Starting phenix.real_space_refine
on Tue Mar  3 11:04:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uak_26427/03_2026/7uak_26427.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uak_26427/03_2026/7uak_26427.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uak_26427/03_2026/7uak_26427.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uak_26427/03_2026/7uak_26427.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uak_26427/03_2026/7uak_26427.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uak_26427/03_2026/7uak_26427.map"
  }
  resolution = 3.38
  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=   0.004
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    1614      2.51       5
     N     450      2.21       5
     O     522      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2586
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 431
          Classifications: {'peptide': 62}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 61}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 0.37, per 1000 atoms: 0.14
  Number of scatterers: 2586
  At special positions: 0
  Unit cell: (95.23, 112.35, 34.24, 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     522      8.00
     N     450      7.00
     C    1614      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.16
  Conformation dependent library (CDL) restraints added in 65.8 milliseconds
  

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  636

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 13 sheets defined
      0.0% alpha, 37.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 56
      removed outlier: 8.984A  pdb=" N   VAL A  49 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 8.809A  pdb=" N   VAL C  52 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   GLY A  51 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 7.432A  pdb=" N   THR C  54 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   GLU A  53 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 8.171A  pdb=" N   ALA C  56 " --> pdb=" O   GLU A  53 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   VAL A  55 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 56
      removed outlier: 8.984A  pdb=" N   VAL A  49 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 8.809A  pdb=" N   VAL C  52 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   GLY A  51 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 7.432A  pdb=" N   THR C  54 " --> pdb=" O   GLY A  51 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   GLU A  53 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 8.171A  pdb=" N   ALA C  56 " --> pdb=" O   GLU A  53 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   VAL A  55 " --> pdb=" O   ALA C  56 " (cutoff:3.500A)
      removed outlier: 8.707A  pdb=" N   VAL E  52 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   GLY C  51 " --> pdb=" O   VAL E  52 " (cutoff:3.500A)
      removed outlier: 7.229A  pdb=" N   THR E  54 " --> pdb=" O   GLY C  51 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   GLU C  53 " --> pdb=" O   THR E  54 " (cutoff:3.500A)
      removed outlier: 7.988A  pdb=" N   ALA E  56 " --> pdb=" O   GLU C  53 " (cutoff:3.500A)
      removed outlier: 6.137A  pdb=" N   VAL C  55 " --> pdb=" O   ALA E  56 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 64
    Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 71
      removed outlier: 6.204A  pdb=" N   ALA A  69 " --> pdb=" O   VAL C  70 " (cutoff:3.500A)
      removed outlier: 7.694A  pdb=" N   THR C  72 " --> pdb=" O   ALA A  69 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   VAL A  71 " --> pdb=" O   THR C  72 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ALA C  69 " --> pdb=" O   VAL E  70 " (cutoff:3.500A)
      removed outlier: 7.975A  pdb=" N   THR E  72 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   VAL C  71 " --> pdb=" O   THR E  72 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 76
      removed outlier: 6.410A  pdb=" N   THR A  75 " --> pdb=" O   ALA C  76 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   THR C  75 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 82
