Starting phenix.real_space_refine
on Tue Feb 11 09:12:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ade_15361/02_2025/8ade_15361.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ade_15361/02_2025/8ade_15361.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ade_15361/02_2025/8ade_15361.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ade_15361/02_2025/8ade_15361.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ade_15361/02_2025/8ade_15361.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ade_15361/02_2025/8ade_15361.cif"
  }
  resolution = 2.78
  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=   0.002
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       7      5.16       5
     C    3255      2.51       5
     N     826      2.21       5
     O     938      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 70 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5026
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 718
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 718
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 4, 'TRANS': 87}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D, G, F
  Time building chain proxies: 2.24, per 1000 atoms: 0.45
  Number of scatterers: 5026
  At special positions: 0
  Unit cell: (68.64, 85.28, 50.96, 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       7     16.00
     O     938      8.00
     N     826      7.00
     C    3255      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: 1.26
  Conformation dependent library (CDL) restraints added in 564.6 milliseconds
  

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1218

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 35.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16
      removed outlier: 6.253A  pdb=" N   LEU A  12 " --> pdb=" O   MET B  13 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   LYS B  15 " --> pdb=" O   LEU A  12 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   VAL A  14 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   LEU B  12 " --> pdb=" O   MET C  13 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   LYS C  15 " --> pdb=" O   LEU B  12 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   VAL B  14 " --> pdb=" O   LYS C  15 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   LEU C  12 " --> pdb=" O   MET D  13 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   LYS D  15 " --> pdb=" O   LEU C  12 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   VAL C  14 " --> pdb=" O   LYS D  15 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   LEU D  12 " --> pdb=" O   MET E  13 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   LYS E  15 " --> pdb=" O   LEU D  12 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   VAL D  14 " --> pdb=" O   LYS E  15 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   LEU E  12 " --> pdb=" O   MET F  13 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   LYS F  15 " --> pdb=" O   LEU E  12 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   VAL E  14 " --> pdb=" O   LYS F  15 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   LEU F  12 " --> pdb=" O   MET G  13 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   LYS G  15 " --> pdb=" O   LEU F  12 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   VAL F  14 " --> pdb=" O   LYS G  15 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21
      removed outlier: 6.802A  pdb=" N   VAL A  20 " --> pdb=" O   ARG B  21 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   VAL B  20 " --> pdb=" O   ARG C  21 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   VAL C  20 " --> pdb=" O   ARG D  21 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   VAL D  20 " --> pdb=" O   ARG E  21 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   VAL E  20 " --> pdb=" O   ARG F  21 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   VAL F  20 " --> pdb=" O   ARG G  21 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 26
    Processing sheet with id=AA4, first strand: chain 'A' and resid 29 through 34
    Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 62
      removed outlier: 6.403A  pdb=" N   THR A  59 " --> pdb=" O   THR B  60 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   GLU B  62 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   GLU A  61 " --> pdb=" O   GLU B  62 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   THR B  59 " --> pdb=" O   THR C  60 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   GLU C  62 " --> pdb=" O   THR B  59 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   GLU B  61 " --> pdb=" O   GLU C  62 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   THR C  59 " --> pdb=" O   THR D  60 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   GLU D  62 " --> pdb=" O   THR C  59 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   GLU C  61 " --> pdb=" O   GLU D  62 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   THR D  59 " --> pdb=" O   THR E  60 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   GLU E  62 " --> pdb=" O   THR D  59 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   GLU D  61 " --> pdb=" O   GLU E  62 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   THR E  59 " --> pdb=" O   THR F  60 " (cutoff:3.500A)
