "
        pdb=" C2'  DC I  72 "
        pdb=" C1'  DC I  72 "
      ideal   model   delta    sigma   weight residual
     101.60   97.87    3.73 1.50e+00 4.44e-01 6.17e+00
  angle pdb=" C   TYR M  69 "
        pdb=" N   ALA M  70 "
        pdb=" CA  ALA M  70 "
      ideal   model   delta    sigma   weight residual
     121.54  126.04   -4.50 1.91e+00 2.74e-01 5.56e+00
  angle pdb=" N   ARG B  23 "
        pdb=" CA  ARG B  23 "
        pdb=" C   ARG B  23 "
      ideal   model   delta    sigma   weight residual
     110.80  115.67   -4.87 2.13e+00 2.20e-01 5.23e+00
  ... (remaining 28018 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.60: 8763
       35.60 -    71.19: 1849
       71.19 -   106.79: 24
      106.79 -   142.38: 0
      142.38 -   177.98: 2
  Dihedral angle restraints: 10638
    sinusoidal: 6875
      harmonic: 3763
  Sorted by residual:
  dihedral pdb=" C4'  DT J 153 "
           pdb=" C3'  DT J 153 "
           pdb=" O3'  DT J 153 "
           pdb=" P    DC J 154 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   42.02  177.98     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CA  LEU A  82 "
           pdb=" C   LEU A  82 "
           pdb=" N   ARG A  83 "
           pdb=" CA  ARG A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.67   19.33     0      5.00e+00 4.00e-02 1.49e+01
  dihedral pdb=" C4'  DG J 119 "
           pdb=" C3'  DG J 119 "
           pdb=" O3'  DG J 119 "
           pdb=" P    DG J 120 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   70.16  149.84     1      3.50e+01 8.16e-04 1.46e+01
  ... (remaining 10635 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 2015
       0.031 -    0.062: 855
       0.062 -    0.093: 194
       0.093 -    0.125: 84
       0.125 -    0.156: 6
  Chirality restraints: 3154
  Sorted by residual:
  chirality pdb=" CB  THR M 102 "
            pdb=" CA  THR M 102 "
            pdb=" OG1 THR M 102 "
            pdb=" CG2 THR M 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.16 2.00e-01 2.50e+01 6.07e-01
  chirality pdb=" CA  ILE N  67 "
            pdb=" N   ILE N  67 "
            pdb=" C   ILE N  67 "
            pdb=" CB  ILE N  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.95e-01
  chirality pdb=" CA  ILE M  94 "
            pdb=" N   ILE M  94 "
            pdb=" C   ILE M  94 "
            pdb=" CB  ILE M  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.69e-01
  ... (remaining 3151 not shown)

  Planarity restraints: 2171
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET M 169 "   -0.038 5.00e-02 4.00e+02   5.73e-02 5.25e+00
        pdb=" N   PRO M 170 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO M 170 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO M 170 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 102 "    0.034 5.00e-02 4.00e+02   5.15e-02 4.24e+00
        pdb=" N   PRO D 103 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H 102 "   -0.027 5.00e-02 4.00e+02   4.12e-02 2.71e+00
        pdb=" N   PRO H 103 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO H 103 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO H 103 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 2168 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 861
        2.71 -     3.25: 16531
        3.25 -     3.80: 35102
        3.80 -     4.35: 44424
        4.35 -     4.90: 64273
  Nonbonded interactions: 161191
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D  90 "
            pdb=" OE1 GLU D  93 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OE1 GLU C  92 "
            pdb=" NH1 ARG M 251 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH1 ARG E 131 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" OE1 GLN M 184 "
            pdb=" NE1 TRP M 196 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" OE1 GLU D  71 "
            pdb=" NZ  LYS F  91 "
     model   vdw
     2.251 3.120
  ... (remaining 161186 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'M'
  selection = chain 'N'
}

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:             1.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.110
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.720
  Check model and map are aligned:         0.130
  Set scattering table:                    0.200
  Process input model:                     46.610
  Find NCS groups from input model:        0.430
  Set up NCS constraints:                  0.090
  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:             0.010
  Load rotamer database and sin/cos tables:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
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      :  0.004   0.041  19486  Z= 0.200
  Angle     :  0.621   7.116  28023  Z= 0.377
  Chirality :  0.037   0.156   3154
  Planarity :  0.004   0.057   2171
  Dihedral  : 26.716 177.979   8228
