Starting phenix.real_space_refine
on Wed Sep 17 03:00:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gz6_51726/09_2025/9gz6_51726.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gz6_51726/09_2025/9gz6_51726.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gz6_51726/09_2025/9gz6_51726.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gz6_51726/09_2025/9gz6_51726.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gz6_51726/09_2025/9gz6_51726.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gz6_51726/09_2025/9gz6_51726.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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: 3
    Type Number    sf(0)   Gaussians
     C    1440      2.51       5
     N     408      2.21       5
     O     468      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2316
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 26, 192
          Classifications: {'peptide': 26}
          Link IDs: {'TRANS': 25}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J, K, L
  Time building chain proxies: 0.41, per 1000 atoms: 0.18
  Number of scatterers: 2316
  At special positions: 0
  Unit cell: (58.855, 69.285, 46.935, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     468      8.00
     N     408      7.00
     C    1440      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=12, symmetry=0
  Number of additional bonds: simple=12, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.34
  Conformation dependent library (CDL) restraints added in 94.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  576

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 7 sheets defined
      0.0% alpha, 57.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 22
      removed outlier: 6.605A  pdb=" N   ALA A  13 " --> pdb=" O   ASN C  14 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   LEU C  16 " --> pdb=" O   ALA A  13 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   PHE A  15 " --> pdb=" O   LEU C  16 " (cutoff:3.500A)
      removed outlier: 7.733A  pdb=" N   HIS C  18 " --> pdb=" O   PHE A  15 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   VAL A  17 " --> pdb=" O   HIS C  18 " (cutoff:3.500A)
      removed outlier: 7.850A  pdb=" N   SER C  20 " --> pdb=" O   VAL A  17 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   SER A  19 " --> pdb=" O   SER C  20 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   ASN C  22 " --> pdb=" O   SER A  19 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   ASN A  21 " --> pdb=" O   ASN C  22 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   ALA C  13 " --> pdb=" O   ASN E  14 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N   LEU E  16 " --> pdb=" O   ALA C  13 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   PHE C  15 " --> pdb=" O   LEU E  16 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   HIS E  18 " --> pdb=" O   PHE C  15 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   VAL C  17 " --> pdb=" O   HIS E  18 " (cutoff:3.500A)
      removed outlier: 7.759A  pdb=" N   SER E  20 " --> pdb=" O   VAL C  17 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   SER C  19 " --> pdb=" O   SER E  20 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   ASN E  22 " --> pdb=" O   SER C  19 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   ASN C  21 " --> pdb=" O   ASN E  22 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ALA E  13 " --> pdb=" O   ASN G  14 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   LEU G  16 " --> pdb=" O   ALA E  13 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   PHE E  15 " --> pdb=" O   LEU G  16 " (cutoff:3.500A)
      removed outlier: 7.642A  pdb=" N   HIS G  18 " --> pdb=" O   PHE E  15 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   VAL E  17 " --> pdb=" O   HIS G  18 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   SER G  20 " --> pdb=" O   VAL E  17 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   SER E  19 " --> pdb=" O   SER G  20 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   ASN G  22 " --> pdb=" O   SER E  19 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   ASN E  21 " --> pdb=" O   ASN G  22 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   ALA G  13 " --> pdb=" O   ASN I  14 " (cutoff:3.500A)
      removed outlier: 8.159A  pdb=" N   LEU I  16 " --> pdb=" O   ALA G  13 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   PHE G  15 " --> pdb=" O   LEU I  16 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   HIS I  18 " --> pdb=" O   PHE G  15 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   VAL G  17 " --> pdb=" O   HIS I  18 " (cutoff:3.500A)
      removed outlier: 7.838A  pdb=" N   SER I  20 " --> pdb=" O   VAL G  17 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   SER G  19 " --> pdb=" O   SER I  20 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ASN I  22 " --> pdb=" O   SER G  19 " (cutoff:3.500A)
      removed outlier: 7.594A  pdb=" N   ASN G  21 " --> pdb=" O   ASN I  22 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   SER K  20 " --> pdb=" O   SER I  19 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ASN I  21 " --> pdb=" O   SER K  20 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   ASN K  22 " --> pdb=" O   ASN I  21 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 31
      removed outlier: 6.614A  pdb=" N   ILE A  26 " --> pdb=" O   LEU C  27 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   SER C  29 " --> pdb=" O   ILE A  26 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   SER A  28 " --> pdb=" O   SER C  29 " (cutoff:3.500A)
