Starting phenix.real_space_refine
on Wed Jul 30 13:28:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zlv_14790/07_2025/7zlv_14790.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zlv_14790/07_2025/7zlv_14790.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.22
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zlv_14790/07_2025/7zlv_14790.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zlv_14790/07_2025/7zlv_14790.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zlv_14790/07_2025/7zlv_14790.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zlv_14790/07_2025/7zlv_14790.cif"
  }
  resolution = 4.22
  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      39      5.16       5
     C    7794      2.51       5
     N    2040      2.21       5
     O    2361      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12234
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "i"
      Number of atoms: 4078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 527, 4078
          Classifications: {'peptide': 527}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 505}
          Chain breaks: 1
  Restraints were copied for chains:
    h, j
  Time building chain proxies: 9.18, per 1000 atoms: 0.75
  Number of scatterers: 12234
  At special positions: 0
  Unit cell: (78.358, 74.305, 274.253, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      39     16.00
     O    2361      8.00
     N    2040      7.00
     C    7794      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: 2.95
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2910

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 39 sheets defined
      2.8% alpha, 34.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.97
  Creating SS restraints...
    Processing helix  chain 'i' and resid 83 through 90
    Processing helix  chain 'i' and resid 258 through 264
      removed outlier: 3.863A  pdb=" N   VAL i 262 " --> pdb=" O   SER i 258 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   ARG i 263 " --> pdb=" O   ALA i 259 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 83 through 90
    Processing helix  chain 'h' and resid 258 through 264
      removed outlier: 3.863A  pdb=" N   VAL h 262 " --> pdb=" O   SER h 258 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   ARG h 263 " --> pdb=" O   ALA h 259 " (cutoff:3.500A)
    Processing helix  chain 'j' and resid 83 through 90
    Processing helix  chain 'j' and resid 258 through 264
      removed outlier: 3.863A  pdb=" N   VAL j 262 " --> pdb=" O   SER j 258 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   ARG j 263 " --> pdb=" O   ALA j 259 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'i' and resid 12 through 17
    Processing sheet with id=AA2, first strand: chain 'i' and resid 47 through 53
      removed outlier: 7.175A  pdb=" N   TYR i  78 " --> pdb=" O   ILE i  35 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'i' and resid 47 through 53
      removed outlier: 3.904A  pdb=" N   GLN i  99 " --> pdb=" O   VAL i  73 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'i' and resid 109 through 115
      removed outlier: 3.669A  pdb=" N   VAL i 128 " --> pdb=" O   PHE i 167 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   PHE i 167 " --> pdb=" O   VAL i 128 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'i' and resid 154 through 159
      removed outlier: 7.272A  pdb=" N   ILE i 141 " --> pdb=" O   TYR i 156 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   VAL i 158 " --> pdb=" O   CYS i 139 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   CYS i 139 " --> pdb=" O   VAL i 158 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   THR i 140 " --> pdb=" O   SER i 180 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'i' and resid 154 through 159
      removed outlier: 7.272A  pdb=" N   ILE i 141 " --> pdb=" O   TYR i 156 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   VAL i 158 " --> pdb=" O   CYS i 139 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   CYS i 139 " --> pdb=" O   VAL i 158 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   THR i 140 " --> pdb=" O   SER i 180 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   TYR i 175 " --> pdb=" O   PHE i 203 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   PHE i 203 " --> pdb=" O   TYR i 175 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'i' and resid 182 through 184
    Processing sheet with id=AA8, first strand: chain 'i' and resid 216 through 223
      removed outlier: 4.366A  pdb=" N   ASN i 217 " --> pdb=" O   ASP i 239 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ASP i 239 " --> pdb=" O   ASN i 217 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS i 221 " --> pdb=" O   ARG i 235 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'i' and resid 270 through 274
      removed outlier: 4.103A  pdb=" N   PHE i 251 " --> pdb=" O   VAL i 274 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'i' and resid 270 through 274
      removed outlier: 4.103A  pdb=" N   PHE i 251 " --> pdb=" O   VAL i 274 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'i' and resid 333 through 335
    Processing sheet with id=AB3, first strand: chain 'i' and resid 413 through 415
      removed outlier: 4.025A  pdb=" N   GLY i 431 " --> pdb=" O   LYS i 440 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LYS i 440 " --> pdb=" O   GLY i 431 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'i' and resid 676 through 679
      removed outlier: 3.828A  pdb=" N   HIS i 686 " --> pdb=" O   LYS i 677 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'h' and resid 12 through 17
    Processing sheet with id=AB6, first strand: chain 'h' and resid 47 through 53
