Starting phenix.real_space_refine
on Tue Feb  3 14:19:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d21_46479/02_2026/9d21_46479.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d21_46479/02_2026/9d21_46479.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d21_46479/02_2026/9d21_46479.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d21_46479/02_2026/9d21_46479.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d21_46479/02_2026/9d21_46479.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d21_46479/02_2026/9d21_46479.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       5      5.16       5
     C    2310      2.51       5
     N     585      2.21       5
     O     660      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3560
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "C"
      Number of atoms: 712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 712
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 4, 'TRANS': 86}
          Chain breaks: 1
  Restraints were copied for chains:
    A, B, D, E
  Time building chain proxies: 0.49, per 1000 atoms: 0.14
  Number of scatterers: 3560
  At special positions: 0
  Unit cell: (67.52, 88.62, 42.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       5     16.00
     O     660      8.00
     N     585      7.00
     C    2310      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: 0.27
  Conformation dependent library (CDL) restraints added in 135.0 milliseconds
  

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  870

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 45.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16
      removed outlier: 6.520A  pdb=" N   LEU A  12 " --> pdb=" O   MET B  13 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   LYS B  15 " --> pdb=" O   LEU A  12 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   VAL A  14 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   MET C  13 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   VAL B  16 " --> pdb=" O   MET C  13 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   LYS C  15 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 22
      removed outlier: 7.162A  pdb=" N   GLY A  22 " --> pdb=" O   ARG B  21 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   ALA C  19 " --> pdb=" O   VAL B  20 " (cutoff:3.500A)
      removed outlier: 7.342A  pdb=" N   GLY B  22 " --> pdb=" O   ALA C  19 " (cutoff:3.500A)
      removed outlier: 8.269A  pdb=" N   ARG C  21 " --> pdb=" O   GLY B  22 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   GLY C  22 " --> pdb=" O   ARG D  21 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   GLY D  22 " --> pdb=" O   ARG E  21 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 32
      removed outlier: 6.490A  pdb=" N   ALA C  25 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   VAL B  28 " --> pdb=" O   ALA C  25 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   ASN C  27 " --> pdb=" O   VAL B  28 " (cutoff:3.500A)
      removed outlier: 7.711A  pdb=" N   VAL B  30 " --> pdb=" O   ASN C  27 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   ALA C  29 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
      removed outlier: 8.135A  pdb=" N   VAL B  32 " --> pdb=" O   ALA C  29 " (cutoff:3.500A)
      removed outlier: 6.913A  pdb=" N   HIS C  31 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 6.885A  pdb=" N   ILE C  26 " --> pdb=" O   ASN D  27 " (cutoff:3.500A)
      removed outlier: 8.264A  pdb=" N   ALA D  29 " --> pdb=" O   ILE C  26 " (cutoff:3.500A)
      removed outlier: 6.394A  pdb=" N   VAL C  28 " --> pdb=" O   ALA D  29 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   HIS D  31 " --> pdb=" O   VAL C  28 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   VAL C  30 " --> pdb=" O   HIS D  31 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 62
      removed outlier: 6.255A  pdb=" N   THR A  59 " --> pdb=" O   ALA B  60 " (cutoff:3.500A)
      removed outlier: 7.947A  pdb=" N   GLU B  62 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   GLU A  61 " --> pdb=" O   GLU B  62 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   THR C  59 " --> pdb=" O   ALA D  60 " (cutoff:3.500A)
      removed outlier: 7.977A  pdb=" N   GLU D  62 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   GLU C  61 " --> pdb=" O   GLU D  62 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   THR D  59 " --> pdb=" O   ALA E  60 " (cutoff:3.500A)
      removed outlier: 8.035A  pdb=" N   GLU E  62 " --> pdb=" O   THR D  59 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   GLU D  61 " --> pdb=" O   GLU E  62 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 66
      removed outlier: 6.429A  pdb=" N   VAL C  65 " --> pdb=" O   GLU B  66 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 73
      removed outlier: 6.710A  pdb=" N   LYS A  70 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 7.873A  pdb=" N   ILE B  73 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   GLU A  72 " --> pdb=" O   ILE B  73 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LYS C  70 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   ILE D  73 " --> pdb=" O   LYS C  70 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   GLU C  72 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LYS D  70 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   ILE E  73 " --> pdb=" O   LYS D  70 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   GLU D  72 " --> pdb=" O   ILE E  73 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 79