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.00 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.23), residues: 1272
  helix:  1.53 (0.21), residues: 592
  sheet:  0.23 (0.33), residues: 238
  loop : -0.18 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP M 196 
 HIS   0.005   0.001   HIS M 110 
 PHE   0.013   0.002   PHE C  25 
 TYR   0.022   0.002   TYR G  50 
 ARG   0.009   0.001   ARG H  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09742 ( 1103)
  hydrogen bonds       : angle       4.53669 ( 2712)
  covalent geometry    : bond        0.00436 (19486)
  covalent geometry    : angle       0.62113 (28023)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 280
  time to evaluate  : 1.345 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7366 (mm-30)
REVERT: C   71 ARG cc_start: 0.8219 (ttp-170) cc_final: 0.7953 (ttm-80)
REVERT: D   59 MET cc_start: 0.8102 (tpt) cc_final: 0.7660 (tpt)
REVERT: D   86 ARG cc_start: 0.8279 (mtp85) cc_final: 0.8036 (mmt-90)
REVERT: E   60 LEU cc_start: 0.8527 (mt) cc_final: 0.8224 (mt)
REVERT: F   55 ARG cc_start: 0.8681 (mtt90) cc_final: 0.8464 (mtm-85)
REVERT: F   79 LYS cc_start: 0.8084 (mttp) cc_final: 0.7858 (mttp)
REVERT: F   85 ASP cc_start: 0.7515 (m-30) cc_final: 0.7300 (m-30)
REVERT: G   73 ASN cc_start: 0.7897 (t0) cc_final: 0.7286 (t0)
REVERT: H   83 TYR cc_start: 0.8482 (m-10) cc_final: 0.8188 (m-10)
REVERT: M   68 TYR cc_start: 0.8352 (p90) cc_final: 0.8068 (p90)
REVERT: M  155 GLN cc_start: 0.7442 (tt0) cc_final: 0.7188 (tt0)
REVERT: U   70 TYR cc_start: 0.8753 (t80) cc_final: 0.8436 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 280
  average time/residue: 0.4032
  time to fit residues: 155.9790
Evaluate side-chains
  237 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 1.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 135 optimal weight:    0.7980
   chunk 122 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 82 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 126 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 76 optimal weight:    4.9990
   chunk 93 optimal weight:   10.0000
   chunk 146 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  24 GLN
C 104 GLN
D  47 GLN
E 125 GLN
F  25 ASN
F  27 GLN
G  24 GLN
G 110 ASN
N  95 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.155122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.110857 restraints weight = 26363.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 1.31
r_work: 0.3262 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.1118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  19486  Z= 0.157
  Angle     :  0.560   6.466  28023  Z= 0.333
  Chirality :  0.035   0.148   3154
  Planarity :  0.004   0.055   2171
  Dihedral  : 29.688 179.099   5718
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  :  6.17 %
    Favored  : 92.29 %
  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:  1.49 (0.23), residues: 1272
  helix:  2.12 (0.21), residues: 592
  sheet:  0.73 (0.35), residues: 214
  loop : -0.33 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP M 196 
 HIS   0.004   0.001   HIS M  31 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.013   0.001   TYR G  50 
 ARG   0.007   0.000   ARG U  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03440 ( 1103)
  hydrogen bonds       : angle       3.45533 ( 2712)
  covalent geometry    : bond        0.00342 (19486)
  covalent geometry    : angle       0.55975 (28023)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 254
  time to evaluate  : 1.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   26 ILE cc_start: 0.8302 (tp) cc_final: 0.7947 (tp)
REVERT: C   64 GLU cc_start: 0.8071 (tt0) cc_final: 0.7799 (tt0)
REVERT: D   86 ARG cc_start: 0.8664 (mtp85) cc_final: 0.8442 (mmt-90)
REVERT: F   85 ASP cc_start: 0.7709 (m-30) cc_final: 0.7422 (m-30)
REVERT: G   73 ASN cc_start: 0.8041 (t0) cc_final: 0.7452 (t0)
REVERT: H   83 TYR cc_start: 0.8851 (m-10) cc_final: 0.8470 (m-10)
REVERT: M  155 GLN cc_start: 0.7673 (tt0) cc_final: 0.7376 (tt0)
REVERT: N   38 VAL cc_start: 0.8148 (t) cc_final: 0.7714 (t)
  outliers start: 17
  outliers final: 12
  residues processed: 261
  average time/residue: 0.4111
  time to fit residues: 147.4400
Evaluate side-chains
  239 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 227
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain M residue  238 GLU
Chi-restraints excluded: chain N residue  191 ARG
Chi-restraints excluded: chain N residue  264 SER
Chi-restraints excluded: chain U residue   86 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 109 optimal weight:   20.0000
   chunk 19 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 114 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9990
   chunk 85 optimal weight:    3.9990
   chunk 94 optimal weight:    5.9990
   chunk 149 optimal weight:    3.9990