      removed outlier: 7.175A  pdb=" N   TYR h  78 " --> pdb=" O   ILE h  35 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'h' and resid 47 through 53
      removed outlier: 3.904A  pdb=" N   GLN h  99 " --> pdb=" O   VAL h  73 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'h' and resid 109 through 115
      removed outlier: 3.670A  pdb=" N   VAL h 128 " --> pdb=" O   PHE h 167 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   PHE h 167 " --> pdb=" O   VAL h 128 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'h' and resid 154 through 159
      removed outlier: 7.273A  pdb=" N   ILE h 141 " --> pdb=" O   TYR h 156 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   VAL h 158 " --> pdb=" O   CYS h 139 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   CYS h 139 " --> pdb=" O   VAL h 158 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   THR h 140 " --> pdb=" O   SER h 180 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'h' and resid 154 through 159
      removed outlier: 7.273A  pdb=" N   ILE h 141 " --> pdb=" O   TYR h 156 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   VAL h 158 " --> pdb=" O   CYS h 139 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   CYS h 139 " --> pdb=" O   VAL h 158 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   THR h 140 " --> pdb=" O   SER h 180 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   TYR h 175 " --> pdb=" O   PHE h 203 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   PHE h 203 " --> pdb=" O   TYR h 175 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'h' and resid 182 through 184
    Processing sheet with id=AC3, first strand: chain 'h' and resid 216 through 223
      removed outlier: 4.366A  pdb=" N   ASN h 217 " --> pdb=" O   ASP h 239 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ASP h 239 " --> pdb=" O   ASN h 217 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS h 221 " --> pdb=" O   ARG h 235 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'h' and resid 270 through 274
      removed outlier: 4.103A  pdb=" N   PHE h 251 " --> pdb=" O   VAL h 274 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'h' and resid 270 through 274
      removed outlier: 4.103A  pdb=" N   PHE h 251 " --> pdb=" O   VAL h 274 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'h' and resid 333 through 335
    Processing sheet with id=AC7, first strand: chain 'h' and resid 413 through 415
      removed outlier: 4.025A  pdb=" N   GLY h 431 " --> pdb=" O   LYS h 440 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LYS h 440 " --> pdb=" O   GLY h 431 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'h' and resid 676 through 679
      removed outlier: 3.829A  pdb=" N   HIS h 686 " --> pdb=" O   LYS h 677 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'j' and resid 12 through 17
    Processing sheet with id=AD1, first strand: chain 'j' and resid 47 through 53
      removed outlier: 7.175A  pdb=" N   TYR j  78 " --> pdb=" O   ILE j  35 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'j' and resid 47 through 53
      removed outlier: 3.903A  pdb=" N   GLN j  99 " --> pdb=" O   VAL j  73 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'j' and resid 109 through 115
      removed outlier: 3.670A  pdb=" N   VAL j 128 " --> pdb=" O   PHE j 167 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   PHE j 167 " --> pdb=" O   VAL j 128 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'j' and resid 154 through 159
      removed outlier: 7.273A  pdb=" N   ILE j 141 " --> pdb=" O   TYR j 156 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   VAL j 158 " --> pdb=" O   CYS j 139 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   CYS j 139 " --> pdb=" O   VAL j 158 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   THR j 140 " --> pdb=" O   SER j 180 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'j' and resid 154 through 159
      removed outlier: 7.273A  pdb=" N   ILE j 141 " --> pdb=" O   TYR j 156 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   VAL j 158 " --> pdb=" O   CYS j 139 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   CYS j 139 " --> pdb=" O   VAL j 158 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   THR j 140 " --> pdb=" O   SER j 180 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   TYR j 175 " --> pdb=" O   PHE j 203 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   PHE j 203 " --> pdb=" O   TYR j 175 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'j' and resid 182 through 184
    Processing sheet with id=AD7, first strand: chain 'j' and resid 216 through 223
      removed outlier: 4.366A  pdb=" N   ASN j 217 " --> pdb=" O   ASP j 239 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ASP j 239 " --> pdb=" O   ASN j 217 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LYS j 221 " --> pdb=" O   ARG j 235 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'j' and resid 270 through 274
      removed outlier: 4.103A  pdb=" N   PHE j 251 " --> pdb=" O   VAL j 274 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'j' and resid 270 through 274
      removed outlier: 4.103A  pdb=" N   PHE j 251 " --> pdb=" O   VAL j 274 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'j' and resid 333 through 335
    Processing sheet with id=AE2, first strand: chain 'j' and resid 413 through 415
      removed outlier: 4.025A  pdb=" N   GLY j 431 " --> pdb=" O   LYS j 440 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LYS j 440 " --> pdb=" O   GLY j 431 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'j' and resid 676 through 679
      removed outlier: 3.828A  pdb=" N   HIS j 686 " --> pdb=" O   LYS j 677 " (cutoff:3.500A)

    351 hydrogen bonds defined for protein.
    945 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: 3.99