      removed outlier: 7.177A  pdb=" N   TRP A  79 " --> pdb=" O   TYR B  78 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   LYS C  76 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 7.407A  pdb=" N   TRP B  79 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
      removed outlier: 8.229A  pdb=" N   TYR C  78 " --> pdb=" O   TRP B  79 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   TRP C  79 " --> pdb=" O   TYR D  78 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   TRP D  79 " --> pdb=" O   TYR E  78 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 98
      removed outlier: 6.977A  pdb=" N   VAL C  93 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   THR B  96 " --> pdb=" O   VAL C  93 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   PHE C  95 " --> pdb=" O   THR B  96 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   ASN B  98 " --> pdb=" O   PHE C  95 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   ALA C  97 " --> pdb=" O   ASN B  98 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 103 through 108
      removed outlier: 6.562A  pdb=" N   ARG A 104 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   ILE B 107 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   THR A 106 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   ARG C 104 " --> pdb=" O   TYR D 105 " (cutoff:3.500A)
      removed outlier: 7.413A  pdb=" N   ILE D 107 " --> pdb=" O   ARG C 104 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   THR C 106 " --> pdb=" O   ILE D 107 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ARG D 104 " --> pdb=" O   TYR E 105 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   ILE E 107 " --> pdb=" O   ARG D 104 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   THR D 106 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 115
      removed outlier: 6.816A  pdb=" N   TYR A 114 " --> pdb=" O   SER B 115 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   TYR C 114 " --> pdb=" O   SER D 115 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   TYR D 114 " --> pdb=" O   SER E 115 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 118 through 122
      removed outlier: 5.517A  pdb=" N   THR C 118 " --> pdb=" O   THR B 119 " (cutoff:3.500A)
      removed outlier: 7.344A  pdb=" N   VAL B 121 " --> pdb=" O   THR C 118 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   ALA C 120 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   THR D 119 " --> pdb=" O   ALA E 120 " (cutoff:3.500A)
      removed outlier: 8.428A  pdb=" N   VAL E 122 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   VAL D 121 " --> pdb=" O   VAL E 122 " (cutoff:3.500A)

    76 hydrogen bonds defined for protein.
    228 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.32

  Time building geometry restraints manager: 0.37 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1110
        1.34 -     1.45: 497
        1.45 -     1.57: 2028
        1.57 -     1.68: 0
        1.68 -     1.80: 10
  Bond restraints: 3645
  Sorted by residual:
  bond pdb=" CG  LEU E 110 "
       pdb=" CD1 LEU E 110 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.61e+00
  bond pdb=" CG  LEU C 110 "
       pdb=" CD1 LEU C 110 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.56e+00
  bond pdb=" CG  LEU A 110 "
       pdb=" CD1 LEU A 110 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.55e+00
  bond pdb=" CG  LEU B 110 "
       pdb=" CD1 LEU B 110 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.55e+00
  bond pdb=" CG  LEU D 110 "
       pdb=" CD1 LEU D 110 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.55e+00
  ... (remaining 3640 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.34: 4622
        1.34 -     2.69: 242
        2.69 -     4.03: 53
        4.03 -     5.38: 33
        5.38 -     6.72: 10
  Bond angle restraints: 4960
  Sorted by residual:
  angle pdb=" C   THR E 119 "
        pdb=" CA  THR E 119 "
        pdb=" CB  THR E 119 "
      ideal   model   delta    sigma   weight residual
     109.71  116.43   -6.72 1.83e+00 2.99e-01 1.35e+01
  angle pdb=" C   THR C 119 "
        pdb=" CA  THR C 119 "
        pdb=" CB  THR C 119 "
      ideal   model   delta    sigma   weight residual
     109.71  116.43   -6.72 1.83e+00 2.99e-01 1.35e+01
  angle pdb=" C   THR B 119 "
        pdb=" CA  THR B 119 "
        pdb=" CB  THR B 119 "
      ideal   model   delta    sigma   weight residual
     109.71  116.42   -6.71 1.83e+00 2.99e-01 1.34e+01
  angle pdb=" C   THR D 119 "
        pdb=" CA  THR D 119 "
        pdb=" CB  THR D 119 "
      ideal   model   delta    sigma   weight residual
     109.71  116.39   -6.68 1.83e+00 2.99e-01 1.33e+01
  angle pdb=" C   THR A 119 "
        pdb=" CA  THR A 119 "
        pdb=" CB  THR A 119 "
      ideal   model   delta    sigma   weight residual
     109.71  116.38   -6.67 1.83e+00 2.99e-01 1.33e+01
  ... (remaining 4955 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 1820