   chunk 148 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 HIS
B  93 GLN
C 104 GLN
D  47 GLN
E  68 GLN
E 125 GLN
M 110 HIS
U 103 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.150488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.105316 restraints weight = 26182.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 1.32
r_work: 0.3176 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3029 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  19486  Z= 0.267
  Angle     :  0.610   6.189  28023  Z= 0.356
  Chirality :  0.039   0.146   3154
  Planarity :  0.005   0.056   2171
  Dihedral  : 30.122 176.680   5718
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  9.25 %
    Favored  : 88.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.23), residues: 1272
  helix:  1.89 (0.21), residues: 592
  sheet:  0.31 (0.34), residues: 240
  loop : -0.37 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP N 185 
 HIS   0.007   0.001   HIS M 110 
 PHE   0.015   0.002   PHE C  25 
 TYR   0.023   0.002   TYR U  90 
 ARG   0.007   0.001   ARG U  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04228 ( 1103)
  hydrogen bonds       : angle       3.50148 ( 2712)
  covalent geometry    : bond        0.00608 (19486)
  covalent geometry    : angle       0.60998 (28023)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 240
  time to evaluate  : 1.438 
Fit side-chains
REVERT: B   26 ILE cc_start: 0.8636 (tp) cc_final: 0.8338 (tp)
REVERT: C   64 GLU cc_start: 0.8209 (tt0) cc_final: 0.8002 (tt0)
REVERT: G   73 ASN cc_start: 0.8061 (t0) cc_final: 0.7477 (t0)
REVERT: H   83 TYR cc_start: 0.8705 (m-10) cc_final: 0.8300 (m-10)
REVERT: M   61 LYS cc_start: 0.8294 (mppt) cc_final: 0.8007 (mmtm)
REVERT: N   38 VAL cc_start: 0.7918 (t) cc_final: 0.7696 (t)
REVERT: N  101 ASP cc_start: 0.7522 (m-30) cc_final: 0.6874 (m-30)
REVERT: U  114 LYS cc_start: 0.8179 (ttpt) cc_final: 0.7629 (ttpp)
  outliers start: 26
  outliers final: 23
  residues processed: 250
  average time/residue: 0.3790
  time to fit residues: 133.4074
Evaluate side-chains
  240 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 217
  time to evaluate  : 1.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  116 LYS
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain M residue  162 GLU
Chi-restraints excluded: chain M residue  165 THR
Chi-restraints excluded: chain M residue  177 THR
Chi-restraints excluded: chain M residue  220 THR
Chi-restraints excluded: chain M residue  238 GLU
Chi-restraints excluded: chain N residue   91 SER
Chi-restraints excluded: chain N residue  191 ARG
Chi-restraints excluded: chain N residue  264 SER
Chi-restraints excluded: chain U residue   52 VAL
Chi-restraints excluded: chain U residue   86 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 153 optimal weight:    1.9990
   chunk 133 optimal weight:    0.0870
   chunk 26 optimal weight:    0.9980
   chunk 124 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9980
   chunk 63 optimal weight:    5.9990
   chunk 102 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.7558

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
C 104 GLN
D  47 GLN
E  68 GLN
E 125 GLN
F  75 HIS
M 155 GLN
N  95 ASN
** N 261 GLN ** 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 = 0.4096 r_free = 0.4096 target = 0.156577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.113254 restraints weight = 25734.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3537 rms_B_bonded: 1.43
r_work: 0.3353 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  19486  Z= 0.150
  Angle     :  0.538   5.888  28023  Z= 0.321
  Chirality :  0.034   0.141   3154
  Planarity :  0.004   0.049   2171
  Dihedral  : 29.817 178.005   5718
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 10.70 %
    Favored  : 87.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.24), residues: 1272
  helix:  2.30 (0.21), residues: 592
  sheet:  0.26 (0.34), residues: 246
  loop : -0.29 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP M 196 
 HIS   0.002   0.001   HIS B  75 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.012   0.001   TYR M 199 
 ARG   0.006   0.000   ARG U  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03294 ( 1103)
  hydrogen bonds       : angle       3.20876 ( 2712)
  covalent geometry    : bond        0.00327 (19486)
  covalent geometry    : angle       0.53760 (28023)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 245
  time to evaluate  : 1.415 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.8515 (ttpp) cc_final: 0.8246 (ttpt)
REVERT: B   26 ILE cc_start: 0.8224 (tp) cc_final: 0.7915 (tp)
REVERT: C   64 GLU cc_start: 0.8216 (tt0) cc_final: 0.7965 (tt0)
REVERT: D   59 MET cc_start: 0.8651 (tpt) cc_final: 0.8218 (tpt)
REVERT: D   89 ILE cc_start: 0.8888 (mt) cc_final: 0.8550 (mt)
REVERT: G   73 ASN cc_start: 0.8027 (t0) cc_final: 0.7441 (t0)