  Time building geometry restraints manager: 3.50 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3966
        1.34 -     1.46: 2810
        1.46 -     1.58: 5647
        1.58 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 12495
  Sorted by residual:
  bond pdb=" N   MET j   1 "
       pdb=" CA  MET j   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.88e+00
  bond pdb=" N   MET h   1 "
       pdb=" CA  MET h   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.86e+00
  bond pdb=" N   MET i   1 "
       pdb=" CA  MET i   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.82e+00
  bond pdb=" N   VAL i 639 "
       pdb=" CA  VAL i 639 "
    ideal  model  delta    sigma   weight residual
    1.459  1.472 -0.014 1.22e-02 6.72e+03 1.25e+00
  bond pdb=" N   VAL j 639 "
       pdb=" CA  VAL j 639 "
    ideal  model  delta    sigma   weight residual
    1.459  1.472 -0.013 1.22e-02 6.72e+03 1.22e+00
  ... (remaining 12490 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.93: 15455
        0.93 -     1.86: 1217
        1.86 -     2.79: 237
        2.79 -     3.72: 71
        3.72 -     4.65: 21
  Bond angle restraints: 17001
  Sorted by residual:
  angle pdb=" N   PRO h 439 "
        pdb=" CA  PRO h 439 "
        pdb=" C   PRO h 439 "
      ideal   model   delta    sigma   weight residual
     111.03  114.57   -3.54 1.54e+00 4.22e-01 5.28e+00
  angle pdb=" N   PRO i 439 "
        pdb=" CA  PRO i 439 "
        pdb=" C   PRO i 439 "
      ideal   model   delta    sigma   weight residual
     111.03  114.54   -3.51 1.54e+00 4.22e-01 5.20e+00
  angle pdb=" N   PRO j 439 "
        pdb=" CA  PRO j 439 "
        pdb=" C   PRO j 439 "
      ideal   model   delta    sigma   weight residual
     111.03  114.53   -3.50 1.54e+00 4.22e-01 5.18e+00
  angle pdb=" N   ASN j 682 "
        pdb=" CA  ASN j 682 "
        pdb=" C   ASN j 682 "
      ideal   model   delta    sigma   weight residual
     110.61  113.26   -2.65 1.25e+00 6.40e-01 4.48e+00
  angle pdb=" N   ALA i 641 "
        pdb=" CA  ALA i 641 "
        pdb=" C   ALA i 641 "
      ideal   model   delta    sigma   weight residual
     107.73  111.11   -3.38 1.61e+00 3.86e-01 4.41e+00
  ... (remaining 16996 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 6690
       17.55 -    35.10: 594
       35.10 -    52.66: 87
       52.66 -    70.21: 6
       70.21 -    87.76: 12
  Dihedral angle restraints: 7389
    sinusoidal: 2829
      harmonic: 4560
  Sorted by residual:
  dihedral pdb=" CA  THR h 321 "
           pdb=" C   THR h 321 "
           pdb=" N   PRO h 322 "
           pdb=" CA  PRO h 322 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.25   24.75     0      5.00e+00 4.00e-02 2.45e+01
  dihedral pdb=" CA  THR i 321 "
           pdb=" C   THR i 321 "
           pdb=" N   PRO i 322 "
           pdb=" CA  PRO i 322 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.29   24.71     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  THR j 321 "
           pdb=" C   THR j 321 "
           pdb=" N   PRO j 322 "
           pdb=" CA  PRO j 322 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.30   24.70     0      5.00e+00 4.00e-02 2.44e+01
  ... (remaining 7386 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1157
       0.032 -    0.065: 444
       0.065 -    0.097: 148
       0.097 -    0.130: 148
       0.130 -    0.162: 29
  Chirality restraints: 1926
  Sorted by residual:
  chirality pdb=" CA  ILE j 414 "
            pdb=" N   ILE j 414 "
            pdb=" C   ILE j 414 "
            pdb=" CB  ILE j 414 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.55e-01
  chirality pdb=" CA  ILE i 414 "
            pdb=" N   ILE i 414 "
            pdb=" C   ILE i 414 "
            pdb=" CB  ILE i 414 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.48e-01
  chirality pdb=" CA  ILE h 414 "
            pdb=" N   ILE h 414 "
            pdb=" C   ILE h 414 "
            pdb=" CB  ILE h 414 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.48e-01
  ... (remaining 1923 not shown)

  Planarity restraints: 2184
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR h 321 "    0.050 5.00e-02 4.00e+02   7.54e-02 9.08e+00
        pdb=" N   PRO h 322 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO h 322 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO h 322 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR i 321 "   -0.050 5.00e-02 4.00e+02   7.53e-02 9.08e+00
        pdb=" N   PRO i 322 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO i 322 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO i 322 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR j 321 "   -0.050 5.00e-02 4.00e+02   7.52e-02 9.06e+00
        pdb=" N   PRO j 322 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO j 322 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO j 322 "   -0.041 5.00e-02 4.00e+02
  ... (remaining 2181 not shown)