       16.00 -    32.00: 230
       32.00 -    47.99: 85
       47.99 -    63.99: 5
       63.99 -    79.99: 15
  Dihedral angle restraints: 2155
    sinusoidal: 815
      harmonic: 1340
  Sorted by residual:
  dihedral pdb=" CA  GLY B  22 "
           pdb=" C   GLY B  22 "
           pdb=" N   SER B  23 "
           pdb=" CA  SER B  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.78   18.22     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  GLY D  22 "
           pdb=" C   GLY D  22 "
           pdb=" N   SER D  23 "
           pdb=" CA  SER D  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.79   18.21     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  GLY C  22 "
           pdb=" C   GLY C  22 "
           pdb=" N   SER C  23 "
           pdb=" CA  SER C  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.80   18.20     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 2152 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 318
       0.037 -    0.074: 151
       0.074 -    0.111: 96
       0.111 -    0.149: 15
       0.149 -    0.186: 5
  Chirality restraints: 585
  Sorted by residual:
  chirality pdb=" CA  SER D  23 "
            pdb=" N   SER D  23 "
            pdb=" C   SER D  23 "
            pdb=" CB  SER D  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.62e-01
  chirality pdb=" CA  SER B  23 "
            pdb=" N   SER B  23 "
            pdb=" C   SER B  23 "
            pdb=" CB  SER B  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.60e-01
  chirality pdb=" CA  SER A  23 "
            pdb=" N   SER A  23 "
            pdb=" C   SER A  23 "
            pdb=" CB  SER A  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.43e-01
  ... (remaining 582 not shown)

  Planarity restraints: 610
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 114 "   -0.009 2.00e-02 2.50e+03   2.03e-02 8.23e+00
        pdb=" CG  TYR E 114 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 114 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 114 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 114 "    0.013 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 114 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 114 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR E 114 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 114 "   -0.009 2.00e-02 2.50e+03   2.03e-02 8.21e+00
        pdb=" CG  TYR D 114 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 114 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 114 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 114 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 114 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 114 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR D 114 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 114 "   -0.009 2.00e-02 2.50e+03   2.02e-02 8.19e+00
        pdb=" CG  TYR C 114 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 114 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 114 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 114 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 114 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 114 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR C 114 "    0.001 2.00e-02 2.50e+03
  ... (remaining 607 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 825
        2.81 -     3.33: 3103
        3.33 -     3.85: 6230
        3.85 -     4.38: 6809
        4.38 -     4.90: 12101
  Nonbonded interactions: 29068
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D  99 "
            pdb=" NH2 ARG D 103 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" OD1 ASP E  99 "
            pdb=" NH2 ARG E 103 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" OD1 ASP C  99 "
            pdb=" NH2 ARG C 103 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" OD1 ASP B  99 "
            pdb=" NH2 ARG B 103 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" OD1 ASP A  99 "
            pdb=" NH2 ARG A 103 "
     model   vdw
     2.286 3.120
  ... (remaining 29063 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'A'
  selection = chain 'B'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     3.960
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6998
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   0.042   3645  Z= 0.177
  Angle     :  0.821   6.721   4960  Z= 0.461
  Chirality :  0.056   0.186    585
  Planarity :  0.006   0.057    610
  Dihedral  : 17.576  79.987   1285
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 18.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.05 %
    Favored  : 91.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 19.48 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.45 (0.34), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.62 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  34 
 TYR   0.044   0.004   TYR E 114 
 PHE   0.017   0.003   PHE A  33 
 TRP   0.002   0.001   TRP E  79 
 HIS   0.001   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 3645)
  covalent geometry    : angle       0.82083 ( 4960)
  hydrogen bonds       : bond        0.20272 (   76)
  hydrogen bonds       : angle       9.87148 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.137 