      removed outlier: 8.313A  pdb=" N   GLU F  62 " --> pdb=" O   THR E  59 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   GLU E  61 " --> pdb=" O   GLU F  62 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   THR F  59 " --> pdb=" O   THR G  60 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   GLU G  62 " --> pdb=" O   THR F  59 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   GLU F  61 " --> pdb=" O   GLU G  62 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 72 through 73
      removed outlier: 6.474A  pdb=" N   GLU A  72 " --> pdb=" O   ILE B  73 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   GLU B  72 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   GLU C  72 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   GLU D  72 " --> pdb=" O   ILE E  73 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   GLU E  72 " --> pdb=" O   ILE F  73 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   GLU F  72 " --> pdb=" O   ILE G  73 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 80
      removed outlier: 7.031A  pdb=" N   TRP A  79 " --> pdb=" O   TYR B  78 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   LYS B  80 " --> pdb=" O   TRP A  79 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   TRP B  79 " --> pdb=" O   TYR C  78 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   LYS C  80 " --> pdb=" O   TRP B  79 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   TRP C  79 " --> pdb=" O   TYR D  78 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   LYS D  80 " --> pdb=" O   TRP C  79 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   TRP D  79 " --> pdb=" O   TYR E  78 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   LYS E  80 " --> pdb=" O   TRP D  79 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   TRP E  79 " --> pdb=" O   TYR F  78 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   LYS F  80 " --> pdb=" O   TRP E  79 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   TRP F  79 " --> pdb=" O   TYR G  78 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   LYS G  80 " --> pdb=" O   TRP F  79 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 93 through 98
    Processing sheet with id=AA9, first strand: chain 'A' and resid 104 through 106
    Processing sheet with id=AB1, first strand: chain 'A' and resid 109 through 110
      removed outlier: 6.486A  pdb=" N   ALA A 109 " --> pdb=" O   LEU B 110 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   ALA B 109 " --> pdb=" O   LEU C 110 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ALA C 109 " --> pdb=" O   LEU D 110 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ALA D 109 " --> pdb=" O   LEU E 110 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   ALA E 109 " --> pdb=" O   LEU F 110 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ALA F 109 " --> pdb=" O   LEU G 110 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 114 through 115
      removed outlier: 6.857A  pdb=" N   TYR A 114 " --> pdb=" O   SER B 115 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   TYR B 114 " --> pdb=" O   SER C 115 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   TYR C 114 " --> pdb=" O   SER D 115 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   TYR D 114 " --> pdb=" O   SER E 115 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   TYR E 114 " --> pdb=" O   SER F 115 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   TYR F 114 " --> pdb=" O   SER G 115 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 118 through 122

    114 hydrogen bonds defined for protein.
    342 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: 1.44

  Time building geometry restraints manager: 1.45 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: 902
        1.33 -     1.45: 1317
        1.45 -     1.57: 2912
        1.57 -     1.69: 0
        1.69 -     1.81: 14
  Bond restraints: 5145
  Sorted by residual:
  bond pdb=" N   ILE A  26 "
       pdb=" CA  ILE A  26 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.042 1.11e-02 8.12e+03 1.40e+01
  bond pdb=" N   ILE C  26 "
       pdb=" CA  ILE C  26 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.042 1.11e-02 8.12e+03 1.40e+01
  bond pdb=" N   ILE E  26 "
       pdb=" CA  ILE E  26 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.11e-02 8.12e+03 1.37e+01
  bond pdb=" N   ILE D  26 "
       pdb=" CA  ILE D  26 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.11e-02 8.12e+03 1.36e+01
  bond pdb=" N   ILE G  26 "
       pdb=" CA  ILE G  26 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.11e-02 8.12e+03 1.36e+01
  ... (remaining 5140 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 4654
        1.46 -     2.91: 1910
        2.91 -     4.37: 366
        4.37 -     5.83: 42
        5.83 -     7.28: 28
  Bond angle restraints: 7000
  Sorted by residual:
  angle pdb=" C   PRO B  24 "
        pdb=" CA  PRO B  24 "
        pdb=" CB  PRO B  24 "
      ideal   model   delta    sigma   weight residual
     110.95  104.89    6.06 1.31e+00 5.83e-01 2.14e+01
  angle pdb=" C   PRO C  24 "
        pdb=" CA  PRO C  24 "
        pdb=" CB  PRO C  24 "
      ideal   model   delta    sigma   weight residual
     110.95  104.91    6.04 1.31e+00 5.83e-01 2.13e+01
  angle pdb=" C   PRO E  24 "