REVERT: H   83 TYR cc_start: 0.8826 (m-10) cc_final: 0.8508 (m-10)
REVERT: M   61 LYS cc_start: 0.8398 (mppt) cc_final: 0.8176 (mmtm)
REVERT: M   98 GLU cc_start: 0.6936 (mp0) cc_final: 0.6403 (pm20)
REVERT: N   98 GLU cc_start: 0.7890 (mp0) cc_final: 0.7669 (pm20)
REVERT: N  152 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8171 (mt0)
REVERT: U   83 ASN cc_start: 0.8236 (p0) cc_final: 0.7971 (p0)
REVERT: U  114 LYS cc_start: 0.8105 (ttpt) cc_final: 0.7759 (ttpp)
  outliers start: 20
  outliers final: 18
  residues processed: 253
  average time/residue: 0.3972
  time to fit residues: 139.2324
Evaluate side-chains
  250 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 232
  time to evaluate  : 1.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  116 LYS
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain M residue  162 GLU
Chi-restraints excluded: chain M residue  165 THR
Chi-restraints excluded: chain M residue  177 THR
Chi-restraints excluded: chain M residue  200 ILE
Chi-restraints excluded: chain M residue  238 GLU
Chi-restraints excluded: chain M residue  257 ASP
Chi-restraints excluded: chain N residue  169 MET
Chi-restraints excluded: chain N residue  191 ARG
Chi-restraints excluded: chain N residue  264 SER
Chi-restraints excluded: chain U residue   86 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 138 optimal weight:    3.9990
   chunk 17 optimal weight:    7.9990
   chunk 147 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 112 optimal weight:    4.9990
   chunk 141 optimal weight:    3.9990
   chunk 135 optimal weight:    0.9990
   chunk 133 optimal weight:    3.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
D  47 GLN
E 125 GLN
F  27 GLN
N  95 ASN
** N 261 GLN ** 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 = 0.4083 r_free = 0.4083 target = 0.155579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.114366 restraints weight = 25981.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.44
r_work: 0.3343 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  19486  Z= 0.176
  Angle     :  0.548   6.136  28023  Z= 0.324
  Chirality :  0.035   0.148   3154
  Planarity :  0.004   0.050   2171
  Dihedral  : 29.834 176.627   5718
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 11.24 %
    Favored  : 86.31 %
  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:  1.58 (0.24), residues: 1272
  helix:  2.36 (0.21), residues: 592
  sheet:  0.31 (0.34), residues: 240
  loop : -0.31 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP M 185 
 HIS   0.003   0.001   HIS M 110 
 PHE   0.009   0.001   PHE G  25 
 TYR   0.022   0.001   TYR U  70 
 ARG   0.008   0.000   ARG H  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03411 ( 1103)
  hydrogen bonds       : angle       3.19696 ( 2712)
  covalent geometry    : bond        0.00394 (19486)
  covalent geometry    : angle       0.54769 (28023)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 220
  time to evaluate  : 1.322 
Fit side-chains
REVERT: A   79 LYS cc_start: 0.8580 (ttpp) cc_final: 0.8285 (ttpt)
REVERT: B   26 ILE cc_start: 0.8273 (tp) cc_final: 0.7959 (tp)
REVERT: C   64 GLU cc_start: 0.8261 (tt0) cc_final: 0.8020 (tt0)
REVERT: C   91 GLU cc_start: 0.7914 (tt0) cc_final: 0.7665 (tt0)
REVERT: G   73 ASN cc_start: 0.8054 (t0) cc_final: 0.7500 (t0)
REVERT: H   33 ARG cc_start: 0.7249 (mmt90) cc_final: 0.6682 (mtp-110)
REVERT: H   83 TYR cc_start: 0.8697 (m-10) cc_final: 0.8384 (m-10)
REVERT: M   98 GLU cc_start: 0.6879 (mp0) cc_final: 0.6342 (pm20)
REVERT: N  152 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8157 (mt0)
REVERT: U  114 LYS cc_start: 0.8067 (ttpt) cc_final: 0.7835 (ttpp)
  outliers start: 27
  outliers final: 21
  residues processed: 235
  average time/residue: 0.3861
  time to fit residues: 126.6314
Evaluate side-chains
  233 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 212
  time to evaluate  : 1.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain D residue  116 LYS
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain M residue   99 SER
Chi-restraints excluded: chain M residue  162 GLU
Chi-restraints excluded: chain M residue  177 THR
Chi-restraints excluded: chain M residue  238 GLU
Chi-restraints excluded: chain M residue  257 ASP
Chi-restraints excluded: chain N residue   91 SER
Chi-restraints excluded: chain N residue  191 ARG
Chi-restraints excluded: chain U residue   86 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 129 optimal weight:    0.4980
   chunk 137 optimal weight:    0.0370
   chunk 14 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 72 optimal weight:   40.0000
   chunk 73 optimal weight:   20.0000
   overall best weight:    0.8260

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
D  47 GLN
E 125 GLN
F  27 GLN
N  95 ASN