    Processing sheet with id=AA7, first strand: chain 'A' and resid 88 through 94
      removed outlier: 8.104A  pdb=" N   ALA A  89 " --> pdb=" O   ALA C  90 " (cutoff:3.500A)
      removed outlier: 7.652A  pdb=" N   THR C  92 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 9.118A  pdb=" N   ALA A  91 " --> pdb=" O   THR C  92 " (cutoff:3.500A)
      removed outlier: 8.471A  pdb=" N   PHE C  94 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   GLY A  93 " --> pdb=" O   PHE C  94 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   LYS C  96 " --> pdb=" O   GLY A  93 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   ALA E  89 " --> pdb=" O   ILE C  88 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   ALA C  90 " --> pdb=" O   ALA E  89 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   PHE C  94 " --> pdb=" O   GLY E  93 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   VAL E  95 " --> pdb=" O   PHE C  94 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   LYS C  96 " --> pdb=" O   VAL E  95 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 49 through 56
      removed outlier: 8.787A  pdb=" N   VAL B  49 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 8.520A  pdb=" N   VAL D  52 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   GLY B  51 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   THR D  54 " --> pdb=" O   GLY B  51 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   GLU B  53 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      removed outlier: 7.717A  pdb=" N   ALA D  56 " --> pdb=" O   GLU B  53 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   VAL B  55 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   VAL D  52 " --> pdb=" O   GLY F  51 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   GLU F  53 " --> pdb=" O   VAL D  52 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   THR D  54 " --> pdb=" O   GLU F  53 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   VAL F  55 " --> pdb=" O   THR D  54 " (cutoff:3.500A)
      removed outlier: 7.122A  pdb=" N   ALA D  56 " --> pdb=" O   VAL F  55 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 63 through 64
    Processing sheet with id=AB1, first strand: chain 'B' and resid 69 through 71
      removed outlier: 6.349A  pdb=" N   ALA B  69 " --> pdb=" O   VAL D  70 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   ALA D  69 " --> pdb=" O   VAL F  70 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 75 through 76
      removed outlier: 6.679A  pdb=" N   THR B  75 " --> pdb=" O   ALA D  76 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   THR D  75 " --> pdb=" O   ALA F  76 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 81 through 82
    Processing sheet with id=AB4, first strand: chain 'B' and resid 88 through 96
      removed outlier: 8.156A  pdb=" N   ALA B  89 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   THR D  92 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 9.125A  pdb=" N   ALA B  91 " --> pdb=" O   THR D  92 " (cutoff:3.500A)
      removed outlier: 8.484A  pdb=" N   PHE D  94 " --> pdb=" O   ALA B  91 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   GLY B  93 " --> pdb=" O   PHE D  94 " (cutoff:3.500A)
      removed outlier: 7.755A  pdb=" N   LYS D  96 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   VAL B  95 " --> pdb=" O   LYS D  96 " (cutoff:3.500A)
      removed outlier: 8.158A  pdb=" N   ALA D  89 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
      removed outlier: 7.641A  pdb=" N   THR F  92 " --> pdb=" O   ALA D  89 " (cutoff:3.500A)
      removed outlier: 9.154A  pdb=" N   ALA D  91 " --> pdb=" O   THR F  92 " (cutoff:3.500A)
      removed outlier: 8.512A  pdb=" N   PHE F  94 " --> pdb=" O   ALA D  91 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   GLY D  93 " --> pdb=" O   PHE F  94 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   LYS F  96 " --> pdb=" O   GLY D  93 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   VAL D  95 " --> pdb=" O   LYS F  96 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4

    16 hydrogen bonds defined for protein.