        pdb=" CA  PRO E  24 "
        pdb=" CB  PRO E  24 "
      ideal   model   delta    sigma   weight residual
     110.95  104.91    6.04 1.31e+00 5.83e-01 2.13e+01
  angle pdb=" C   PRO A  24 "
        pdb=" CA  PRO A  24 "
        pdb=" CB  PRO A  24 "
      ideal   model   delta    sigma   weight residual
     110.95  104.92    6.03 1.31e+00 5.83e-01 2.12e+01
  angle pdb=" C   PRO D  24 "
        pdb=" CA  PRO D  24 "
        pdb=" CB  PRO D  24 "
      ideal   model   delta    sigma   weight residual
     110.95  104.93    6.02 1.31e+00 5.83e-01 2.11e+01
  ... (remaining 6995 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.52: 2737
       11.52 -    23.03: 238
       23.03 -    34.55: 42
       34.55 -    46.07: 0
       46.07 -    57.58: 14
  Dihedral angle restraints: 3031
    sinusoidal: 1148
      harmonic: 1883
  Sorted by residual:
  dihedral pdb=" C   PRO C  24 "
           pdb=" N   PRO C  24 "
           pdb=" CA  PRO C  24 "
           pdb=" CB  PRO C  24 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -112.66   -8.04     0      2.50e+00 1.60e-01 1.03e+01
  dihedral pdb=" C   PRO B  24 "
           pdb=" N   PRO B  24 "
           pdb=" CA  PRO B  24 "
           pdb=" CB  PRO B  24 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -112.66   -8.04     0      2.50e+00 1.60e-01 1.03e+01
  dihedral pdb=" C   PRO E  24 "
           pdb=" N   PRO E  24 "
           pdb=" CA  PRO E  24 "
           pdb=" CB  PRO E  24 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -112.67   -8.03     0      2.50e+00 1.60e-01 1.03e+01
  ... (remaining 3028 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 209
       0.047 -    0.094: 249
       0.094 -    0.141: 203
       0.141 -    0.189: 116
       0.189 -    0.236: 49
  Chirality restraints: 826
  Sorted by residual:
  chirality pdb=" CA  ILE F  68 "
            pdb=" N   ILE F  68 "
            pdb=" C   ILE F  68 "
            pdb=" CB  ILE F  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  ILE E  68 "
            pdb=" N   ILE E  68 "
            pdb=" C   ILE E  68 "
            pdb=" CB  ILE E  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CA  ILE C  68 "
            pdb=" N   ILE C  68 "
            pdb=" C   ILE C  68 "
            pdb=" CB  ILE C  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 823 not shown)

  Planarity restraints: 861
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR C 114 "    0.013 2.00e-02 2.50e+03   2.58e-02 6.64e+00
        pdb=" C   TYR C 114 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   TYR C 114 "    0.017 2.00e-02 2.50e+03
        pdb=" N   SER C 115 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 114 "    0.012 2.00e-02 2.50e+03   2.55e-02 6.52e+00
        pdb=" C   TYR A 114 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   TYR A 114 "    0.017 2.00e-02 2.50e+03
        pdb=" N   SER A 115 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR E 114 "    0.012 2.00e-02 2.50e+03   2.55e-02 6.51e+00
        pdb=" C   TYR E 114 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   TYR E 114 "    0.017 2.00e-02 2.50e+03
        pdb=" N   SER E 115 "    0.015 2.00e-02 2.50e+03
  ... (remaining 858 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 406
        2.75 -     3.29: 5005
        3.29 -     3.82: 8088
        3.82 -     4.36: 11472
        4.36 -     4.90: 20635
  Nonbonded interactions: 45606
  Sorted by model distance:
  nonbonded pdb=" O   SER A 117 "
            pdb=" OG  SER B 117 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   SER D 117 "
            pdb=" OG  SER E 117 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   SER C 117 "
            pdb=" OG  SER D 117 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   SER B 117 "
            pdb=" OG  SER C 117 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   SER F 117 "
            pdb=" OG  SER G 117 "
     model   vdw
     2.213 3.040
  ... (remaining 45601 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
}

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:             1.430
  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:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.570
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  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:11.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
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      :  0.012   0.042   5145  Z= 0.832
  Angle     :  1.581   7.283   7000  Z= 1.154
  Chirality :  0.107   0.236    826
  Planarity :  0.005   0.026    861
  Dihedral  :  9.637  57.583   1813
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.12 (0.23), residues: 616
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.13 (0.18), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.001   TRP E  79 
 HIS   0.003   0.001   HIS B  90 
 PHE   0.004   0.001   PHE G  33 
 TYR   0.006   0.001   TYR C 116 
 ARG   0.002   0.001   ARG C  34 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 THR cc_start: 0.8874 (m) cc_final: 0.8558 (p)
REVERT: C  123 THR cc_start: 0.7245 (t) cc_final: 0.6610 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 1.2375
  time to fit residues: 231.2026
Evaluate side-chains
  132 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.2980
   chunk 25 optimal weight:    0.9990