Fit side-chains
REVERT: D   66 GLU cc_start: 0.7572 (tt0) cc_final: 0.6830 (tm-30)
REVERT: E  103 ARG cc_start: 0.6858 (mtm-85) cc_final: 0.5259 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.0497
  time to fit residues: 5.3101
Evaluate side-chains
  51 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.3980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.153412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.142747 restraints weight = 6339.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.4338 rms_B_bonded: 1.89
r_work: 0.4254 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.4148 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.4148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3645  Z= 0.187
  Angle     :  0.683   6.288   4960  Z= 0.362
  Chirality :  0.056   0.190    585
  Planarity :  0.005   0.048    610
  Dihedral  :  5.630  21.709    490
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 19.22 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.46 (0.34), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.63 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D  21 
 TYR   0.018   0.003   TYR B 116 
 PHE   0.009   0.002   PHE A  33 
 TRP   0.006   0.001   TRP A  79 
 HIS   0.003   0.001   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00437 ( 3645)
  covalent geometry    : angle       0.68349 ( 4960)
  hydrogen bonds       : bond        0.02964 (   76)
  hydrogen bonds       : angle       6.68786 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.144 
Fit side-chains
REVERT: C   13 MET cc_start: 0.7905 (tpp) cc_final: 0.7616 (tpp)
REVERT: A   72 GLU cc_start: 0.7015 (mm-30) cc_final: 0.6807 (mm-30)
REVERT: D   66 GLU cc_start: 0.8233 (tt0) cc_final: 0.7620 (tm-30)
REVERT: D  105 TYR cc_start: 0.8160 (m-80) cc_final: 0.7696 (m-80)
REVERT: E  103 ARG cc_start: 0.7862 (mtm-85) cc_final: 0.5418 (mmm160)
  outliers start: 8
  outliers final: 6
  residues processed: 68
  average time/residue: 0.0520
  time to fit residues: 4.6911
Evaluate side-chains
  48 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Chi-restraints excluded: chain E residue   18 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 12 optimal weight:    0.4980
   chunk 35 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  90 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.159188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.139293 restraints weight = 6868.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.4297 rms_B_bonded: 1.92
r_work: 0.4219 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.4117 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3645  Z= 0.185
  Angle     :  0.656   5.154   4960  Z= 0.351
  Chirality :  0.055   0.181    585
  Planarity :  0.005   0.040    610
  Dihedral  :  5.627  20.195    490
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 22.08 %
    Favored  : 75.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.43 (0.34), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.61 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  21 
 TYR   0.017   0.003   TYR A 105 
 PHE   0.008   0.002   PHE E  87 
 TRP   0.005   0.001   TRP A  79 
 HIS   0.004   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 3645)
  covalent geometry    : angle       0.65608 ( 4960)
  hydrogen bonds       : bond        0.02484 (   76)
  hydrogen bonds       : angle       5.97635 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.140 
Fit side-chains
REVERT: C   13 MET cc_start: 0.7916 (tpp) cc_final: 0.7715 (tpp)
REVERT: D   66 GLU cc_start: 0.8209 (tt0) cc_final: 0.7643 (tm-30)
REVERT: E   72 GLU cc_start: 0.5626 (pm20) cc_final: 0.5353 (pm20)
REVERT: E  103 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.5390 (mmm160)
  outliers start: 10
  outliers final: 8
  residues processed: 56
  average time/residue: 0.0315
  time to fit residues: 2.4717
Evaluate side-chains
  46 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain D residue   77 SER
Chi-restraints excluded: chain E residue   13 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0970
   chunk 38 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 19 optimal weight:    0.1980
   chunk 44 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0270
   overall best weight:    0.4636

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

Flipped N/Q/H residues before XYZ refinement:
C  90 HIS
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  90 HIS
B  90 HIS
D  90 HIS
E  90 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.153692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.143076 restraints weight = 6144.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.4313 rms_B_bonded: 1.94
r_work: 0.4238 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.4132 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.4132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3645  Z= 0.144
  Angle     :  0.618   4.987   4960  Z= 0.337
  Chirality :  0.054   0.179    585
  Planarity :  0.004   0.043    610
  Dihedral  :  5.486  20.688    490
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 23.12 %
    Favored  : 75.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.46 (0.34), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.63 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  34 