** N 261 GLN ** 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 = 0.4087 r_free = 0.4087 target = 0.156552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.114481 restraints weight = 26189.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 1.41
r_work: 0.3323 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3172 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  19486  Z= 0.154
  Angle     :  0.533   6.823  28023  Z= 0.316
  Chirality :  0.034   0.144   3154
  Planarity :  0.004   0.050   2171
  Dihedral  : 29.723 175.823   5718
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 11.97 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.24), residues: 1272
  helix:  2.49 (0.21), residues: 592
  sheet:  0.23 (0.33), residues: 246
  loop : -0.27 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP N 185 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.007   0.001   PHE G  25 
 TYR   0.013   0.001   TYR M 199 
 ARG   0.006   0.000   ARG U  56 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03239 ( 1103)
  hydrogen bonds       : angle       3.09502 ( 2712)
  covalent geometry    : bond        0.00339 (19486)
  covalent geometry    : angle       0.53310 (28023)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 214
  time to evaluate  : 1.383 
Fit side-chains
REVERT: B   26 ILE cc_start: 0.8154 (tp) cc_final: 0.7856 (tp)
REVERT: C   64 GLU cc_start: 0.8254 (tt0) cc_final: 0.8019 (tt0)
REVERT: C   91 GLU cc_start: 0.7949 (tt0) cc_final: 0.7674 (tt0)
REVERT: D   59 MET cc_start: 0.8754 (tpt) cc_final: 0.8286 (tpt)
REVERT: G   73 ASN cc_start: 0.8094 (t0) cc_final: 0.7550 (t0)
REVERT: H   33 ARG cc_start: 0.7101 (mmt90) cc_final: 0.6600 (mtp-110)
REVERT: M   98 GLU cc_start: 0.6916 (mp0) cc_final: 0.6381 (pm20)
REVERT: N  152 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8131 (mt0)
REVERT: N  191 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7377 (ttp-170)
REVERT: U   83 ASN cc_start: 0.8196 (p0) cc_final: 0.7893 (p0)
REVERT: U  114 LYS cc_start: 0.7995 (ttpt) cc_final: 0.7758 (ttpp)
  outliers start: 28
  outliers final: 23
  residues processed: 230
  average time/residue: 0.4076
  time to fit residues: 129.0490
Evaluate side-chains
  234 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 210
  time to evaluate  : 1.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain D residue  116 LYS
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain M residue   99 SER
Chi-restraints excluded: chain M residue  152 GLN
Chi-restraints excluded: chain M residue  162 GLU
Chi-restraints excluded: chain M residue  177 THR
Chi-restraints excluded: chain M residue  200 ILE
Chi-restraints excluded: chain M residue  230 MET
Chi-restraints excluded: chain M residue  238 GLU
Chi-restraints excluded: chain M residue  257 ASP
Chi-restraints excluded: chain N residue   91 SER
Chi-restraints excluded: chain N residue  191 ARG
Chi-restraints excluded: chain N residue  264 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 154 optimal weight:    5.9990
   chunk 140 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 59 optimal weight:    4.9990
   chunk 89 optimal weight:    6.9990
   chunk 4 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 138 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
C  84 GLN
C 104 GLN
D  47 GLN
E 125 GLN
F  27 GLN
N  95 ASN
** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.157510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.115730 restraints weight = 25768.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 1.42
r_work: 0.3357 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  19486  Z= 0.151
  Angle     :  0.530   9.874  28023  Z= 0.314
  Chirality :  0.034   0.142   3154
  Planarity :  0.004   0.049   2171
  Dihedral  : 29.689 175.591   5718
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 12.69 %
    Favored  : 84.86 %
  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:  1.78 (0.24), residues: 1272
  helix:  2.57 (0.21), residues: 592
  sheet:  0.35 (0.33), residues: 244
  loop : -0.25 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP N 185 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.007   0.001   PHE G  25 
 TYR   0.016   0.001   TYR U  70 
 ARG   0.006   0.000   ARG E 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03190 ( 1103)
  hydrogen bonds       : angle       3.03842 ( 2712)
  covalent geometry    : bond        0.00333 (19486)
  covalent geometry    : angle       0.52988 (28023)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 219
  time to evaluate  : 1.370 
Fit side-chains
REVERT: B   26 ILE cc_start: 0.8088 (tp) cc_final: 0.7785 (tp)
REVERT: C   64 GLU cc_start: 0.8263 (tt0) cc_final: 0.8029 (tt0)
REVERT: C   91 GLU cc_start: 0.7909 (tt0) cc_final: 0.7660 (tt0)
REVERT: G   73 ASN cc_start: 0.8095 (t0) cc_final: 0.7560 (t0)
REVERT: H   33 ARG cc_start: 0.7090 (mmt90) cc_final: 0.6630 (mtp-110)
REVERT: M   98 GLU cc_start: 0.6956 (mp0) cc_final: 0.6373 (pm20)