      removed outlier: 8.221A  pdb=" N   ASN C  31 " --> pdb=" O   SER A  28 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   THR A  30 " --> pdb=" O   ASN C  31 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   ILE C  26 " --> pdb=" O   LEU E  27 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   SER E  29 " --> pdb=" O   ILE C  26 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   SER C  28 " --> pdb=" O   SER E  29 " (cutoff:3.500A)
      removed outlier: 8.064A  pdb=" N   ASN E  31 " --> pdb=" O   SER C  28 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   THR C  30 " --> pdb=" O   ASN E  31 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ILE G  26 " --> pdb=" O   LEU I  27 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   SER I  29 " --> pdb=" O   ILE G  26 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   SER G  28 " --> pdb=" O   SER I  29 " (cutoff:3.500A)
      removed outlier: 8.071A  pdb=" N   ASN I  31 " --> pdb=" O   SER G  28 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   THR G  30 " --> pdb=" O   ASN I  31 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ILE I  26 " --> pdb=" O   LEU K  27 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   SER K  29 " --> pdb=" O   ILE I  26 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   SER I  28 " --> pdb=" O   SER K  29 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   ASN K  31 " --> pdb=" O   SER I  28 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   THR I  30 " --> pdb=" O   ASN K  31 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36
    Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 22
      removed outlier: 6.546A  pdb=" N   ALA B  13 " --> pdb=" O   ASN D  14 " (cutoff:3.500A)
      removed outlier: 8.002A  pdb=" N   LEU D  16 " --> pdb=" O   ALA B  13 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   PHE B  15 " --> pdb=" O   LEU D  16 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   HIS D  18 " --> pdb=" O   PHE B  15 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   VAL B  17 " --> pdb=" O   HIS D  18 " (cutoff:3.500A)
      removed outlier: 7.837A  pdb=" N   SER D  20 " --> pdb=" O   VAL B  17 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   SER B  19 " --> pdb=" O   SER D  20 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ASN D  22 " --> pdb=" O   SER B  19 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   ASN B  21 " --> pdb=" O   ASN D  22 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ASN F  22 " --> pdb=" O   ASN D  21 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   ALA F  13 " --> pdb=" O   ASN H  14 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   LEU H  16 " --> pdb=" O   ALA F  13 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   PHE F  15 " --> pdb=" O   LEU H  16 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   HIS H  18 " --> pdb=" O   PHE F  15 " (cutoff:3.500A)
      removed outlier: 5.925A  pdb=" N   VAL F  17 " --> pdb=" O   HIS H  18 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   SER H  20 " --> pdb=" O   VAL F  17 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   SER F  19 " --> pdb=" O   SER H  20 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   ASN H  22 " --> pdb=" O   SER F  19 " (cutoff:3.500A)
      removed outlier: 7.429A  pdb=" N   ASN F  21 " --> pdb=" O   ASN H  22 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   ALA H  13 " --> pdb=" O   ASN J  14 " (cutoff:3.500A)
      removed outlier: 8.090A  pdb=" N   LEU J  16 " --> pdb=" O   ALA H  13 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   PHE H  15 " --> pdb=" O   LEU J  16 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   HIS J  18 " --> pdb=" O   PHE H  15 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   VAL H  17 " --> pdb=" O   HIS J  18 " (cutoff:3.500A)
      removed outlier: 7.759A  pdb=" N   SER J  20 " --> pdb=" O   VAL H  17 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   SER H  19 " --> pdb=" O   SER J  20 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   ASN J  22 " --> pdb=" O   SER H  19 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   ASN H  21 " --> pdb=" O   ASN J  22 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   SER L  20 " --> pdb=" O   SER J  19 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ASN J  21 " --> pdb=" O   SER L  20 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   ASN L  22 " --> pdb=" O   ASN J  21 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 31
      removed outlier: 3.510A  pdb=" N   SER D  29 " --> pdb=" O   SER B  28 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   ILE H  26 " --> pdb=" O   LEU J  27 " (cutoff:3.500A)
      removed outlier: 7.802A  pdb=" N   SER J  29 " --> pdb=" O   ILE H  26 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   SER H  28 " --> pdb=" O   SER J  29 " (cutoff:3.500A)
      removed outlier: 8.020A  pdb=" N   ASN J  31 " --> pdb=" O   SER H  28 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   THR H  30 " --> pdb=" O   ASN J  31 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   ILE J  26 " --> pdb=" O   LEU L  27 " (cutoff:3.500A)
      removed outlier: 8.129A  pdb=" N   SER L  29 " --> pdb=" O   ILE J  26 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   SER J  28 " --> pdb=" O   SER L  29 " (cutoff:3.500A)
      removed outlier: 8.191A  pdb=" N   ASN L  31 " --> pdb=" O   SER J  28 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   THR J  30 " --> pdb=" O   ASN L  31 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 35 through 36
    Processing sheet with id=AA7, first strand: chain 'J' and resid 35 through 36