 TYR   0.011   0.002   TYR B 105 
 PHE   0.008   0.001   PHE E  87 
 TRP   0.004   0.001   TRP A  79 
 HIS   0.003   0.001   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 3645)
  covalent geometry    : angle       0.61803 ( 4960)
  hydrogen bonds       : bond        0.01986 (   76)
  hydrogen bonds       : angle       5.70418 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.142 
Fit side-chains
REVERT: C   13 MET cc_start: 0.7936 (tpp) cc_final: 0.7673 (tpp)
REVERT: A   90 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.7162 (m90)
REVERT: D   66 GLU cc_start: 0.8193 (tt0) cc_final: 0.7580 (tm-30)
REVERT: E  103 ARG cc_start: 0.7999 (mtm-85) cc_final: 0.5477 (mmm160)
  outliers start: 6
  outliers final: 5
  residues processed: 51
  average time/residue: 0.0583
  time to fit residues: 3.8961
Evaluate side-chains
  47 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain E residue   13 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
C  90 HIS
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  90 HIS
D  90 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.144791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.134492 restraints weight = 6375.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.4220 rms_B_bonded: 1.92
r_work: 0.4151 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.4049 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.4049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.3511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.046   3645  Z= 0.294
  Angle     :  0.745   6.960   4960  Z= 0.402
  Chirality :  0.056   0.176    585
  Planarity :  0.005   0.036    610
  Dihedral  :  5.979  19.747    490
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 22.08 %
    Favored  : 73.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.41 (0.34), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.59 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E 103 
 TYR   0.019   0.003   TYR C 114 
 PHE   0.014   0.002   PHE A  87 
 TRP   0.006   0.002   TRP B  79 
 HIS   0.019   0.002   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00703 ( 3645)
  covalent geometry    : angle       0.74505 ( 4960)
  hydrogen bonds       : bond        0.02372 (   76)
  hydrogen bonds       : angle       5.76246 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 39
  time to evaluate  : 0.102 
Fit side-chains
REVERT: C   13 MET cc_start: 0.8101 (tpp) cc_final: 0.7876 (tpp)
REVERT: A   90 HIS cc_start: 0.7598 (OUTLIER) cc_final: 0.7380 (m90)
REVERT: D  103 ARG cc_start: 0.7753 (mtm-85) cc_final: 0.7490 (mtm-85)
  outliers start: 16
  outliers final: 12
  residues processed: 51
  average time/residue: 0.0356
  time to fit residues: 2.4974
Evaluate side-chains
  49 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 36
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain D residue   77 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   18 ASP
Chi-restraints excluded: chain E residue   77 SER
Chi-restraints excluded: chain E residue   84 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 14 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.146934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.136691 restraints weight = 6280.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.4242 rms_B_bonded: 1.91
r_work: 0.4152 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.4045 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.3587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3645  Z= 0.175
  Angle     :  0.651   5.208   4960  Z= 0.355
  Chirality :  0.054   0.176    585
  Planarity :  0.004   0.037    610
  Dihedral  :  5.793  21.869    490
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.80 %
    Favored  : 89.20 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 21.82 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.44 (0.34), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.61 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  34 
 TYR   0.015   0.002   TYR C 114 
 PHE   0.006   0.001   PHE A  33 
 TRP   0.003   0.001   TRP A  79 
 HIS   0.006   0.001   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 3645)
  covalent geometry    : angle       0.65143 ( 4960)
  hydrogen bonds       : bond        0.01969 (   76)
  hydrogen bonds       : angle       5.56298 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.088 
Fit side-chains
REVERT: C   13 MET cc_start: 0.8052 (tpp) cc_final: 0.7736 (tpp)
REVERT: B   23 SER cc_start: 0.8620 (p) cc_final: 0.8322 (m)
  outliers start: 13
  outliers final: 9
  residues processed: 53
  average time/residue: 0.0242
  time to fit residues: 1.8856
Evaluate side-chains
  45 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain D residue   77 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 38 optimal weight:    0.4980
   chunk 11 optimal weight:    3.9990
   chunk 42 optimal weight:    0.6980
   chunk 36 optimal weight:    0.2980
   chunk 14 optimal weight:    0.6980
   chunk 3 optimal weight:    0.6980
   chunk 7 optimal weight:    0.2980
   chunk 1 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0980
   overall best weight:    0.3780