    48 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: 0.23

  Time building geometry restraints manager: 0.21 seconds

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

  Histogram of bond lengths:
        1.22 -     1.28: 456
        1.28 -     1.35: 402
        1.35 -     1.41: 96
        1.41 -     1.48: 438
        1.48 -     1.55: 1206
  Bond restraints: 2598
  Sorted by residual:
  bond pdb=" N   GLU B  46 "
       pdb=" CA  GLU B  46 "
    ideal  model  delta    sigma   weight residual
    1.456  1.479 -0.023 1.25e-02 6.40e+03 3.39e+00
  bond pdb=" N   GLU A  46 "
       pdb=" CA  GLU A  46 "
    ideal  model  delta    sigma   weight residual
    1.456  1.479 -0.023 1.25e-02 6.40e+03 3.36e+00
  bond pdb=" N   GLU D  46 "
       pdb=" CA  GLU D  46 "
    ideal  model  delta    sigma   weight residual
    1.456  1.478 -0.023 1.25e-02 6.40e+03 3.31e+00
  bond pdb=" N   GLU E  46 "
       pdb=" CA  GLU E  46 "
    ideal  model  delta    sigma   weight residual
    1.456  1.478 -0.022 1.25e-02 6.40e+03 3.16e+00
  bond pdb=" N   GLU F  46 "
       pdb=" CA  GLU F  46 "
    ideal  model  delta    sigma   weight residual
    1.456  1.478 -0.022 1.25e-02 6.40e+03 3.15e+00
  ... (remaining 2593 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 3329
        1.23 -     2.45: 127
        2.45 -     3.68: 36
        3.68 -     4.91: 6
        4.91 -     6.13: 12
  Bond angle restraints: 3510
  Sorted by residual:
  angle pdb=" C   GLU E  46 "
        pdb=" CA  GLU E  46 "
        pdb=" CB  GLU E  46 "
      ideal   model   delta    sigma   weight residual
     109.64  115.00   -5.36 1.77e+00 3.19e-01 9.19e+00
  angle pdb=" C   GLU B  46 "
        pdb=" CA  GLU B  46 "
        pdb=" CB  GLU B  46 "
      ideal   model   delta    sigma   weight residual
     109.64  115.00   -5.36 1.77e+00 3.19e-01 9.16e+00
  angle pdb=" C   GLU D  46 "
        pdb=" CA  GLU D  46 "
        pdb=" CB  GLU D  46 "
      ideal   model   delta    sigma   weight residual
     109.64  114.99   -5.35 1.77e+00 3.19e-01 9.12e+00
  angle pdb=" C   GLU F  46 "
        pdb=" CA  GLU F  46 "
        pdb=" CB  GLU F  46 "
      ideal   model   delta    sigma   weight residual
     109.64  114.97   -5.33 1.77e+00 3.19e-01 9.08e+00
  angle pdb=" C   GLU A  46 "
        pdb=" CA  GLU A  46 "
        pdb=" CB  GLU A  46 "
      ideal   model   delta    sigma   weight residual
     109.64  114.97   -5.33 1.77e+00 3.19e-01 9.06e+00
  ... (remaining 3505 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.04: 1206
       10.04 -    20.08: 204
       20.08 -    30.12: 72
       30.12 -    40.16: 24
       40.16 -    50.20: 18
  Dihedral angle restraints: 1524
    sinusoidal: 516
      harmonic: 1008
  Sorted by residual:
  dihedral pdb=" CA  GLU D  46 "
           pdb=" C   GLU D  46 "
           pdb=" N   GLY D  47 "
           pdb=" CA  GLY D  47 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.27  -23.73     0      5.00e+00 4.00e-02 2.25e+01
  dihedral pdb=" CA  GLU C  46 "
           pdb=" C   GLU C  46 "
           pdb=" N   GLY C  47 "
           pdb=" CA  GLY C  47 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.28  -23.72     0      5.00e+00 4.00e-02 2.25e+01
  dihedral pdb=" CA  GLU A  46 "
           pdb=" C   GLU A  46 "
           pdb=" N   GLY A  47 "
           pdb=" CA  GLY A  47 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.28  -23.72     0      5.00e+00 4.00e-02 2.25e+01
  ... (remaining 1521 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 310
       0.035 -    0.071: 54
       0.071 -    0.106: 48
       0.106 -    0.141: 38
       0.141 -    0.177: 6
  Chirality restraints: 456
  Sorted by residual:
  chirality pdb=" CB  VAL E  77 "
            pdb=" CA  VAL E  77 "
            pdb=" CG1 VAL E  77 "
            pdb=" CG2 VAL E  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.80e-01
  chirality pdb=" CB  VAL D  77 "
            pdb=" CA  VAL D  77 "
            pdb=" CG1 VAL D  77 "
            pdb=" CG2 VAL D  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.76e-01
  chirality pdb=" CB  VAL C  77 "
            pdb=" CA  VAL C  77 "
            pdb=" CG1 VAL C  77 "
            pdb=" CG2 VAL C  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 7.72e-01
  ... (remaining 453 not shown)

  Planarity restraints: 438