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

  Time building geometry restraints manager: 0.31 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 372
        1.29 -     1.35: 384
        1.35 -     1.41: 264
        1.41 -     1.48: 396
        1.48 -     1.54: 924
  Bond restraints: 2340
  Sorted by residual:
  bond pdb=" N   SER F  34 "
       pdb=" CA  SER F  34 "
    ideal  model  delta    sigma   weight residual
    1.455  1.462 -0.006 1.33e-02 5.65e+03 2.30e-01
  bond pdb=" N   SER C  34 "
       pdb=" CA  SER C  34 "
    ideal  model  delta    sigma   weight residual
    1.455  1.462 -0.006 1.33e-02 5.65e+03 2.23e-01
  bond pdb=" N   SER B  34 "
       pdb=" CA  SER B  34 "
    ideal  model  delta    sigma   weight residual
    1.455  1.461 -0.006 1.33e-02 5.65e+03 2.10e-01
  bond pdb=" N   SER I  34 "
       pdb=" CA  SER I  34 "
    ideal  model  delta    sigma   weight residual
    1.455  1.461 -0.006 1.33e-02 5.65e+03 2.07e-01
  bond pdb=" N   SER H  34 "
       pdb=" CA  SER H  34 "
    ideal  model  delta    sigma   weight residual
    1.455  1.461 -0.006 1.33e-02 5.65e+03 1.96e-01
  ... (remaining 2335 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 2859
        1.30 -     2.61: 238
        2.61 -     3.91: 35
        3.91 -     5.22: 36
        5.22 -     6.52: 12
  Bond angle restraints: 3180
  Sorted by residual:
  angle pdb=" N   ASN D  22 "
        pdb=" CA  ASN D  22 "
        pdb=" C   ASN D  22 "
      ideal   model   delta    sigma   weight residual
     108.73  112.94   -4.21 1.63e+00 3.76e-01 6.66e+00
  angle pdb=" N   ASN C  22 "
        pdb=" CA  ASN C  22 "
        pdb=" C   ASN C  22 "
      ideal   model   delta    sigma   weight residual
     108.73  112.92   -4.19 1.63e+00 3.76e-01 6.62e+00
  angle pdb=" N   ASN A  22 "
        pdb=" CA  ASN A  22 "
        pdb=" C   ASN A  22 "
      ideal   model   delta    sigma   weight residual
     108.73  112.92   -4.19 1.63e+00 3.76e-01 6.59e+00
  angle pdb=" N   ASN J  22 "
        pdb=" CA  ASN J  22 "
        pdb=" C   ASN J  22 "
      ideal   model   delta    sigma   weight residual
     108.73  112.91   -4.18 1.63e+00 3.76e-01 6.56e+00
  angle pdb=" N   ASN B  22 "
        pdb=" CA  ASN B  22 "
        pdb=" C   ASN B  22 "
      ideal   model   delta    sigma   weight residual
     108.73  112.90   -4.17 1.63e+00 3.76e-01 6.53e+00
  ... (remaining 3175 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -     7.46: 1044
        7.46 -    14.91: 168
       14.91 -    22.36: 52
       22.36 -    29.81: 32
       29.81 -    37.26: 12
  Dihedral angle restraints: 1308
    sinusoidal: 420
      harmonic: 888
  Sorted by residual:
  dihedral pdb=" N   ASN J  21 "
           pdb=" CA  ASN J  21 "
           pdb=" CB  ASN J  21 "
           pdb=" CG  ASN J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -89.48   29.48     3      1.50e+01 4.44e-03 4.61e+00
  dihedral pdb=" N   ASN E  21 "
           pdb=" CA  ASN E  21 "
           pdb=" CB  ASN E  21 "
           pdb=" CG  ASN E  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -89.48   29.48     3      1.50e+01 4.44e-03 4.61e+00
  dihedral pdb=" N   ASN I  21 "
           pdb=" CA  ASN I  21 "
           pdb=" CB  ASN I  21 "
           pdb=" CG  ASN I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -89.47   29.47     3      1.50e+01 4.44e-03 4.61e+00
  ... (remaining 1305 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.027: 156
       0.027 -    0.051: 151
       0.051 -    0.076: 65
       0.076 -    0.100: 0
       0.100 -    0.125: 12
  Chirality restraints: 384
  Sorted by residual:
  chirality pdb=" CA  ILE B  26 "
            pdb=" N   ILE B  26 "
            pdb=" C   ILE B  26 "
            pdb=" CB  ILE B  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.89e-01
  chirality pdb=" CA  ILE E  26 "
            pdb=" N   ILE E  26 "
            pdb=" C   ILE E  26 "
            pdb=" CB  ILE E  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  chirality pdb=" CA  ILE H  26 "
            pdb=" N   ILE H  26 "
            pdb=" C   ILE H  26 "
            pdb=" CB  ILE H  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.80e-01
  ... (remaining 381 not shown)