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  90 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.154186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.143912 restraints weight = 6438.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.4325 rms_B_bonded: 1.87
r_work: 0.4259 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.4155 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.4155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.3679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   3645  Z= 0.129
  Angle     :  0.595   4.879   4960  Z= 0.322
  Chirality :  0.054   0.185    585
  Planarity :  0.004   0.045    610
  Dihedral  :  5.465  19.963    490
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.97 %
    Favored  : 91.03 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 23.64 %
    Favored  : 74.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.39 (0.35), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.26), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 103 
 TYR   0.016   0.002   TYR B 116 
 PHE   0.009   0.001   PHE E  87 
 TRP   0.002   0.001   TRP A  79 
 HIS   0.006   0.001   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 3645)
  covalent geometry    : angle       0.59474 ( 4960)
  hydrogen bonds       : bond        0.01787 (   76)
  hydrogen bonds       : angle       5.29780 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.082 
Fit side-chains
REVERT: C   13 MET cc_start: 0.8147 (tpp) cc_final: 0.7853 (tpp)
REVERT: E  103 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.5417 (mmm160)
  outliers start: 7
  outliers final: 6
  residues processed: 47
  average time/residue: 0.0438
  time to fit residues: 2.7913
Evaluate side-chains
  43 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain D residue   77 SER
Chi-restraints excluded: chain E residue   84 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 29 optimal weight:    0.2980
   chunk 31 optimal weight:    4.9990
   overall best weight:    1.8588

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.143483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.133707 restraints weight = 6497.789|
|-----------------------------------------------------------------------------|
r_work (start): 0.4213 rms_B_bonded: 1.77
r_work: 0.4148 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.4049 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.4049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.4089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043   3645  Z= 0.313
  Angle     :  0.764   7.032   4960  Z= 0.411
  Chirality :  0.057   0.180    585
  Planarity :  0.005   0.037    610
  Dihedral  :  6.176  20.753    490
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 16.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.26 %
    Favored  : 88.74 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 22.60 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.38 (0.35), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 103 
 TYR   0.022   0.003   TYR C 116 
 PHE   0.009   0.003   PHE D  87 
 TRP   0.006   0.002   TRP D  79 
 HIS   0.005   0.001   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00745 ( 3645)
  covalent geometry    : angle       0.76353 ( 4960)
  hydrogen bonds       : bond        0.02326 (   76)
  hydrogen bonds       : angle       5.76368 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 0.112 
Fit side-chains
REVERT: C   13 MET cc_start: 0.8295 (tpp) cc_final: 0.8061 (tpp)
REVERT: B   13 MET cc_start: 0.7832 (tpt) cc_final: 0.7568 (tpt)
  outliers start: 9
  outliers final: 9
  residues processed: 42
  average time/residue: 0.0268
  time to fit residues: 1.6469
Evaluate side-chains
  41 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 32
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain D residue   77 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   77 SER
Chi-restraints excluded: chain E residue   84 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 5 optimal weight:    0.4980
   chunk 13 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0870
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  90 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.148151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.138291 restraints weight = 6339.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.4276 rms_B_bonded: 1.87
r_work: 0.4224 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.4120 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.4120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.4050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080   3645  Z= 0.159
  Angle     :  0.633   5.486   4960  Z= 0.342
  Chirality :  0.054   0.175    585
  Planarity :  0.004   0.037    610
  Dihedral  :  5.751  21.193    490
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.66 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 22.60 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.46 (0.35), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.63 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 103 
 TYR   0.020   0.002   TYR C 105 
 PHE   0.008   0.001   PHE E  87 
 TRP   0.004   0.001   TRP A  79 
 HIS   0.002   0.000   HIS E  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 3645)
  covalent geometry    : angle       0.63306 ( 4960)