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E  94 "    0.000 2.00e-02 2.50e+03   9.16e-03 1.47e+00
        pdb=" CG  PHE E  94 "    0.014 2.00e-02 2.50e+03
        pdb=" CD1 PHE E  94 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 PHE E  94 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE E  94 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE E  94 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE E  94 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  94 "    0.000 2.00e-02 2.50e+03   9.03e-03 1.43e+00
        pdb=" CG  PHE A  94 "    0.014 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  94 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  94 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  94 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  94 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  94 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  94 "   -0.001 2.00e-02 2.50e+03   8.95e-03 1.40e+00
        pdb=" CG  PHE B  94 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  94 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  94 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  94 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  94 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  94 "    0.002 2.00e-02 2.50e+03
  ... (remaining 435 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 1110
        2.91 -     3.40: 2293
        3.40 -     3.90: 4080
        3.90 -     4.40: 3915
        4.40 -     4.90: 8123
  Nonbonded interactions: 19521
  Sorted by model distance:
  nonbonded pdb=" N   ASP B  98 "
            pdb=" OD1 ASP B  98 "
     model   vdw
     2.407 3.120
  nonbonded pdb=" N   ASP C  98 "
            pdb=" OD1 ASP C  98 "
     model   vdw
     2.407 3.120
  nonbonded pdb=" N   ASP D  98 "
            pdb=" OD1 ASP D  98 "
     model   vdw
     2.407 3.120
  nonbonded pdb=" N   ASP E  98 "
            pdb=" OD1 ASP E  98 "
     model   vdw
     2.407 3.120
  nonbonded pdb=" N   ASP F  98 "
            pdb=" OD1 ASP F  98 "
     model   vdw
     2.407 3.120
  ... (remaining 19516 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'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.190
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6421
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   0.042   2598  Z= 0.181
  Angle     :  0.696   6.133   3510  Z= 0.404
  Chirality :  0.053   0.177    456
  Planarity :  0.002   0.010    438
  Dihedral  : 13.749  50.196    888
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.44 %
    Favored  : 85.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 are not related in a simple way.
  whole: -2.82 (0.41), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.31), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR E  39 
 PHE   0.015   0.007   PHE E  94 
 HIS   0.002   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 2598)
  covalent geometry    : angle       0.69649 ( 3510)
  hydrogen bonds       : bond        0.20850 (   16)
  hydrogen bonds       : angle       8.17976 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.076 
Fit side-chains
REVERT: E   79 GLN cc_start: 0.8009 (mp10) cc_final: 0.7802 (mp10)
REVERT: F   57 GLU cc_start: 0.7570 (mp0) cc_final: 0.6840 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 19
  average time/residue: 0.0512
  time to fit residues: 1.2688
Evaluate side-chains
  16 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0980
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    2.2188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.140922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.105467 restraints weight = 3100.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3962 rms_B_bonded: 2.88
r_work: 0.3848 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3715 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   2598  Z= 0.231
  Angle     :  0.702   5.776   3510  Z= 0.387
  Chirality :  0.052   0.128    456
  Planarity :  0.003   0.011    438
  Dihedral  :  6.771  26.266    372
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.22 %
    Favored  : 82.78 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  :  6.44 %
    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 are not related in a simple way.