  Planarity restraints: 408
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE L  23 "   -0.001 2.00e-02 2.50e+03   1.18e-02 2.43e+00
        pdb=" CG  PHE L  23 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 PHE L  23 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 PHE L  23 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE L  23 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 PHE L  23 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE L  23 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D  23 "   -0.001 2.00e-02 2.50e+03   1.17e-02 2.39e+00
        pdb=" CG  PHE D  23 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 PHE D  23 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 PHE D  23 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE D  23 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 PHE D  23 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE D  23 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE J  23 "   -0.001 2.00e-02 2.50e+03   1.17e-02 2.38e+00
        pdb=" CG  PHE J  23 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 PHE J  23 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 PHE J  23 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE J  23 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 PHE J  23 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE J  23 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 405 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 412
        2.79 -     3.32: 1963
        3.32 -     3.84: 3778
        3.84 -     4.37: 4360
        4.37 -     4.90: 7380
  Nonbonded interactions: 17893
  Sorted by model distance:
  nonbonded pdb=" O   SER H  34 "
            pdb=" O   GLY J  33 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   SER B  34 "
            pdb=" O   GLY D  33 "
     model   vdw
     2.412 3.040
  nonbonded pdb=" O   SER E  34 "
            pdb=" O   GLY G  33 "
     model   vdw
     2.424 3.040
  nonbonded pdb=" N   NH2 H  38 "
            pdb=" O   TYR J  37 "
     model   vdw
     2.434 3.120
  nonbonded pdb=" O   SER A  34 "
            pdb=" O   GLY C  33 "
     model   vdw
     2.466 3.040
  ... (remaining 17888 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.850
  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:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.450
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
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      :  0.008   0.103   2352  Z= 0.743
  Angle     :  0.956   6.523   3180  Z= 0.510
  Chirality :  0.042   0.125    384
  Planarity :  0.003   0.012    408
  Dihedral  : 10.538  37.257    732
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.82 (0.29), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.22), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.002   TYR K  37 
 PHE   0.020   0.005   PHE L  23 
 HIS   0.001   0.000   HIS E  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 2340)
  covalent geometry    : angle       0.95557 ( 3180)
  hydrogen bonds       : bond        0.27642 (   47)
  hydrogen bonds       : angle       8.77112 (  141)
  Misc. bond           : bond        0.10202 (   12)

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.090 
Fit side-chains
REVERT: C   14 ASN cc_start: 0.7932 (t0) cc_final: 0.7632 (t0)
REVERT: D   14 ASN cc_start: 0.7937 (t0) cc_final: 0.7594 (t0)
REVERT: F   14 ASN cc_start: 0.7743 (t0) cc_final: 0.7542 (t0)
REVERT: G   22 ASN cc_start: 0.8492 (t0) cc_final: 0.8150 (t0)
REVERT: L   14 ASN cc_start: 0.7940 (t0) cc_final: 0.7685 (t0)
REVERT: L   32 VAL cc_start: 0.8716 (t) cc_final: 0.8429 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0265
  time to fit residues: 3.1912
Evaluate side-chains
  66 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 12 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 18 optimal weight:    9.9990
   chunk 6 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
C  31 ASN
** D  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  31 ASN
** F  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  31 ASN
I  35 ASN
** J  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.146737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.128833 restraints weight = 3671.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.4061 rms_B_bonded: 3.32
r_work: 0.3958 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2352  Z= 0.103
  Angle     :  0.576   4.885   3180  Z= 0.287
  Chirality :  0.039   0.126    384
  Planarity :  0.002   0.007    408
  Dihedral  :  4.992  11.429    312
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 18.94 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.25 (0.26), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.47 (0.20), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR K  37 
 PHE   0.010   0.001   PHE H  23 
 HIS   0.001   0.000   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 2340)
  covalent geometry    : angle       0.57637 ( 3180)
  hydrogen bonds       : bond        0.02324 (   47)
  hydrogen bonds       : angle       6.32985 (  141)
  Misc. bond           : bond        0.00067 (   12)

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.096 
Fit side-chains
REVERT: C   36 THR cc_start: 0.8553 (m) cc_final: 0.8265 (p)
REVERT: D   14 ASN cc_start: 0.7743 (t0) cc_final: 0.7450 (t0)
REVERT: G   22 ASN cc_start: 0.8688 (t0) cc_final: 0.8391 (t0)
REVERT: K   22 ASN cc_start: 0.8434 (t0) cc_final: 0.7913 (t0)
REVERT: L   14 ASN cc_start: 0.7654 (t0) cc_final: 0.7251 (t0)
REVERT: L   32 VAL cc_start: 0.8866 (t) cc_final: 0.8592 (p)
  outliers start: 8
  outliers final: 6
  residues processed: 78
  average time/residue: 0.0232
  time to fit residues: 2.6612
Evaluate side-chains
  71 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain E residue   31 ASN
Chi-restraints excluded: chain I residue   31 ASN
Chi-restraints excluded: chain K residue   12 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 5 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** D  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  22 ASN
** F  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  31 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 = 0.4039 r_free = 0.4039 target = 0.135475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.117789 restraints weight = 5039.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 3.74
r_work: 0.3753 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.3529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.023   2352  Z= 0.299
  Angle     :  0.646   4.646   3180  Z= 0.356
  Chirality :  0.043   0.140    384
  Planarity :  0.003   0.008    408
  Dihedral  :  6.009  14.426    312
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 16.67 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.02 (0.23), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.05 (0.18), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR L  37 
 PHE   0.017   0.003   PHE I  15 
 HIS   0.001   0.000   HIS K  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00639 ( 2340)
  covalent geometry    : angle       0.64602 ( 3180)
  hydrogen bonds       : bond        0.04266 (   47)
  hydrogen bonds       : angle       5.85063 (  141)
  Misc. bond           : bond        0.00136 (   12)