  Histogram of nonbonded interaction distances:
        1.81 -     2.43: 118
        2.43 -     3.05: 8777
        3.05 -     3.67: 18272
        3.67 -     4.28: 26892
        4.28 -     4.90: 44598
  Nonbonded interactions: 98657
  Sorted by model distance:
  nonbonded pdb=" O   LEU h 651 "
            pdb=" NE  ARG j 662 "
     model   vdw
     1.813 3.120
  nonbonded pdb=" NE  ARG i 662 "
            pdb=" O   LEU j 651 "
     model   vdw
     1.877 3.120
  nonbonded pdb=" O   LEU i 651 "
            pdb=" NE  ARG h 662 "
     model   vdw
     1.905 3.120
  nonbonded pdb=" O   VAL i 645 "
            pdb=" O   ALA h 641 "
     model   vdw
     1.935 3.040
  nonbonded pdb=" O   VAL h 645 "
            pdb=" O   ALA j 641 "
     model   vdw
     1.979 3.040
  ... (remaining 98652 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'i'
  selection = chain 'h'
  selection = chain 'j'
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.220
  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:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     32.640
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6751
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      :  0.003   0.032  12495  Z= 0.135
  Angle     :  0.596   4.650  17001  Z= 0.338
  Chirality :  0.050   0.162   1926
  Planarity :  0.006   0.110   2184
  Dihedral  : 13.596  87.761   4479
  Min Nonbonded Distance : 1.813

Molprobity Statistics.
  All-atom Clashscore : 25.16
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 10.52 %
    Favored  : 89.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.64 (0.19), residues: 1569
  helix: -1.46 (1.01), residues: 39
  sheet: -1.44 (0.26), residues: 381
  loop : -3.06 (0.16), residues: 1149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP j 300 
 HIS   0.004   0.001   HIS j 630 
 PHE   0.008   0.001   PHE h 101 
 TYR   0.011   0.001   TYR j  71 
 ARG   0.005   0.001   ARG h 458 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.26352 (  276)
  hydrogen bonds       : angle      12.55220 (  945)
  covalent geometry    : bond        0.00265 (12495)
  covalent geometry    : angle       0.59571 (17001)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 1.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: i  633 MET cc_start: 0.1901 (mmt) cc_final: -0.0124 (mtt)
REVERT: i  676 MET cc_start: -0.0860 (pmm) cc_final: -0.1637 (pmm)
REVERT: h  433 ASP cc_start: 0.4555 (t0) cc_final: 0.4339 (t0)
REVERT: h  633 MET cc_start: 0.1119 (mmt) cc_final: 0.0243 (mtt)
REVERT: h  676 MET cc_start: -0.0972 (pmm) cc_final: -0.1362 (pmm)
REVERT: j  108 ARG cc_start: 0.6533 (mmp-170) cc_final: 0.6220 (mmm160)
REVERT: j  433 ASP cc_start: 0.4134 (t0) cc_final: 0.3834 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.2170
  time to fit residues: 46.5353
Evaluate side-chains
  98 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 1.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    0.7980
   chunk 118 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 91 optimal weight:    0.8980
   chunk 141 optimal weight:    3.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
i 217 ASN
** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.100307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.082810 restraints weight = 48188.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.084335 restraints weight = 29715.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.085361 restraints weight = 20069.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3584
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3584 r_free = 0.3584    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3584 r_free = 0.3584    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3584
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  12495  Z= 0.232
  Angle     :  0.760   7.854  17001  Z= 0.409
  Chirality :  0.055   0.187   1926
  Planarity :  0.007   0.112   2184
  Dihedral  :  7.128  37.574   1704
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 18.21
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 11.54 %
    Favored  : 88.27 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  : 10.81 %
    Favored  : 89.04 %
  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: -3.67 (0.18), residues: 1569
  helix: -0.60 (1.31), residues: 24
  sheet: -1.33 (0.24), residues: 402
  loop : -3.16 (0.15), residues: 1143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP j 429 
 HIS   0.009   0.002   HIS i 630 
 PHE   0.024   0.002   PHE j 261 
 TYR   0.013   0.002   TYR j 138 
 ARG   0.006   0.001   ARG i 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04424 (  276)
  hydrogen bonds       : angle       8.10440 (  945)
  covalent geometry    : bond        0.00517 (12495)
  covalent geometry    : angle       0.75993 (17001)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 124
  time to evaluate  : 1.339 
Fit side-chains
   revert: symmetry clash
REVERT: i  433 ASP cc_start: 0.5781 (t0) cc_final: 0.5490 (t0)
REVERT: h  108 ARG cc_start: 0.6659 (mmp-170) cc_final: 0.6247 (mmp-170)
REVERT: h  433 ASP cc_start: 0.5725 (t0) cc_final: 0.5511 (t0)
REVERT: j  108 ARG cc_start: 0.6803 (mmp-170) cc_final: 0.6572 (mmm160)
REVERT: j  433 ASP cc_start: 0.5075 (t0) cc_final: 0.4802 (t0)
  outliers start: 2
  outliers final: 1
  residues processed: 126
  average time/residue: 0.2257
  time to fit residues: 43.2237
Evaluate side-chains
  96 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 1.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 56 optimal weight:    0.2980
   chunk 148 optimal weight:    3.9990
   chunk 104 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 126 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   chunk 133 optimal weight:    3.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
i 217 ASN
** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.102908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.084767 restraints weight = 47688.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.086391 restraints weight = 28777.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.087502 restraints weight = 19101.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3622
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3622 r_free = 0.3622    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3622 r_free = 0.3622    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3622
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6909
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12495  Z= 0.153
  Angle     :  0.668   6.811  17001  Z= 0.361
  Chirality :  0.052   0.214   1926
  Planarity :  0.005   0.065   2184
  Dihedral  :  6.722  36.078   1704
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.24 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  4.84 %
    Favored  : 95.09 %
  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: -3.49 (0.18), residues: 1569
  helix: -0.68 (1.22), residues: 24
  sheet: -1.63 (0.22), residues: 474
  loop : -2.88 (0.16), residues: 1071