   chunk 49 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.155716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.131825 restraints weight = 6016.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.4147 rms_B_bonded: 2.53
r_work: 0.4039 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3917 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5145  Z= 0.338
  Angle     :  0.677   6.850   7000  Z= 0.353
  Chirality :  0.050   0.164    826
  Planarity :  0.005   0.045    861
  Dihedral  :  5.178  16.565    693
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 17.95 %
    Favored  : 78.75 %
  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: -3.22 (0.25), residues: 616
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.45 (0.19), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP D  79 
 HIS   0.002   0.001   HIS B  88 
 PHE   0.013   0.002   PHE B  33 
 TYR   0.016   0.002   TYR E 114 
 ARG   0.009   0.001   ARG E 104 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.8124 (ttt) cc_final: 0.7725 (tpt)
REVERT: B   92 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7172 (tm-30)
REVERT: B   99 ASP cc_start: 0.7206 (t0) cc_final: 0.6802 (t0)
REVERT: B  104 ARG cc_start: 0.8308 (ttp-110) cc_final: 0.7813 (ttm110)
REVERT: C   92 GLU cc_start: 0.8335 (pt0) cc_final: 0.7374 (tm-30)
REVERT: D   13 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.7429 (tmt)
REVERT: D   35 LYS cc_start: 0.8417 (ttmm) cc_final: 0.8032 (ttmm)
REVERT: D   92 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7394 (tm-30)
REVERT: E   21 ARG cc_start: 0.8363 (mmm160) cc_final: 0.7828 (tpp80)
REVERT: E   35 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8331 (ttmm)
REVERT: F   13 MET cc_start: 0.7757 (tmt) cc_final: 0.7533 (tmt)
REVERT: F   34 ARG cc_start: 0.7991 (tpt-90) cc_final: 0.7708 (ttt90)
REVERT: G   13 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7246 (tmt)
REVERT: G   89 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8054 (mt-10)
REVERT: G   99 ASP cc_start: 0.6939 (t0) cc_final: 0.6622 (t70)
  outliers start: 18
  outliers final: 4
  residues processed: 147
  average time/residue: 1.5448
  time to fit residues: 234.0679
Evaluate side-chains
  122 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   92 GLU
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain D residue   13 MET
Chi-restraints excluded: chain E residue   35 LYS
Chi-restraints excluded: chain G residue   13 MET
Chi-restraints excluded: chain G residue  104 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 4 optimal weight:    0.3980
   chunk 5 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.147678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.123376 restraints weight = 6169.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.4054 rms_B_bonded: 2.52
r_work: 0.3935 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3809 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.3681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5145  Z= 0.311
  Angle     :  0.632   7.194   7000  Z= 0.330
  Chirality :  0.050   0.174    826
  Planarity :  0.005   0.047    861
  Dihedral  :  5.141  15.816    693
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.33 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.11 (0.26), residues: 616
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.37 (0.20), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  79 
 HIS   0.002   0.001   HIS D  88 
 PHE   0.010   0.002   PHE B  33 
 TYR   0.019   0.002   TYR C 114 
 ARG   0.008   0.001   ARG E 104 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.8182 (ttt) cc_final: 0.7811 (tpt)
REVERT: B   92 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7363 (tm-30)
REVERT: B  104 ARG cc_start: 0.8358 (ttp-110) cc_final: 0.7818 (ttm110)
REVERT: C   92 GLU cc_start: 0.8634 (pt0) cc_final: 0.7661 (tm-30)
REVERT: D   13 MET cc_start: 0.7774 (tmt) cc_final: 0.7482 (tmt)
REVERT: D   35 LYS cc_start: 0.8608 (ttmm) cc_final: 0.8183 (ttmm)
REVERT: D   92 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7748 (tm-30)
REVERT: E   21 ARG cc_start: 0.8326 (mmm160) cc_final: 0.7885 (tpp80)
REVERT: E   35 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8139 (ttmm)
REVERT: E  104 ARG cc_start: 0.8336 (ttm110) cc_final: 0.7986 (ttp-110)
REVERT: F   13 MET cc_start: 0.7793 (tmt) cc_final: 0.7464 (tmt)
REVERT: F   21 ARG cc_start: 0.8203 (mmm-85) cc_final: 0.7842 (tpp80)
REVERT: F   76 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8324 (mptt)
REVERT: G   13 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7359 (tmt)
REVERT: G   89 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8101 (mt-10)
  outliers start: 17
  outliers final: 6
  residues processed: 128
  average time/residue: 1.7189
  time to fit residues: 226.4102
Evaluate side-chains
  117 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   92 GLU
Chi-restraints excluded: chain C residue   76 LYS
Chi-restraints excluded: chain E residue   35 LYS
Chi-restraints excluded: chain F residue   76 LYS
Chi-restraints excluded: chain G residue   13 MET
Chi-restraints excluded: chain G residue   59 THR
Chi-restraints excluded: chain G residue  104 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 35 optimal weight:    0.4980
   chunk 28 optimal weight:    0.4980