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.091 
Fit side-chains
REVERT: C   22 ASN cc_start: 0.8778 (t0) cc_final: 0.8151 (t0)
REVERT: F   32 VAL cc_start: 0.8735 (t) cc_final: 0.8427 (p)
REVERT: K   32 VAL cc_start: 0.8921 (t) cc_final: 0.8693 (p)
REVERT: L   32 VAL cc_start: 0.8957 (t) cc_final: 0.8723 (p)
  outliers start: 14
  outliers final: 13
  residues processed: 58
  average time/residue: 0.0239
  time to fit residues: 2.0672
Evaluate side-chains
  63 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain A residue   31 ASN
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain E residue   36 THR
Chi-restraints excluded: chain F residue   36 THR
Chi-restraints excluded: chain G residue   36 THR
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   36 THR
Chi-restraints excluded: chain I residue   36 THR
Chi-restraints excluded: chain J residue   31 ASN
Chi-restraints excluded: chain J residue   36 THR
Chi-restraints excluded: chain K residue   36 THR
Chi-restraints excluded: chain L residue   36 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 4 optimal weight:    9.9990
   chunk 1 optimal weight:    8.9990
   chunk 3 optimal weight:    6.9990
   chunk 20 optimal weight:    8.9990
   chunk 12 optimal weight:    9.9990
   chunk 19 optimal weight:    7.9990
   chunk 9 optimal weight:    7.9990
   chunk 2 optimal weight:    7.9990
   chunk 18 optimal weight:    7.9990
   chunk 6 optimal weight:    8.9990
   overall best weight:    7.7990

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

Flipped N/Q/H residues before XYZ refinement:
** D  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  31 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.133868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.115920 restraints weight = 5066.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3864 rms_B_bonded: 3.57
r_work: 0.3753 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.4121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.037   2352  Z= 0.467
  Angle     :  0.766   5.384   3180  Z= 0.430
  Chirality :  0.046   0.136    384
  Planarity :  0.004   0.013    408
  Dihedral  :  6.718  20.099    312
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  6.82 %
    Allowed  : 17.05 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.44 (0.25), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.37 (0.19), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR H  37 
 PHE   0.024   0.004   PHE J  15 
 HIS   0.001   0.001   HIS L  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.01000 ( 2340)
  covalent geometry    : angle       0.76620 ( 3180)
  hydrogen bonds       : bond        0.05326 (   47)
  hydrogen bonds       : angle       5.68075 (  141)
  Misc. bond           : bond        0.00137 (   12)

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 49
  time to evaluate  : 0.094 
Fit side-chains
REVERT: B   32 VAL cc_start: 0.8610 (t) cc_final: 0.8343 (p)
REVERT: C   22 ASN cc_start: 0.8728 (t0) cc_final: 0.8120 (t0)
REVERT: D   14 ASN cc_start: 0.7891 (t0) cc_final: 0.7659 (t0)
REVERT: E   29 SER cc_start: 0.8864 (p) cc_final: 0.8637 (p)
REVERT: F   32 VAL cc_start: 0.8684 (t) cc_final: 0.8461 (p)
REVERT: J   32 VAL cc_start: 0.8679 (t) cc_final: 0.8459 (p)
REVERT: L   32 VAL cc_start: 0.8879 (t) cc_final: 0.8541 (p)
  outliers start: 18
  outliers final: 17
  residues processed: 57
  average time/residue: 0.0238
  time to fit residues: 2.0270
Evaluate side-chains
  64 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 47
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain A residue   31 ASN
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue   31 ASN
Chi-restraints excluded: chain E residue   31 ASN
Chi-restraints excluded: chain E residue   36 THR
Chi-restraints excluded: chain F residue   36 THR
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain G residue   36 THR
Chi-restraints excluded: chain H residue   30 THR
Chi-restraints excluded: chain H residue   36 THR
Chi-restraints excluded: chain I residue   31 ASN
Chi-restraints excluded: chain I residue   36 THR
Chi-restraints excluded: chain J residue   31 ASN
Chi-restraints excluded: chain J residue   36 THR
Chi-restraints excluded: chain K residue   31 ASN
Chi-restraints excluded: chain L residue   36 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    7.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  31 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.137488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.118781 restraints weight = 5259.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3892 rms_B_bonded: 3.85
r_work: 0.3777 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.4025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.010   2352  Z= 0.099
  Angle     :  0.469   3.767   3180  Z= 0.257
  Chirality :  0.038   0.122    384
  Planarity :  0.001   0.005    408
  Dihedral  :  5.331  14.894    312
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 22.73 %
    Favored  : 75.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.42 (0.25), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.36 (0.19), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.000   TYR B  37 
 PHE   0.005   0.001   PHE J  15 
 HIS   0.002   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 ( 2340)
  covalent geometry    : angle       0.46907 ( 3180)
  hydrogen bonds       : bond        0.02691 (   47)
  hydrogen bonds       : angle       5.23270 (  141)
  Misc. bond           : bond        0.00026 (   12)