  hydrogen bonds       : bond        0.01844 (   76)
  hydrogen bonds       : angle       5.43882 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 37
  time to evaluate  : 0.083 
Fit side-chains
REVERT: C   13 MET cc_start: 0.8174 (tpp) cc_final: 0.7906 (tpp)
REVERT: B   13 MET cc_start: 0.7761 (tpt) cc_final: 0.7502 (tpt)
REVERT: E  103 ARG cc_start: 0.7528 (mtm-85) cc_final: 0.5067 (mmm160)
  outliers start: 9
  outliers final: 9
  residues processed: 45
  average time/residue: 0.0301
  time to fit residues: 1.8801
Evaluate side-chains
  44 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain D residue   77 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   84 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0980
   chunk 42 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  90 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.147635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.137712 restraints weight = 6336.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.4255 rms_B_bonded: 1.87
r_work: 0.4203 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.4101 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.4101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.4095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   3645  Z= 0.191
  Angle     :  0.659   6.012   4960  Z= 0.355
  Chirality :  0.055   0.179    585
  Planarity :  0.004   0.036    610
  Dihedral  :  5.794  21.342    490
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 14.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.26 %
    Favored  : 88.74 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 21.82 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.40 (0.35), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.58 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 103 
 TYR   0.021   0.003   TYR C 105 
 PHE   0.008   0.002   PHE A  87 
 TRP   0.003   0.001   TRP A  79 
 HIS   0.005   0.001   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 3645)
  covalent geometry    : angle       0.65861 ( 4960)
  hydrogen bonds       : bond        0.01955 (   76)
  hydrogen bonds       : angle       5.42685 (  228)

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

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

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  870 Ramachandran restraints generated.
    435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 34
  time to evaluate  : 0.083 
Fit side-chains
REVERT: C   13 MET cc_start: 0.8209 (tpp) cc_final: 0.7927 (tpp)
REVERT: B   13 MET cc_start: 0.7797 (tpt) cc_final: 0.7543 (tpt)
REVERT: E   21 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.6173 (tpm170)
REVERT: E  103 ARG cc_start: 0.7670 (mtm-85) cc_final: 0.5140 (mmm160)
  outliers start: 12
  outliers final: 11
  residues processed: 43
  average time/residue: 0.0362
  time to fit residues: 2.0617
Evaluate side-chains
  44 residues out of total 385 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 32
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   26 ILE
Chi-restraints excluded: chain C residue   77 SER
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain B residue   66 GLU
Chi-restraints excluded: chain B residue   77 SER
Chi-restraints excluded: chain D residue   77 SER
Chi-restraints excluded: chain D residue  117 SER
Chi-restraints excluded: chain E residue   21 ARG
Chi-restraints excluded: chain E residue   26 ILE
Chi-restraints excluded: chain E residue   84 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0970
   chunk 27 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 10 optimal weight:    0.2980
   chunk 8 optimal weight:    0.8980
   chunk 1 optimal weight:    0.1980
   chunk 9 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  90 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.148970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.139373 restraints weight = 6272.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.4288 rms_B_bonded: 1.85
r_work: 0.4225 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.4121 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.4126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073   3645  Z= 0.151
  Angle     :  0.637   5.897   4960  Z= 0.343
  Chirality :  0.055   0.181    585
  Planarity :  0.004   0.034    610
  Dihedral  :  5.693  21.307    490
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 14.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.49 %
    Favored  : 88.51 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 22.08 %
    Favored  : 75.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.38 (0.35), residues: 435
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.27), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 103 
 TYR   0.021   0.003   TYR C 105 
 PHE   0.009   0.001   PHE A  87 
 TRP   0.002   0.001   TRP A  79 
 HIS   0.005   0.001   HIS A  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 3645)
  covalent geometry    : angle       0.63674 ( 4960)
  hydrogen bonds       : bond        0.01847 (   76)
  hydrogen bonds       : angle       5.30312 (  228)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 821.29 seconds
wall clock time: 14 minutes 50.06 seconds (890.06 seconds total)