   chunk 51 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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**
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.145198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.120719 restraints weight = 6180.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.4014 rms_B_bonded: 2.51
r_work: 0.3891 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3767 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.4011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5145  Z= 0.310
  Angle     :  0.607   6.500   7000  Z= 0.318
  Chirality :  0.049   0.138    826
  Planarity :  0.004   0.042    861
  Dihedral  :  5.135  16.621    693
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 19.78 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.95 (0.26), residues: 616
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.24 (0.20), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP F  79 
 HIS   0.002   0.001   HIS D  88 
 PHE   0.008   0.002   PHE B  33 
 TYR   0.017   0.002   TYR C 114 
 ARG   0.007   0.001   ARG F 104 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.8148 (ttt) cc_final: 0.7772 (tpt)
REVERT: B   92 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7667 (tm-30)
REVERT: B  104 ARG cc_start: 0.8315 (ttp-110) cc_final: 0.7888 (ttm110)
REVERT: C   92 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7684 (tm-30)
REVERT: D   13 MET cc_start: 0.7877 (tmt) cc_final: 0.7501 (tmt)
REVERT: D   21 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7787 (mmm-85)
REVERT: D   35 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8171 (ttmm)
REVERT: D   92 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7757 (tm-30)
REVERT: E   13 MET cc_start: 0.7834 (tmt) cc_final: 0.6895 (tmt)
REVERT: E   21 ARG cc_start: 0.8346 (mmm160) cc_final: 0.7878 (tpp80)
REVERT: F   13 MET cc_start: 0.7833 (tmt) cc_final: 0.7595 (tmt)
REVERT: F   21 ARG cc_start: 0.8175 (mmm-85) cc_final: 0.7807 (tpp80)
REVERT: F   35 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8217 (ttmt)
REVERT: F   76 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8198 (mptt)
REVERT: G   13 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7392 (tmt)
REVERT: G   80 LYS cc_start: 0.8392 (tttt) cc_final: 0.8127 (tttm)
REVERT: G   89 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8112 (mt-10)
  outliers start: 24
  outliers final: 5
  residues processed: 118
  average time/residue: 1.8436
  time to fit residues: 223.6996
Evaluate side-chains
  112 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   92 GLU
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain D residue   21 ARG
Chi-restraints excluded: chain F residue   35 LYS
Chi-restraints excluded: chain F residue   76 LYS
Chi-restraints excluded: chain G residue   13 MET
Chi-restraints excluded: chain G residue   59 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0770
   chunk 47 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0980
   chunk 43 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.5340

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

Flipped N/Q/H residues before XYZ refinement:
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.154420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.130975 restraints weight = 5674.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 2.47
r_work: 0.3940 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3809 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.4215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5145  Z= 0.284
  Angle     :  0.596   5.840   7000  Z= 0.312
  Chirality :  0.049   0.145    826
  Planarity :  0.005   0.055    861
  Dihedral  :  5.093  16.531    693
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 21.79 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.27), residues: 616
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.16 (0.21), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  79 
 HIS   0.002   0.000   HIS A  88 
 PHE   0.006   0.001   PHE E  64 
 TYR   0.014   0.002   TYR C 114 
 ARG   0.011   0.001   ARG D 104 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.8179 (ttt) cc_final: 0.7804 (tpt)
REVERT: A   92 GLU cc_start: 0.8451 (pt0) cc_final: 0.7658 (tm-30)
REVERT: B   61 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7404 (mt-10)
REVERT: B   92 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7612 (tm-30)
REVERT: B  104 ARG cc_start: 0.8187 (ttp-110) cc_final: 0.7701 (ttm110)
REVERT: C   92 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7707 (tm-30)
REVERT: D   13 MET cc_start: 0.7840 (tmt) cc_final: 0.7444 (tmt)
REVERT: D   35 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8209 (ttmm)
REVERT: D   92 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7632 (tm-30)
REVERT: E   13 MET cc_start: 0.7859 (tmt) cc_final: 0.6872 (tmt)
REVERT: F   13 MET cc_start: 0.7763 (tmt) cc_final: 0.7231 (tmt)
REVERT: F   21 ARG cc_start: 0.8157 (mmm-85) cc_final: 0.7762 (tpp80)
REVERT: F   35 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8092 (ttmt)
REVERT: F   76 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8118 (mptt)
REVERT: G   13 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7323 (tmt)
REVERT: G   80 LYS cc_start: 0.8186 (tttt) cc_final: 0.7902 (tttm)