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.097 
Fit side-chains
REVERT: C   22 ASN cc_start: 0.8636 (t0) cc_final: 0.8216 (t0)
REVERT: E   29 SER cc_start: 0.8685 (p) cc_final: 0.8458 (p)
REVERT: H   32 VAL cc_start: 0.8817 (t) cc_final: 0.8401 (m)
REVERT: J   32 VAL cc_start: 0.8594 (t) cc_final: 0.8287 (p)
REVERT: L   32 VAL cc_start: 0.8851 (t) cc_final: 0.8578 (p)
  outliers start: 4
  outliers final: 4
  residues processed: 62
  average time/residue: 0.0245
  time to fit residues: 2.2470
Evaluate side-chains
  49 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain H residue   36 THR
Chi-restraints excluded: chain I residue   31 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 18 optimal weight:    7.9990
   chunk 11 optimal weight:    0.9990
   chunk 4 optimal weight:    8.9990
   chunk 2 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  22 ASN
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  22 ASN
** G  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN
** I  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  22 ASN
L  31 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.133600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.115599 restraints weight = 4878.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 3.72
r_work: 0.3760 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.4373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   2352  Z= 0.277
  Angle     :  0.581   4.154   3180  Z= 0.325
  Chirality :  0.041   0.129    384
  Planarity :  0.002   0.009    408
  Dihedral  :  5.771  16.164    312
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 18.18 %
    Favored  : 75.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.42 (0.28), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.36 (0.21), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR K  37 
 PHE   0.014   0.003   PHE J  15 
 HIS   0.001   0.000   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00586 ( 2340)
  covalent geometry    : angle       0.58121 ( 3180)
  hydrogen bonds       : bond        0.03831 (   47)
  hydrogen bonds       : angle       5.33905 (  141)
  Misc. bond           : bond        0.00081 (   12)

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 42
  time to evaluate  : 0.097 
Fit side-chains
REVERT: C   22 ASN cc_start: 0.8802 (t0) cc_final: 0.8209 (t0)
REVERT: E   29 SER cc_start: 0.8787 (p) cc_final: 0.8559 (p)
REVERT: H   31 ASN cc_start: 0.7813 (m-40) cc_final: 0.7527 (m-40)
REVERT: H   32 VAL cc_start: 0.8647 (t) cc_final: 0.8268 (m)
REVERT: J   32 VAL cc_start: 0.8658 (t) cc_final: 0.8323 (p)
REVERT: L   32 VAL cc_start: 0.8875 (t) cc_final: 0.8593 (p)
  outliers start: 16
  outliers final: 13
  residues processed: 48
  average time/residue: 0.0246
  time to fit residues: 1.7671
Evaluate side-chains
  55 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain A residue   31 ASN
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   31 ASN
Chi-restraints excluded: chain E residue   31 ASN
Chi-restraints excluded: chain F residue   36 THR
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain H residue   27 LEU
Chi-restraints excluded: chain H residue   36 THR
Chi-restraints excluded: chain I residue   31 ASN
Chi-restraints excluded: chain J residue   31 ASN
Chi-restraints excluded: chain K residue   31 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 21 optimal weight:    0.3980
   chunk 13 optimal weight:    0.6980
   chunk 2 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 7 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 20 optimal weight:    7.9990
   chunk 4 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  31 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.136446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.117461 restraints weight = 5080.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3889 rms_B_bonded: 3.88
r_work: 0.3781 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.4383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.014   2352  Z= 0.134
  Angle     :  0.471   3.538   3180  Z= 0.263
  Chirality :  0.038   0.124    384
  Planarity :  0.001   0.005    408
  Dihedral  :  5.186  14.259    312
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 20.08 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.44 (0.28), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.37 (0.22), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR B  37 
 PHE   0.007   0.001   PHE D  15 
 HIS   0.002   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 2340)
  covalent geometry    : angle       0.47126 ( 3180)
  hydrogen bonds       : bond        0.02810 (   47)
  hydrogen bonds       : angle       5.00305 (  141)
  Misc. bond           : bond        0.00033 (   12)