  whole: -3.25 (0.38), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.47 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR F  39 
 PHE   0.013   0.003   PHE D  94 
 HIS   0.009   0.004   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 ( 2598)
  covalent geometry    : angle       0.70213 ( 3510)
  hydrogen bonds       : bond        0.02716 (   16)
  hydrogen bonds       : angle       5.22727 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 23
  time to evaluate  : 0.089 
Fit side-chains
REVERT: A   57 GLU cc_start: 0.7772 (mp0) cc_final: 0.7313 (mp0)
REVERT: B   58 LYS cc_start: 0.7627 (ptpt) cc_final: 0.7392 (ptpt)
REVERT: E   58 LYS cc_start: 0.7358 (ptpt) cc_final: 0.7154 (ptpt)
REVERT: F   58 LYS cc_start: 0.7400 (ptpt) cc_final: 0.7021 (ptpt)
  outliers start: 7
  outliers final: 7
  residues processed: 28
  average time/residue: 0.0549
  time to fit residues: 1.8539
Evaluate side-chains
  25 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 18
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain F residue   59 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 24 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.2784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.141943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.105887 restraints weight = 3071.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3963 rms_B_bonded: 2.84
r_work: 0.3846 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3713 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
moved from start:          0.3207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2598  Z= 0.140
  Angle     :  0.591   5.011   3510  Z= 0.324
  Chirality :  0.049   0.137    456
  Planarity :  0.002   0.007    438
  Dihedral  :  6.280  26.561    372
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.33 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  :  9.85 %
    Favored  : 87.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.30 (0.38), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.51 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR B  39 
 PHE   0.008   0.002   PHE A  94 
 HIS   0.004   0.002   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 2598)
  covalent geometry    : angle       0.59104 ( 3510)
  hydrogen bonds       : bond        0.02205 (   16)
  hydrogen bonds       : angle       4.22572 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 21
  time to evaluate  : 0.097 
Fit side-chains
REVERT: A   57 GLU cc_start: 0.7705 (mp0) cc_final: 0.7074 (mp0)
REVERT: D   58 LYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6741 (ptpt)
REVERT: E   58 LYS cc_start: 0.7444 (ptpt) cc_final: 0.7148 (ptpt)
REVERT: F   58 LYS cc_start: 0.7216 (ptpt) cc_final: 0.6843 (ptpt)
  outliers start: 8
  outliers final: 5
  residues processed: 26
  average time/residue: 0.0762
  time to fit residues: 2.3407
Evaluate side-chains
  25 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 19
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain F residue   59 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 12 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 2 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   chunk 20 optimal weight:    4.9990
   chunk 19 optimal weight:    5.9990
   overall best weight:    2.5186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.135368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.100291 restraints weight = 3136.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3918 rms_B_bonded: 2.78
r_work: 0.3798 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3663 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.3963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   2598  Z= 0.247
  Angle     :  0.685   4.869   3510  Z= 0.381
  Chirality :  0.052   0.134    456
  Planarity :  0.003   0.008    438
  Dihedral  :  6.861  26.038    372
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.50 %
    Favored  : 82.50 %
  Rotamer:
    Outliers :  7.20 %
    Allowed  :  9.85 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.57 (0.35), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.71 (0.27), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR F  39 
 PHE   0.007   0.002   PHE B  94 
 HIS   0.007   0.004   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 2598)
  covalent geometry    : angle       0.68512 ( 3510)
  hydrogen bonds       : bond        0.03197 (   16)
  hydrogen bonds       : angle       4.22584 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 29
  time to evaluate  : 0.091 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.4884 (OUTLIER) cc_final: 0.4570 (tt)
REVERT: A   57 GLU cc_start: 0.7850 (mp0) cc_final: 0.7305 (mp0)
REVERT: A   58 LYS cc_start: 0.7710 (ptpt) cc_final: 0.7046 (ptpt)
REVERT: D   58 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7216 (ptpt)
REVERT: E   57 GLU cc_start: 0.8067 (mp0) cc_final: 0.7720 (mp0)
REVERT: F   58 LYS cc_start: 0.7266 (ptpt) cc_final: 0.6921 (ptpt)
  outliers start: 19
  outliers final: 12
  residues processed: 43
  average time/residue: 0.0918
  time to fit residues: 4.5267
Evaluate side-chains
  38 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 24
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain B residue   65 ASN
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   65 ASN