REVERT: N  152 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8127 (mt0)
REVERT: N  191 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7363 (ttp-170)
REVERT: N  216 LYS cc_start: 0.8409 (tppt) cc_final: 0.8122 (tptm)
REVERT: U  114 LYS cc_start: 0.8050 (ttpt) cc_final: 0.7824 (ttpp)
  outliers start: 27
  outliers final: 23
  residues processed: 232
  average time/residue: 0.4009
  time to fit residues: 130.0265
Evaluate side-chains
  241 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 217
  time to evaluate  : 1.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain D residue  116 LYS
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain M residue   99 SER
Chi-restraints excluded: chain M residue  152 GLN
Chi-restraints excluded: chain M residue  162 GLU
Chi-restraints excluded: chain M residue  177 THR
Chi-restraints excluded: chain M residue  230 MET
Chi-restraints excluded: chain M residue  238 GLU
Chi-restraints excluded: chain M residue  257 ASP
Chi-restraints excluded: chain N residue   91 SER
Chi-restraints excluded: chain N residue  191 ARG
Chi-restraints excluded: chain N residue  264 SER
Chi-restraints excluded: chain U residue   68 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 129 optimal weight:    5.9990
   chunk 108 optimal weight:    8.9990
   chunk 93 optimal weight:   10.0000
   chunk 73 optimal weight:   20.0000
   chunk 4 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 141 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 126 optimal weight:    0.3980
   chunk 123 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
C  84 GLN
C 104 GLN
D  47 GLN
E 125 GLN
F  27 GLN
N  95 ASN
** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.157518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.114631 restraints weight = 25669.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 1.39
r_work: 0.3372 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  19486  Z= 0.154
  Angle     :  0.535   8.990  28023  Z= 0.315
  Chirality :  0.034   0.143   3154
  Planarity :  0.004   0.048   2171
  Dihedral  : 29.673 174.496   5718
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 12.42 %
    Favored  : 84.77 %
  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:  1.80 (0.24), residues: 1272
  helix:  2.57 (0.21), residues: 592
  sheet:  0.34 (0.34), residues: 236
  loop : -0.19 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP M 185 
 HIS   0.002   0.001   HIS B  75 
 PHE   0.008   0.001   PHE G  25 
 TYR   0.014   0.001   TYR H  83 
 ARG   0.007   0.000   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03223 ( 1103)
  hydrogen bonds       : angle       3.02454 ( 2712)
  covalent geometry    : bond        0.00342 (19486)
  covalent geometry    : angle       0.53546 (28023)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 220
  time to evaluate  : 1.428 
Fit side-chains
REVERT: B   26 ILE cc_start: 0.8141 (tp) cc_final: 0.7846 (tp)
REVERT: C   64 GLU cc_start: 0.8242 (tt0) cc_final: 0.8020 (tt0)
REVERT: C   91 GLU cc_start: 0.7892 (tt0) cc_final: 0.7639 (tt0)
REVERT: G   73 ASN cc_start: 0.8101 (t0) cc_final: 0.7589 (t0)
REVERT: G   99 ARG cc_start: 0.8237 (mmm160) cc_final: 0.7991 (mmm160)
REVERT: H   33 ARG cc_start: 0.7082 (mmt90) cc_final: 0.6691 (mtp-110)
REVERT: M   98 GLU cc_start: 0.6893 (mp0) cc_final: 0.6297 (pm20)
REVERT: M  162 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6973 (pm20)
REVERT: N  152 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8133 (mt0)
REVERT: N  191 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7332 (ttp-170)
REVERT: U  114 LYS cc_start: 0.8019 (ttpt) cc_final: 0.7790 (ttpp)
  outliers start: 31
  outliers final: 25
  residues processed: 236
  average time/residue: 0.3971
  time to fit residues: 130.9602
Evaluate side-chains
  244 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 217
  time to evaluate  : 1.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain D residue  116 LYS
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain M residue   99 SER
Chi-restraints excluded: chain M residue  152 GLN
Chi-restraints excluded: chain M residue  162 GLU
Chi-restraints excluded: chain M residue  177 THR
Chi-restraints excluded: chain M residue  230 MET
Chi-restraints excluded: chain M residue  238 GLU
Chi-restraints excluded: chain M residue  257 ASP
Chi-restraints excluded: chain N residue   30 MET
Chi-restraints excluded: chain N residue   91 SER
Chi-restraints excluded: chain N residue  191 ARG
Chi-restraints excluded: chain N residue  264 SER
Chi-restraints excluded: chain U residue   68 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 113 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:   10.0000
   chunk 55 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0970
   chunk 25 optimal weight:    0.7980
   chunk 114 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 66 optimal weight:    0.6980