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP j 350 
 HIS   0.006   0.001   HIS i 630 
 PHE   0.013   0.002   PHE h 401 
 TYR   0.010   0.001   TYR i 138 
 ARG   0.008   0.001   ARG j 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03768 (  276)
  hydrogen bonds       : angle       7.24693 (  945)
  covalent geometry    : bond        0.00326 (12495)
  covalent geometry    : angle       0.66760 (17001)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 1.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: i  433 ASP cc_start: 0.5637 (t0) cc_final: 0.5277 (t0)
REVERT: h  433 ASP cc_start: 0.5268 (t0) cc_final: 0.4934 (t0)
REVERT: h  633 MET cc_start: 0.1554 (mmt) cc_final: 0.0725 (mtt)
REVERT: j  433 ASP cc_start: 0.4901 (t0) cc_final: 0.4612 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 133
  average time/residue: 0.2214
  time to fit residues: 44.5481
Evaluate side-chains
  91 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 1.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 95 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 65 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0470
   chunk 39 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.7478

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

Flipped N/Q/H residues before XYZ refinement:
** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
j 397 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.103577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.085548 restraints weight = 45325.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.087197 restraints weight = 27058.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.088398 restraints weight = 17907.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3637
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3637 r_free = 0.3637    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3637 r_free = 0.3637    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3637
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6880
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12495  Z= 0.140
  Angle     :  0.645   7.291  17001  Z= 0.348
  Chirality :  0.051   0.231   1926
  Planarity :  0.005   0.064   2184
  Dihedral  :  6.489  35.998   1704
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.94 %
    Favored  : 89.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.31 (0.18), residues: 1569
  helix: -0.17 (1.25), residues: 24
  sheet: -1.55 (0.23), residues: 444
  loop : -2.72 (0.16), residues: 1101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP i 266 
 HIS   0.004   0.001   HIS i 630 
 PHE   0.012   0.002   PHE h 401 
 TYR   0.012   0.001   TYR h 138 
 ARG   0.005   0.001   ARG j 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03339 (  276)
  hydrogen bonds       : angle       6.68881 (  945)
  covalent geometry    : bond        0.00307 (12495)
  covalent geometry    : angle       0.64501 (17001)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 1.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: i  162 MET cc_start: 0.6373 (tpp) cc_final: 0.6170 (tpp)
REVERT: i  433 ASP cc_start: 0.5713 (t0) cc_final: 0.5487 (t0)
REVERT: h  257 ASP cc_start: 0.5953 (t0) cc_final: 0.5542 (t70)
REVERT: h  433 ASP cc_start: 0.4991 (t0) cc_final: 0.4778 (t0)
REVERT: h  633 MET cc_start: 0.1342 (mmt) cc_final: 0.0250 (mtt)
REVERT: j  257 ASP cc_start: 0.6150 (t0) cc_final: 0.5916 (t70)
REVERT: j  433 ASP cc_start: 0.4652 (t0) cc_final: 0.4433 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.2202
  time to fit residues: 43.7785
Evaluate side-chains
  90 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 130 optimal weight:    0.0570
   chunk 120 optimal weight:    6.9990
   chunk 101 optimal weight:    5.9990
   chunk 49 optimal weight:    6.9990
   chunk 96 optimal weight:    9.9990
   chunk 107 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.9902

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

Flipped N/Q/H residues before XYZ refinement:
** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
h 217 ASN
** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.103200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.084946 restraints weight = 47094.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.086642 restraints weight = 28354.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.087783 restraints weight = 18839.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3625
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3625 r_free = 0.3625    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3625 r_free = 0.3625    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3625
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12495  Z= 0.154
  Angle     :  0.642   6.814  17001  Z= 0.345
  Chirality :  0.051   0.174   1926
  Planarity :  0.005   0.059   2184
  Dihedral  :  6.428  38.676   1704
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.56 %
    Favored  : 90.25 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.97 %
    Favored  : 97.96 %
  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: -3.28 (0.19), residues: 1569
  helix:  0.11 (1.25), residues: 24
  sheet: -1.54 (0.23), residues: 468
  loop : -2.71 (0.16), residues: 1077