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   77 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    2.1188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.136454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.101687 restraints weight = 3188.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 2.86
r_work: 0.3819 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3680 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   2598  Z= 0.211
  Angle     :  0.646   4.566   3510  Z= 0.358
  Chirality :  0.051   0.140    456
  Planarity :  0.003   0.010    438
  Dihedral  :  6.676  25.493    372
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.06 %
    Favored  : 81.94 %
  Rotamer:
    Outliers :  6.82 %
    Allowed  : 10.98 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.56 (0.35), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.27), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR D  39 
 PHE   0.005   0.002   PHE D  94 
 HIS   0.005   0.003   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 2598)
  covalent geometry    : angle       0.64595 ( 3510)
  hydrogen bonds       : bond        0.02666 (   16)
  hydrogen bonds       : angle       3.94265 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 26
  time to evaluate  : 0.060 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.4795 (OUTLIER) cc_final: 0.4479 (tt)
REVERT: A   57 GLU cc_start: 0.7779 (mp0) cc_final: 0.7194 (mp0)
REVERT: A   58 LYS cc_start: 0.7763 (ptpt) cc_final: 0.7508 (ptpt)
REVERT: B   38 LEU cc_start: 0.4342 (OUTLIER) cc_final: 0.3641 (tt)
REVERT: D   58 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7153 (ptpt)
REVERT: E   38 LEU cc_start: 0.4594 (OUTLIER) cc_final: 0.4117 (tt)
REVERT: E   57 GLU cc_start: 0.8055 (mp0) cc_final: 0.7608 (mp0)
REVERT: F   38 LEU cc_start: 0.4834 (OUTLIER) cc_final: 0.4301 (tt)
REVERT: F   58 LYS cc_start: 0.7228 (ptpt) cc_final: 0.6873 (ptpt)
  outliers start: 18
  outliers final: 12
  residues processed: 41
  average time/residue: 0.0733
  time to fit residues: 3.4510
Evaluate side-chains
  42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 25
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   65 ASN
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   65 ASN
Chi-restraints excluded: chain F residue   77 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 31 optimal weight:    0.4980
   chunk 21 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 2 optimal weight:    0.1980
   chunk 8 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.141760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.106365 restraints weight = 3052.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3971 rms_B_bonded: 2.82
r_work: 0.3857 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3718 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.4093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   2598  Z= 0.109
  Angle     :  0.560   4.479   3510  Z= 0.306
  Chirality :  0.049   0.131    456
  Planarity :  0.002   0.009    438
  Dihedral  :  5.856  22.828    372
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.72 %
    Favored  : 85.28 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 15.91 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.33 (0.38), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.53 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR B  39 
 PHE   0.005   0.001   PHE D  94 
 HIS   0.003   0.002   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 2598)
  covalent geometry    : angle       0.55965 ( 3510)
  hydrogen bonds       : bond        0.01765 (   16)
  hydrogen bonds       : angle       3.72237 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 20
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.7644 (mp0) cc_final: 0.6920 (mp0)
REVERT: A   58 LYS cc_start: 0.7391 (ptpt) cc_final: 0.6970 (ptpt)
REVERT: B   38 LEU cc_start: 0.4201 (OUTLIER) cc_final: 0.3360 (tt)
REVERT: B   57 GLU cc_start: 0.7599 (mp0) cc_final: 0.7363 (mp0)
REVERT: D   58 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6775 (ptpt)
REVERT: E   38 LEU cc_start: 0.4098 (OUTLIER) cc_final: 0.3682 (tt)
REVERT: E   57 GLU cc_start: 0.8165 (mp0) cc_final: 0.7618 (mp0)
REVERT: F   38 LEU cc_start: 0.3920 (OUTLIER) cc_final: 0.3261 (tt)
  outliers start: 12
  outliers final: 6
  residues processed: 30
  average time/residue: 0.0853
  time to fit residues: 2.9786
Evaluate side-chains
  30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 20
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   59 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 29 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   overall best weight:    1.4782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.132890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.096865 restraints weight = 3080.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3909 rms_B_bonded: 2.94
r_work: 0.3798 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3663 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.4254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2598  Z= 0.155
  Angle     :  0.589   4.352   3510  Z= 0.324
  Chirality :  0.049   0.130    456
  Planarity :  0.002   0.009    438
  Dihedral  :  6.077  23.759    372
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.78 %
    Favored  : 82.22 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 15.91 %
    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 are not related in a simple way.