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.116 
Fit side-chains
REVERT: C   22 ASN cc_start: 0.8701 (t0) cc_final: 0.8229 (t0)
REVERT: C   32 VAL cc_start: 0.8703 (t) cc_final: 0.8475 (p)
REVERT: E   29 SER cc_start: 0.8571 (p) cc_final: 0.8359 (p)
REVERT: H   31 ASN cc_start: 0.7814 (m-40) cc_final: 0.7498 (m-40)
REVERT: H   32 VAL cc_start: 0.8688 (t) cc_final: 0.8313 (m)
REVERT: H   36 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8514 (p)
REVERT: J   32 VAL cc_start: 0.8644 (t) cc_final: 0.8304 (p)
REVERT: J   35 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8324 (t0)
REVERT: L   32 VAL cc_start: 0.8845 (t) cc_final: 0.8560 (p)
  outliers start: 8
  outliers final: 5
  residues processed: 47
  average time/residue: 0.0238
  time to fit residues: 1.6821
Evaluate side-chains
  47 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain H residue   27 LEU
Chi-restraints excluded: chain H residue   36 THR
Chi-restraints excluded: chain I residue   31 ASN
Chi-restraints excluded: chain I residue   36 THR
Chi-restraints excluded: chain J residue   35 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 20 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  31 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.135446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.117618 restraints weight = 4450.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 3.49
r_work: 0.3768 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.4607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.035   2352  Z= 0.388
  Angle     :  0.653   4.745   3180  Z= 0.369
  Chirality :  0.042   0.127    384
  Planarity :  0.003   0.008    408
  Dihedral  :  6.084  16.909    312
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.99 %
    Favored  : 92.01 %
  Rotamer:
    Outliers :  6.44 %
    Allowed  : 17.42 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.66 (0.28), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.55 (0.21), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.006   0.001   TYR K  37 
 PHE   0.019   0.004   PHE J  15 
 HIS   0.002   0.001   HIS L  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00826 ( 2340)
  covalent geometry    : angle       0.65314 ( 3180)
  hydrogen bonds       : bond        0.04723 (   47)
  hydrogen bonds       : angle       5.44794 (  141)
  Misc. bond           : bond        0.00119 (   12)

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 37
  time to evaluate  : 0.096 
Fit side-chains
REVERT: C   22 ASN cc_start: 0.8738 (t0) cc_final: 0.8125 (t0)
REVERT: C   29 SER cc_start: 0.8993 (p) cc_final: 0.8746 (p)
REVERT: E   29 SER cc_start: 0.8826 (p) cc_final: 0.8595 (p)
REVERT: H   31 ASN cc_start: 0.7830 (m-40) cc_final: 0.7585 (m-40)
REVERT: J   32 VAL cc_start: 0.8652 (t) cc_final: 0.8392 (p)
REVERT: K   29 SER cc_start: 0.9044 (p) cc_final: 0.8823 (p)
REVERT: L   32 VAL cc_start: 0.8858 (t) cc_final: 0.8544 (p)
  outliers start: 17
  outliers final: 16
  residues processed: 41
  average time/residue: 0.0231
  time to fit residues: 1.4394
Evaluate side-chains
  51 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 35
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain A residue   31 ASN
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain B residue   31 ASN
Chi-restraints excluded: chain C residue   31 ASN
Chi-restraints excluded: chain E residue   31 ASN
Chi-restraints excluded: chain F residue   31 ASN
Chi-restraints excluded: chain F residue   36 THR
Chi-restraints excluded: chain G residue   31 ASN
Chi-restraints excluded: chain H residue   27 LEU
Chi-restraints excluded: chain H residue   36 THR
Chi-restraints excluded: chain I residue   31 ASN
Chi-restraints excluded: chain I residue   36 THR
Chi-restraints excluded: chain J residue   31 ASN
Chi-restraints excluded: chain K residue   31 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  31 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.135372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.116735 restraints weight = 4769.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 3.73
r_work: 0.3775 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.4546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.017   2352  Z= 0.177
  Angle     :  0.501   3.704   3180  Z= 0.281
  Chirality :  0.039   0.123    384
  Planarity :  0.002   0.006    408
  Dihedral  :  5.348  14.370    312
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 21.59 %
    Favored  : 74.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.68 (0.28), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.56 (0.21), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR B  37 
 PHE   0.010   0.002   PHE J  15 
 HIS   0.002   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 2340)
  covalent geometry    : angle       0.50102 ( 3180)
  hydrogen bonds       : bond        0.03250 (   47)
  hydrogen bonds       : angle       5.14450 (  141)
  Misc. bond           : bond        0.00050 (   12)