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP i 287 
 HIS   0.006   0.001   HIS h 630 
 PHE   0.014   0.002   PHE j 261 
 TYR   0.013   0.002   TYR i 138 
 ARG   0.006   0.001   ARG j 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03183 (  276)
  hydrogen bonds       : angle       6.49311 (  945)
  covalent geometry    : bond        0.00348 (12495)
  covalent geometry    : angle       0.64213 (17001)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 1.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: i  433 ASP cc_start: 0.5878 (t0) cc_final: 0.5418 (t0)
REVERT: h  257 ASP cc_start: 0.6041 (t0) cc_final: 0.5637 (t70)
REVERT: h  430 MET cc_start: 0.5332 (mpp) cc_final: 0.5048 (mpp)
REVERT: h  433 ASP cc_start: 0.4917 (t0) cc_final: 0.4684 (t0)
REVERT: h  627 MET cc_start: 0.1603 (ptm) cc_final: 0.1331 (ptp)
REVERT: h  633 MET cc_start: 0.1704 (mmt) cc_final: 0.0632 (mtt)
REVERT: j  433 ASP cc_start: 0.4670 (t0) cc_final: 0.4426 (t0)
REVERT: j  676 MET cc_start: -0.1377 (pmm) cc_final: -0.1730 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 126
  average time/residue: 0.2210
  time to fit residues: 42.2195
Evaluate side-chains
  88 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 1.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 125 optimal weight:    0.5980
   chunk 75 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   chunk 48 optimal weight:    8.9990
   chunk 11 optimal weight:    2.9990
   chunk 134 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
h 217 ASN
j 397 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.103914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.085483 restraints weight = 46762.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.087165 restraints weight = 27990.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.088311 restraints weight = 18486.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3641
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3641 r_free = 0.3641    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3641 r_free = 0.3641    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3641
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6906
moved from start:          0.2895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12495  Z= 0.140
  Angle     :  0.625   5.824  17001  Z= 0.336
  Chirality :  0.051   0.177   1926
  Planarity :  0.005   0.057   2184
  Dihedral  :  6.300  38.448   1704
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.50 %
    Favored  : 90.31 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.33 %
    Favored  : 96.60 %
  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: -3.18 (0.19), residues: 1569
  helix:  0.27 (1.25), residues: 24
  sheet: -1.30 (0.24), residues: 444
  loop : -2.72 (0.16), residues: 1101

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP j 429 
 HIS   0.004   0.001   HIS i 630 
 PHE   0.012   0.002   PHE h 261 
 TYR   0.016   0.001   TYR j 660 
 ARG   0.004   0.001   ARG h 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03072 (  276)
  hydrogen bonds       : angle       6.16829 (  945)
  covalent geometry    : bond        0.00302 (12495)
  covalent geometry    : angle       0.62494 (17001)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 1.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: i  430 MET cc_start: 0.4443 (mpp) cc_final: 0.4184 (mpp)
REVERT: i  433 ASP cc_start: 0.5789 (t0) cc_final: 0.5363 (t0)
REVERT: h  233 ASP cc_start: 0.7595 (t70) cc_final: 0.7367 (t0)
REVERT: h  257 ASP cc_start: 0.5876 (t0) cc_final: 0.5675 (t0)
REVERT: h  633 MET cc_start: 0.1313 (mmt) cc_final: 0.0291 (mtp)
REVERT: j  676 MET cc_start: -0.1432 (pmm) cc_final: -0.1761 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 130
  average time/residue: 0.2191
  time to fit residues: 43.0260
Evaluate side-chains
  88 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 1.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 133 optimal weight:    0.9980
   chunk 86 optimal weight:    0.0570
   chunk 107 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 128 optimal weight:    0.6980
   chunk 138 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 124 optimal weight:    0.1980
   chunk 142 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   overall best weight:    0.7900

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

Flipped N/Q/H residues before XYZ refinement:
** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j 397 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 = 0.3957 r_free = 0.3957 target = 0.104250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.085772 restraints weight = 47043.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.087466 restraints weight = 28375.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.088603 restraints weight = 18734.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3643
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3643 r_free = 0.3643    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3643 r_free = 0.3643    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3643
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6903
moved from start:          0.3101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12495  Z= 0.139
  Angle     :  0.633   6.574  17001  Z= 0.338
  Chirality :  0.052   0.239   1926
  Planarity :  0.005   0.055   2184
  Dihedral  :  6.270  38.299   1704
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.05 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  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: -3.20 (0.19), residues: 1569
  helix:  0.45 (1.26), residues: 24
  sheet: -1.47 (0.23), residues: 474
  loop : -2.67 (0.16), residues: 1071