   chunk 134 optimal weight:    4.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
C  84 GLN
C 104 GLN
D  47 GLN
E 125 GLN
F  27 GLN
** N 261 GLN ** 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 = 0.4114 r_free = 0.4114 target = 0.157923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.114449 restraints weight = 25999.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 1.43
r_work: 0.3373 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  19486  Z= 0.145
  Angle     :  0.536   9.558  28023  Z= 0.316
  Chirality :  0.034   0.141   3154
  Planarity :  0.004   0.061   2171
  Dihedral  : 29.667 174.567   5718
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 13.33 %
    Favored  : 84.32 %
  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:  1.82 (0.23), residues: 1272
  helix:  2.62 (0.21), residues: 592
  sheet:  0.55 (0.36), residues: 210
  loop : -0.31 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP U  78 
 HIS   0.003   0.001   HIS M 110 
 PHE   0.007   0.001   PHE G  25 
 TYR   0.020   0.001   TYR U  70 
 ARG   0.011   0.000   ARG M  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03167 ( 1103)
  hydrogen bonds       : angle       3.02876 ( 2712)
  covalent geometry    : bond        0.00317 (19486)
  covalent geometry    : angle       0.53639 (28023)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 223
  time to evaluate  : 1.480 
Fit side-chains
REVERT: B   26 ILE cc_start: 0.8122 (tp) cc_final: 0.7810 (tp)
REVERT: C   64 GLU cc_start: 0.8258 (tt0) cc_final: 0.8043 (tt0)
REVERT: C   91 GLU cc_start: 0.7891 (tt0) cc_final: 0.7631 (tt0)
REVERT: D   59 MET cc_start: 0.8731 (tpt) cc_final: 0.8290 (tpt)
REVERT: G   73 ASN cc_start: 0.7983 (t0) cc_final: 0.7441 (t0)
REVERT: G   99 ARG cc_start: 0.8236 (mmm160) cc_final: 0.7977 (mmm160)
REVERT: H   33 ARG cc_start: 0.7070 (mmt90) cc_final: 0.6623 (mtp-110)
REVERT: M   98 GLU cc_start: 0.6925 (mp0) cc_final: 0.6329 (pm20)
REVERT: M  162 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6915 (pm20)
REVERT: N  152 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8124 (mt0)
REVERT: N  191 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7333 (ttp-170)
REVERT: U  114 LYS cc_start: 0.8018 (ttpt) cc_final: 0.7791 (ttpp)
  outliers start: 26
  outliers final: 22
  residues processed: 236
  average time/residue: 0.3973
  time to fit residues: 130.0392
Evaluate side-chains
  241 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 217
  time to evaluate  : 1.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain D residue  116 LYS
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain M residue   99 SER
Chi-restraints excluded: chain M residue  152 GLN
Chi-restraints excluded: chain M residue  162 GLU
Chi-restraints excluded: chain M residue  177 THR
Chi-restraints excluded: chain M residue  238 GLU
Chi-restraints excluded: chain M residue  257 ASP
Chi-restraints excluded: chain N residue   30 MET
Chi-restraints excluded: chain N residue   91 SER
Chi-restraints excluded: chain N residue  191 ARG
Chi-restraints excluded: chain N residue  264 SER
Chi-restraints excluded: chain U residue   68 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 160 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 135 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 155 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 147 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
C  84 GLN
C 104 GLN
D  47 GLN
E 125 GLN
** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.157303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.114254 restraints weight = 25690.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 1.40
r_work: 0.3353 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3197 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  19486  Z= 0.160
  Angle     :  0.543   9.437  28023  Z= 0.319
  Chirality :  0.034   0.143   3154
  Planarity :  0.004   0.048   2171
  Dihedral  : 29.668 174.411   5718
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 13.42 %
    Favored  : 84.22 %
  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:  1.77 (0.23), residues: 1272
  helix:  2.56 (0.21), residues: 592
  sheet:  0.38 (0.35), residues: 220
  loop : -0.25 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP M 185 
 HIS   0.003   0.001   HIS M 110 
 PHE   0.008   0.001   PHE G  25 
 TYR   0.013   0.001   TYR M 199 
 ARG   0.011   0.000   ARG M  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03268 ( 1103)
  hydrogen bonds       : angle       3.05369 ( 2712)
  covalent geometry    : bond        0.00356 (19486)
  covalent geometry    : angle       0.54276 (28023)

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

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

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2544 Ramachandran restraints generated.