REVERT: G   89 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8216 (mt-10)
  outliers start: 16
  outliers final: 3
  residues processed: 111
  average time/residue: 1.8422
  time to fit residues: 209.9470
Evaluate side-chains
  109 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   61 GLU
Chi-restraints excluded: chain B residue   92 GLU
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain F residue   35 LYS
Chi-restraints excluded: chain F residue   76 LYS
Chi-restraints excluded: chain G residue   13 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0370
   chunk 47 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0980
   chunk 2 optimal weight:    3.9990
   chunk 38 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.153829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.129955 restraints weight = 5682.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.4050 rms_B_bonded: 2.51
r_work: 0.3930 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3799 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.4358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5145  Z= 0.282
  Angle     :  0.589   5.439   7000  Z= 0.309
  Chirality :  0.049   0.142    826
  Planarity :  0.005   0.055    861
  Dihedral  :  5.079  16.631    693
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 22.71 %
    Favored  : 74.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.74 (0.27), residues: 616
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.08 (0.21), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D  79 
 HIS   0.002   0.001   HIS A  88 
 PHE   0.006   0.001   PHE E  64 
 TYR   0.013   0.002   TYR C 114 
 ARG   0.012   0.001   ARG D 104 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.486 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.8179 (ttt) cc_final: 0.7795 (tpt)
REVERT: A   74 ASP cc_start: 0.8936 (t0) cc_final: 0.8694 (t0)
REVERT: A   92 GLU cc_start: 0.8473 (pt0) cc_final: 0.7629 (tm-30)
REVERT: B   92 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7651 (tm-30)
REVERT: B  104 ARG cc_start: 0.8171 (ttp-110) cc_final: 0.7706 (ttm110)
REVERT: C   92 GLU cc_start: 0.8572 (pt0) cc_final: 0.7724 (tm-30)
REVERT: D   13 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7554 (tmt)
REVERT: D   35 LYS cc_start: 0.8619 (ttmm) cc_final: 0.8313 (ttmm)
REVERT: D   92 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7651 (tm-30)
REVERT: E   13 MET cc_start: 0.7802 (tmt) cc_final: 0.6874 (tmt)
REVERT: E   21 ARG cc_start: 0.8150 (mmm-85) cc_final: 0.7597 (tpp80)
REVERT: F   13 MET cc_start: 0.7770 (tmt) cc_final: 0.7220 (tmt)
REVERT: F   21 ARG cc_start: 0.8222 (mmm-85) cc_final: 0.7764 (tpp80)
REVERT: F   35 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8071 (ttmt)
REVERT: F   76 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8138 (mptt)
REVERT: G   13 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7334 (tmt)
REVERT: G   80 LYS cc_start: 0.8183 (tttt) cc_final: 0.7846 (tttm)
  outliers start: 16
  outliers final: 6
  residues processed: 112
  average time/residue: 1.9352
  time to fit residues: 222.6728
Evaluate side-chains
  107 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   92 GLU
Chi-restraints excluded: chain C residue  104 ARG
Chi-restraints excluded: chain D residue   13 MET
Chi-restraints excluded: chain F residue   35 LYS
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   76 LYS
Chi-restraints excluded: chain G residue   13 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0980
   chunk 0 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  90 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.150847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.126819 restraints weight = 5605.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 2.48
r_work: 0.3895 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3763 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.4449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5145  Z= 0.338
  Angle     :  0.623   6.543   7000  Z= 0.327
  Chirality :  0.050   0.150    826
  Planarity :  0.004   0.057    861
  Dihedral  :  5.173  17.376    693
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 22.53 %
    Favored  : 74.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.60 (0.28), residues: 616
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.21), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F  79 
 HIS   0.004   0.001   HIS F  90 
 PHE   0.006   0.001   PHE A  33 
 TYR   0.012   0.002   TYR C 114 
 ARG   0.011   0.001   ARG F 104 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.8206 (ttt) cc_final: 0.7810 (tpt)
REVERT: A   74 ASP cc_start: 0.9006 (t0) cc_final: 0.8788 (t0)
REVERT: A   92 GLU cc_start: 0.8536 (pt0) cc_final: 0.7655 (tm-30)
REVERT: B   92 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7615 (tm-30)
REVERT: B  104 ARG cc_start: 0.8211 (ttp-110) cc_final: 0.7805 (ttm110)
REVERT: C   92 GLU cc_start: 0.8472 (pt0) cc_final: 0.7723 (tm-30)
REVERT: D   13 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7525 (tmt)
REVERT: D   26 ILE cc_start: 0.8903 (pt) cc_final: 0.8605 (mt)
REVERT: D   35 LYS cc_start: 0.8628 (ttmm) cc_final: 0.8251 (ttmm)
REVERT: D   92 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7677 (tm-30)
REVERT: E   13 MET cc_start: 0.7851 (tmt) cc_final: 0.6888 (tmt)