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.096 
Fit side-chains
REVERT: C   22 ASN cc_start: 0.8698 (t0) cc_final: 0.8280 (t0)
REVERT: C   32 VAL cc_start: 0.8703 (t) cc_final: 0.8444 (p)
REVERT: H   31 ASN cc_start: 0.7793 (m-40) cc_final: 0.7524 (m-40)
REVERT: J   32 VAL cc_start: 0.8654 (t) cc_final: 0.8407 (p)
REVERT: J   35 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8509 (t0)
REVERT: L   32 VAL cc_start: 0.8844 (t) cc_final: 0.8531 (m)
  outliers start: 11
  outliers final: 10
  residues processed: 45
  average time/residue: 0.0232
  time to fit residues: 1.5703
Evaluate side-chains
  49 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 38
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain E residue   31 ASN
Chi-restraints excluded: chain F residue   36 THR
Chi-restraints excluded: chain H residue   27 LEU
Chi-restraints excluded: chain H residue   36 THR
Chi-restraints excluded: chain I residue   31 ASN
Chi-restraints excluded: chain I residue   36 THR
Chi-restraints excluded: chain J residue   35 ASN
Chi-restraints excluded: chain L residue   34 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9990
   chunk 14 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 10 optimal weight:    4.9990
   chunk 13 optimal weight:    8.9990
   chunk 21 optimal weight:    0.0870
   chunk 18 optimal weight:    5.9990
   chunk 1 optimal weight:    0.3980
   chunk 19 optimal weight:   10.0000
   overall best weight:    2.4964

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  31 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.137593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.119104 restraints weight = 4639.080|
|-----------------------------------------------------------------------------|
r_work (start): 0.3905 rms_B_bonded: 3.57
r_work: 0.3799 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.4570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   2352  Z= 0.160
  Angle     :  0.482   3.567   3180  Z= 0.271
  Chirality :  0.038   0.121    384
  Planarity :  0.001   0.006    408
  Dihedral  :  5.180  14.300    312
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 20.83 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.71 (0.28), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.58 (0.22), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR B  37 
 PHE   0.008   0.002   PHE I  15 
 HIS   0.002   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 2340)
  covalent geometry    : angle       0.48247 ( 3180)
  hydrogen bonds       : bond        0.03017 (   47)
  hydrogen bonds       : angle       4.97149 (  141)
  Misc. bond           : bond        0.00045 (   12)

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

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

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  576 Ramachandran restraints generated.
    288 Oldfield, 0 Emsley, 288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.062 
Fit side-chains
REVERT: C   22 ASN cc_start: 0.8668 (t0) cc_final: 0.8250 (t0)
REVERT: C   32 VAL cc_start: 0.8719 (t) cc_final: 0.8475 (p)
REVERT: H   31 ASN cc_start: 0.7757 (m-40) cc_final: 0.7526 (m-40)
REVERT: J   32 VAL cc_start: 0.8683 (t) cc_final: 0.8431 (p)
REVERT: J   35 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8484 (t0)
REVERT: L   32 VAL cc_start: 0.8812 (t) cc_final: 0.8475 (m)
  outliers start: 11
  outliers final: 10
  residues processed: 48
  average time/residue: 0.0194
  time to fit residues: 1.3900
Evaluate side-chains
  51 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 SER
Chi-restraints excluded: chain B residue   19 SER
Chi-restraints excluded: chain B residue   27 LEU
Chi-restraints excluded: chain E residue   31 ASN
Chi-restraints excluded: chain F residue   36 THR
Chi-restraints excluded: chain H residue   27 LEU
Chi-restraints excluded: chain H residue   36 THR
Chi-restraints excluded: chain I residue   31 ASN
Chi-restraints excluded: chain I residue   36 THR
Chi-restraints excluded: chain J residue   35 ASN
Chi-restraints excluded: chain L residue   34 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 14 optimal weight:    0.8980
   chunk 1 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 11 optimal weight:    8.9990
   chunk 21 optimal weight:    6.9990
   chunk 23 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9980
   chunk 9 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   overall best weight:    2.9786

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

Flipped N/Q/H residues before XYZ refinement:
** B  22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  31 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.136042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.117674 restraints weight = 4668.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3910 rms_B_bonded: 3.57
r_work: 0.3805 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.4620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   2352  Z= 0.187
  Angle     :  0.499   3.698   3180  Z= 0.280
  Chirality :  0.038   0.120    384
  Planarity :  0.002   0.009    408
  Dihedral  :  5.284  14.615    312
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 21.21 %
    Favored  : 74.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.72 (0.28), residues: 288
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.59 (0.22), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR B  37 
 PHE   0.010   0.002   PHE J  15 
 HIS   0.001   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 2340)
  covalent geometry    : angle       0.49896 ( 3180)
  hydrogen bonds       : bond        0.03237 (   47)
  hydrogen bonds       : angle       4.96784 (  141)
  Misc. bond           : bond        0.00053 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 686.27 seconds
wall clock time: 12 minutes 37.10 seconds (757.10 seconds total)