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.002   TRP i 429 
 HIS   0.008   0.002   HIS i 630 
 PHE   0.015   0.002   PHE h 401 
 TYR   0.014   0.001   TYR h 660 
 ARG   0.004   0.001   ARG h 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03026 (  276)
  hydrogen bonds       : angle       6.01786 (  945)
  covalent geometry    : bond        0.00305 (12495)
  covalent geometry    : angle       0.63317 (17001)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 1.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: i  108 ARG cc_start: 0.6214 (mmp-170) cc_final: 0.5750 (mmm160)
REVERT: i  421 TRP cc_start: 0.6944 (t60) cc_final: 0.6159 (t60)
REVERT: h  421 TRP cc_start: 0.6486 (t60) cc_final: 0.5710 (t60)
REVERT: h  633 MET cc_start: 0.1150 (mmt) cc_final: 0.0228 (mtp)
REVERT: j  429 TRP cc_start: 0.2753 (t60) cc_final: 0.1931 (t60)
REVERT: j  633 MET cc_start: 0.1398 (mmt) cc_final: 0.0429 (mtp)
REVERT: j  676 MET cc_start: -0.1522 (pmm) cc_final: -0.1836 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.2397
  time to fit residues: 46.1896
Evaluate side-chains
  93 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 1.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 71 optimal weight:    0.5980
   chunk 89 optimal weight:    4.9990
   chunk 127 optimal weight:    3.9990
   chunk 42 optimal weight:   10.0000
   chunk 129 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 137 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 121 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** i 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j 397 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 = 0.3887 r_free = 0.3887 target = 0.100157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.082044 restraints weight = 48077.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.083581 restraints weight = 29403.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.084652 restraints weight = 19691.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3571
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7021
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  12495  Z= 0.267
  Angle     :  0.774   9.798  17001  Z= 0.411
  Chirality :  0.055   0.277   1926
  Planarity :  0.006   0.095   2184
  Dihedral  :  7.074  49.207   1704
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 20.15
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 12.81 %
    Favored  : 87.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  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: -3.50 (0.19), residues: 1569
  helix: -0.45 (1.29), residues: 24
  sheet: -1.50 (0.23), residues: 471
  loop : -2.96 (0.16), residues: 1074

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.003   TRP j 429 
 HIS   0.015   0.003   HIS i 630 
 PHE   0.030   0.003   PHE j 261 
 TYR   0.020   0.002   TYR i 138 
 ARG   0.024   0.001   ARG j 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03446 (  276)
  hydrogen bonds       : angle       6.71382 (  945)
  covalent geometry    : bond        0.00603 (12495)
  covalent geometry    : angle       0.77380 (17001)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 1.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: i  421 TRP cc_start: 0.6487 (t60) cc_final: 0.6088 (t60)
REVERT: i  676 MET cc_start: -0.1685 (pmm) cc_final: -0.1966 (pmm)
REVERT: h  108 ARG cc_start: 0.6530 (mmp-170) cc_final: 0.6295 (mmp-170)
REVERT: h  233 ASP cc_start: 0.7635 (t0) cc_final: 0.7400 (t0)
REVERT: h  421 TRP cc_start: 0.6393 (t60) cc_final: 0.5811 (t60)
REVERT: j  396 ILE cc_start: 0.5534 (mt) cc_final: 0.5315 (tp)
REVERT: j  429 TRP cc_start: 0.3421 (t60) cc_final: 0.1950 (t60)
REVERT: j  633 MET cc_start: 0.1840 (mmt) cc_final: 0.0338 (mtp)
REVERT: j  676 MET cc_start: -0.1503 (pmm) cc_final: -0.1797 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.2212
  time to fit residues: 38.7609
Evaluate side-chains
  84 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 1.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 120 optimal weight:    0.9990
   chunk 125 optimal weight:    0.8980
   chunk 92 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 76 optimal weight:    0.5980
   chunk 104 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 148 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** i 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** i 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** i 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** h 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j 397 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 = 0.3941 r_free = 0.3941 target = 0.103364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.084859 restraints weight = 47656.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.086458 restraints weight = 28742.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.087624 restraints weight = 19193.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3626
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3626 r_free = 0.3626    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3626 r_free = 0.3626    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3626
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
moved from start:          0.3260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12495  Z= 0.148
  Angle     :  0.670   8.462  17001  Z= 0.356
  Chirality :  0.052   0.199   1926
  Planarity :  0.005   0.066   2184
  Dihedral  :  6.696  47.596   1704
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 17.15
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.92 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.39 (0.19), residues: 1569
  helix:  0.07 (1.28), residues: 24
  sheet: -1.62 (0.23), residues: 477
  loop : -2.79 (0.16), residues: 1068