REVERT: E   21 ARG cc_start: 0.8165 (mmm-85) cc_final: 0.7605 (tpp80)
REVERT: F   13 MET cc_start: 0.7791 (tmt) cc_final: 0.7318 (tpt)
REVERT: F   21 ARG cc_start: 0.8210 (mmm-85) cc_final: 0.7749 (tpp80)
REVERT: F   35 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8077 (ttmt)
REVERT: G   13 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7415 (tmt)
REVERT: G   66 GLU cc_start: 0.8324 (tt0) cc_final: 0.8098 (tt0)
REVERT: G   80 LYS cc_start: 0.8192 (tttt) cc_final: 0.7868 (tttm)
  outliers start: 16
  outliers final: 6
  residues processed: 111
  average time/residue: 1.7135
  time to fit residues: 195.6237
Evaluate side-chains
  107 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   92 GLU
Chi-restraints excluded: chain C residue  104 ARG
Chi-restraints excluded: chain D residue   13 MET
Chi-restraints excluded: chain F residue   35 LYS
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain G residue   13 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  90 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.149138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.124880 restraints weight = 5779.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 2.52
r_work: 0.3871 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3740 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.4553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   5145  Z= 0.360
  Angle     :  0.630   7.076   7000  Z= 0.331
  Chirality :  0.050   0.171    826
  Planarity :  0.005   0.062    861
  Dihedral  :  5.244  18.154    693
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 23.08 %
    Favored  : 73.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.57 (0.28), residues: 616
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.95 (0.22), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP D  79 
 HIS   0.006   0.001   HIS F  90 
 PHE   0.007   0.001   PHE A  33 
 TYR   0.012   0.002   TYR C 114 
 ARG   0.012   0.001   ARG F 104 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.8199 (ttt) cc_final: 0.7826 (tpt)
REVERT: A   74 ASP cc_start: 0.9019 (t0) cc_final: 0.8776 (t0)
REVERT: A   92 GLU cc_start: 0.8558 (pt0) cc_final: 0.7704 (tm-30)
REVERT: B   92 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7681 (tm-30)
REVERT: B  104 ARG cc_start: 0.8240 (ttp-110) cc_final: 0.7821 (ttm110)
REVERT: C   92 GLU cc_start: 0.8498 (pt0) cc_final: 0.7744 (tm-30)
REVERT: D   13 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7536 (tmt)
REVERT: D   26 ILE cc_start: 0.8905 (pt) cc_final: 0.8584 (mt)
REVERT: D   35 LYS cc_start: 0.8653 (ttmm) cc_final: 0.8280 (ttmm)
REVERT: D   92 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7846 (tm-30)
REVERT: E   13 MET cc_start: 0.7850 (tmt) cc_final: 0.6903 (tmt)
REVERT: E   21 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7600 (tpp80)
REVERT: F   13 MET cc_start: 0.7807 (tmt) cc_final: 0.7366 (tpt)
REVERT: F   21 ARG cc_start: 0.8214 (mmm-85) cc_final: 0.7744 (tpp80)
REVERT: G   13 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7431 (tmt)
REVERT: G   80 LYS cc_start: 0.8231 (tttt) cc_final: 0.7923 (tttm)
  outliers start: 16
  outliers final: 7
  residues processed: 113
  average time/residue: 1.8392
  time to fit residues: 213.4713
Evaluate side-chains
  111 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   92 GLU
Chi-restraints excluded: chain C residue  104 ARG
Chi-restraints excluded: chain D residue   13 MET
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   76 LYS
Chi-restraints excluded: chain G residue   13 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 49 optimal weight:    0.0870
   chunk 46 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 51 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0030
   chunk 48 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0270
   chunk 33 optimal weight:    0.2980
   chunk 1 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.2026

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

Flipped N/Q/H residues before XYZ refinement:
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.157827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.134422 restraints weight = 5578.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.4098 rms_B_bonded: 2.49
r_work: 0.3975 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3845 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.4662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5145  Z= 0.215
  Angle     :  0.585   6.172   7000  Z= 0.305
  Chirality :  0.050   0.152    826
  Planarity :  0.005   0.061    861
  Dihedral  :  4.955  16.705    693
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 24.91 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.66 (0.28), residues: 616
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.21), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A  79 
 HIS   0.003   0.000   HIS G  90 
 PHE   0.007   0.001   PHE E  64 
 TYR   0.013   0.001   TYR E 114 
 ARG   0.014   0.001   ARG F 104 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.595 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.8171 (ttt) cc_final: 0.7800 (tpt)
REVERT: A   92 GLU cc_start: 0.8533 (pt0) cc_final: 0.7664 (tm-30)
REVERT: B   92 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7573 (tm-30)