    1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 213
  time to evaluate  : 1.328 
Fit side-chains
REVERT: C   64 GLU cc_start: 0.8262 (tt0) cc_final: 0.8039 (tt0)
REVERT: C   91 GLU cc_start: 0.7886 (tt0) cc_final: 0.7649 (tt0)
REVERT: E  115 LYS cc_start: 0.8679 (mtmm) cc_final: 0.8420 (mtmm)
REVERT: G   73 ASN cc_start: 0.8001 (t0) cc_final: 0.7465 (t0)
REVERT: G   99 ARG cc_start: 0.8247 (mmm160) cc_final: 0.8015 (mmm160)
REVERT: H   33 ARG cc_start: 0.7061 (mmt90) cc_final: 0.6666 (mtp-110)
REVERT: M   98 GLU cc_start: 0.6911 (mp0) cc_final: 0.6329 (pm20)
REVERT: M  162 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6976 (pm20)
REVERT: N  152 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8097 (mt0)
REVERT: N  191 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7345 (ttp-170)
REVERT: U  114 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7780 (ttpp)
  outliers start: 26
  outliers final: 23
  residues processed: 227
  average time/residue: 0.3876
  time to fit residues: 122.7126
Evaluate side-chains
  236 residues out of total 1103 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 211
  time to evaluate  : 1.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   90 THR
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain D residue  116 LYS
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   52 THR
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain M residue   99 SER
Chi-restraints excluded: chain M residue  152 GLN
Chi-restraints excluded: chain M residue  162 GLU
Chi-restraints excluded: chain M residue  177 THR
Chi-restraints excluded: chain M residue  238 GLU
Chi-restraints excluded: chain M residue  257 ASP
Chi-restraints excluded: chain N residue   30 MET
Chi-restraints excluded: chain N residue   91 SER
Chi-restraints excluded: chain N residue  191 ARG
Chi-restraints excluded: chain N residue  264 SER
Chi-restraints excluded: chain U residue   68 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 161
   random chunks:
   chunk 7 optimal weight:    6.9990
   chunk 79 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 98 optimal weight:    3.9990
   chunk 125 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 155 optimal weight:    2.9990
   chunk 121 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
C  84 GLN
C 104 GLN
D  47 GLN
N  95 ASN
** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.155805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.113595 restraints weight = 25660.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 1.48
r_work: 0.3342 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  19486  Z= 0.189
  Angle     :  0.556  10.310  28023  Z= 0.325
  Chirality :  0.035   0.150   3154
  Planarity :  0.004   0.047   2171
  Dihedral  : 29.761 173.317   5718
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.60 %
    Favored  : 83.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.24), residues: 1272
  helix:  2.46 (0.21), residues: 592
  sheet:  0.26 (0.34), residues: 240
  loop : -0.25 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP N 185 
 HIS   0.003   0.001   HIS M 110 
 PHE   0.010   0.001   PHE G  25 
 TYR   0.020   0.002   TYR U  70 
 ARG   0.008   0.000   ARG E  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03487 ( 1103)
  hydrogen bonds       : angle       3.14871 ( 2712)
  covalent geometry    : bond        0.00424 (19486)
  covalent geometry    : angle       0.55591 (28023)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11739.57 seconds
wall clock time: 200 minutes 16.40 seconds (12016.40 seconds total)