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP j 429 
 HIS   0.003   0.001   HIS i 630 
 PHE   0.014   0.002   PHE i  58 
 TYR   0.016   0.002   TYR h 138 
 ARG   0.010   0.001   ARG j 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03017 (  276)
  hydrogen bonds       : angle       6.21448 (  945)
  covalent geometry    : bond        0.00328 (12495)
  covalent geometry    : angle       0.66990 (17001)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 1.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: i  249 ARG cc_start: 0.7383 (tpt-90) cc_final: 0.7179 (tpt-90)
REVERT: i  421 TRP cc_start: 0.6491 (t60) cc_final: 0.6107 (t60)
REVERT: h  233 ASP cc_start: 0.7563 (t0) cc_final: 0.7349 (t0)
REVERT: h  421 TRP cc_start: 0.6270 (t60) cc_final: 0.5658 (t60)
REVERT: j  429 TRP cc_start: 0.3431 (t60) cc_final: 0.1939 (t60)
REVERT: j  676 MET cc_start: -0.1553 (pmm) cc_final: -0.1836 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.2274
  time to fit residues: 44.0203
Evaluate side-chains
  90 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 1.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 116 optimal weight:    0.0980
   chunk 67 optimal weight:    3.9990
   chunk 137 optimal weight:    0.4980
   chunk 123 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 56 optimal weight:    0.0870
   chunk 146 optimal weight:    0.1980
   chunk 107 optimal weight:    0.0370
   chunk 30 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    0.1836

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

Flipped N/Q/H residues before XYZ refinement:
i 217 ASN
j 397 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.105893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.087448 restraints weight = 46422.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.089167 restraints weight = 27832.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.090312 restraints weight = 18245.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3678
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3678 r_free = 0.3678    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3678 r_free = 0.3678    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3678
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6845
moved from start:          0.3601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  12495  Z= 0.109
  Angle     :  0.620   7.322  17001  Z= 0.331
  Chirality :  0.051   0.234   1926
  Planarity :  0.005   0.058   2184
  Dihedral  :  6.037  39.877   1704
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  8.67 %
    Favored  : 91.14 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.23 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.03 (0.19), residues: 1569
  helix:  0.85 (1.30), residues: 24
  sheet: -1.34 (0.24), residues: 456
  loop : -2.56 (0.16), residues: 1089

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP j 429 
 HIS   0.004   0.001   HIS i 630 
 PHE   0.025   0.002   PHE i  58 
 TYR   0.015   0.001   TYR h  23 
 ARG   0.005   0.001   ARG i 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02996 (  276)
  hydrogen bonds       : angle       5.66333 (  945)
  covalent geometry    : bond        0.00239 (12495)
  covalent geometry    : angle       0.61967 (17001)

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

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

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3138 Ramachandran restraints generated.
    1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 137
  time to evaluate  : 1.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: i  627 MET cc_start: 0.2453 (pmm) cc_final: 0.2018 (ttp)
REVERT: h  421 TRP cc_start: 0.6404 (t60) cc_final: 0.5893 (t60)
REVERT: j  108 ARG cc_start: 0.6431 (mmp-170) cc_final: 0.6180 (mmm160)
REVERT: j  240 TRP cc_start: 0.5642 (t60) cc_final: 0.5105 (t60)
REVERT: j  397 ASN cc_start: 0.5567 (OUTLIER) cc_final: 0.5269 (t0)
REVERT: j  633 MET cc_start: 0.1285 (mmt) cc_final: -0.0246 (mtp)
REVERT: j  676 MET cc_start: -0.1351 (pmm) cc_final: -0.1641 (pmm)
  outliers start: 2
  outliers final: 0
  residues processed: 138
  average time/residue: 0.2351
  time to fit residues: 47.9581
Evaluate side-chains
  96 residues out of total 1323 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 1.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 148 optimal weight:    3.9990
   chunk 77 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0970
   chunk 58 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 118 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   chunk 132 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 127 optimal weight:    1.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** i 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** i 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** h 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** j 146 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 = 0.3962 r_free = 0.3962 target = 0.104211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.085556 restraints weight = 47328.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.087236 restraints weight = 28680.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.088369 restraints weight = 18983.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3640
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3640 r_free = 0.3640    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.3639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6909
moved from start:          0.3610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12495  Z= 0.144
  Angle     :  0.643   7.177  17001  Z= 0.342
  Chirality :  0.051   0.196   1926
  Planarity :  0.005   0.093   2184
  Dihedral  :  6.119  41.180   1704
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 17.68
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.24 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.10 (0.19), residues: 1569
  helix:  0.51 (1.28), residues: 24
  sheet: -1.50 (0.23), residues: 486
  loop : -2.55 (0.17), residues: 1059

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP j 429 
 HIS   0.005   0.001   HIS i 630 
 PHE   0.015   0.002   PHE h 261 
 TYR   0.018   0.002   TYR h 660 
 ARG   0.017   0.001   ARG i 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02956 (  276)
  hydrogen bonds       : angle       5.82573 (  945)
  covalent geometry    : bond        0.00325 (12495)
  covalent geometry    : angle       0.64271 (17001)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4429.69 seconds
wall clock time: 79 minutes 14.63 seconds (4754.63 seconds total)