REVERT: B  104 ARG cc_start: 0.8180 (ttp-110) cc_final: 0.7731 (ttm110)
REVERT: C   92 GLU cc_start: 0.8589 (pt0) cc_final: 0.7750 (tm-30)
REVERT: D   13 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7560 (tmt)
REVERT: D   26 ILE cc_start: 0.8853 (pt) cc_final: 0.8643 (mt)
REVERT: D   35 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8202 (ttmm)
REVERT: D   77 SER cc_start: 0.8624 (t) cc_final: 0.8374 (t)
REVERT: D   92 GLU cc_start: 0.8377 (tm-30) cc_final: 0.7874 (tm-30)
REVERT: E   13 MET cc_start: 0.7838 (tmt) cc_final: 0.7438 (tpt)
REVERT: E   21 ARG cc_start: 0.8035 (mmm-85) cc_final: 0.7503 (tpp80)
REVERT: F   13 MET cc_start: 0.7798 (tmt) cc_final: 0.7223 (tmt)
REVERT: F   21 ARG cc_start: 0.8192 (mmm-85) cc_final: 0.7739 (tpp80)
REVERT: F   76 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8060 (mptt)
REVERT: G   13 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7376 (tmt)
REVERT: G   80 LYS cc_start: 0.8082 (tttt) cc_final: 0.7771 (tttm)
  outliers start: 11
  outliers final: 3
  residues processed: 106
  average time/residue: 1.8904
  time to fit residues: 206.0529
Evaluate side-chains
  104 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   92 GLU
Chi-restraints excluded: chain D residue   13 MET
Chi-restraints excluded: chain F residue   76 LYS
Chi-restraints excluded: chain G residue   13 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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**
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.151003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.126471 restraints weight = 5649.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.4021 rms_B_bonded: 2.51
r_work: 0.3898 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3768 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.4692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5145  Z= 0.349
  Angle     :  0.644   7.658   7000  Z= 0.336
  Chirality :  0.051   0.185    826
  Planarity :  0.004   0.042    861
  Dihedral  :  5.124  18.639    693
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 25.64 %
    Favored  : 72.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.29), residues: 616
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.91 (0.22), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP D  79 
 HIS   0.002   0.001   HIS A  88 
 PHE   0.007   0.002   PHE G  33 
 TYR   0.012   0.002   TYR C 114 
 ARG   0.014   0.001   ARG E 104 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 MET cc_start: 0.8226 (ttt) cc_final: 0.7836 (tpt)
REVERT: A   74 ASP cc_start: 0.9007 (t0) cc_final: 0.8806 (t0)
REVERT: A   92 GLU cc_start: 0.8548 (pt0) cc_final: 0.7690 (tm-30)
REVERT: B   92 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7740 (tm-30)
REVERT: B  104 ARG cc_start: 0.8242 (ttp-110) cc_final: 0.7849 (ttm110)
REVERT: C   92 GLU cc_start: 0.8487 (pt0) cc_final: 0.7764 (tm-30)
REVERT: D   13 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7537 (tmt)
REVERT: D   26 ILE cc_start: 0.8928 (pt) cc_final: 0.8661 (mt)
REVERT: D   35 LYS cc_start: 0.8631 (ttmm) cc_final: 0.8263 (ttmm)
REVERT: D   92 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7851 (tm-30)
REVERT: E   13 MET cc_start: 0.7807 (tmt) cc_final: 0.6920 (tmt)
REVERT: E   21 ARG cc_start: 0.8133 (mmm-85) cc_final: 0.7568 (tpp80)
REVERT: F   13 MET cc_start: 0.7804 (tmt) cc_final: 0.7326 (tpt)
REVERT: F   21 ARG cc_start: 0.8221 (mmm-85) cc_final: 0.7768 (tpp80)
REVERT: G   13 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7376 (tmt)
REVERT: G   80 LYS cc_start: 0.8194 (tttt) cc_final: 0.7892 (tttm)
  outliers start: 9
  outliers final: 3
  residues processed: 107
  average time/residue: 1.8379
  time to fit residues: 201.9470
Evaluate side-chains
  108 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain B residue   59 THR
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue   92 GLU
Chi-restraints excluded: chain D residue   13 MET
Chi-restraints excluded: chain G residue   13 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0270
   chunk 37 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.4238

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

Flipped N/Q/H residues before XYZ refinement:
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.155223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.131143 restraints weight = 5727.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.4071 rms_B_bonded: 2.52
r_work: 0.3944 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3812 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.4737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5145  Z= 0.255
  Angle     :  0.609   7.060   7000  Z= 0.317
  Chirality :  0.050   0.211    826
  Planarity :  0.004   0.046    861
  Dihedral  :  5.012  19.012    693
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 26.19 %
    Favored  : 72.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.57 (0.29), residues: 616
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.95 (0.22), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  79 
 HIS   0.001   0.000   HIS A  88 
 PHE   0.007   0.001   PHE E  64 
 TYR   0.012   0.002   TYR C 114 
 ARG   0.014   0.001   ARG E 104 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5088.95 seconds
wall clock time: 90 minutes 41.54 seconds (5441.54 seconds total)