  whole: -3.31 (0.39), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.52 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR D  39 
 PHE   0.004   0.001   PHE D  94 
 HIS   0.004   0.002   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 2598)
  covalent geometry    : angle       0.58920 ( 3510)
  hydrogen bonds       : bond        0.02188 (   16)
  hydrogen bonds       : angle       3.74556 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 26
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LEU cc_start: 0.5125 (OUTLIER) cc_final: 0.4699 (tt)
REVERT: A   57 GLU cc_start: 0.7696 (mp0) cc_final: 0.7042 (mp0)
REVERT: A   58 LYS cc_start: 0.7551 (ptpt) cc_final: 0.7301 (ptpt)
REVERT: B   38 LEU cc_start: 0.4245 (OUTLIER) cc_final: 0.3382 (tt)
REVERT: D   58 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6965 (ptpt)
REVERT: E   38 LEU cc_start: 0.4043 (OUTLIER) cc_final: 0.3640 (tt)
REVERT: E   57 GLU cc_start: 0.8080 (mp0) cc_final: 0.7535 (mp0)
REVERT: F   38 LEU cc_start: 0.3965 (OUTLIER) cc_final: 0.3342 (tt)
  outliers start: 16
  outliers final: 8
  residues processed: 38
  average time/residue: 0.1034
  time to fit residues: 4.4785
Evaluate side-chains
  39 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 26
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   59 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 23 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 24 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9980
   chunk 2 optimal weight:    6.9990
   chunk 15 optimal weight:    7.9990
   overall best weight:    2.1384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.130415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.095000 restraints weight = 3197.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3846 rms_B_bonded: 2.96
r_work: 0.3726 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3586 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.4502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   2598  Z= 0.213
  Angle     :  0.648   4.790   3510  Z= 0.358
  Chirality :  0.051   0.131    456
  Planarity :  0.003   0.010    438
  Dihedral  :  6.505  23.926    372
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.33 %
    Favored  : 81.67 %
  Rotamer:
    Outliers :  7.95 %
    Allowed  : 15.15 %
    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 are not related in a simple way.
  whole: -3.46 (0.37), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.63 (0.28), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.002   0.001   TYR D  39 
 PHE   0.006   0.002   PHE D  94 
 HIS   0.005   0.003   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 2598)
  covalent geometry    : angle       0.64756 ( 3510)
  hydrogen bonds       : bond        0.02716 (   16)
  hydrogen bonds       : angle       3.79132 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 33
  time to evaluate  : 0.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 LEU cc_start: 0.5281 (OUTLIER) cc_final: 0.4923 (tt)
REVERT: A   57 GLU cc_start: 0.7733 (mp0) cc_final: 0.7092 (mp0)
REVERT: A   58 LYS cc_start: 0.7652 (ptpt) cc_final: 0.7386 (ptpt)
REVERT: B   38 LEU cc_start: 0.4125 (OUTLIER) cc_final: 0.3396 (tt)
REVERT: D   58 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6952 (ptpt)
REVERT: E   38 LEU cc_start: 0.4244 (OUTLIER) cc_final: 0.3740 (tt)
REVERT: E   57 GLU cc_start: 0.8111 (mp0) cc_final: 0.7516 (mp0)
REVERT: F   38 LEU cc_start: 0.4520 (OUTLIER) cc_final: 0.3803 (tt)
  outliers start: 21
  outliers final: 12
  residues processed: 49
  average time/residue: 0.0828
  time to fit residues: 4.6338
Evaluate side-chains
  49 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 32
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   58 LYS
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   77 VAL
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   59 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9980
   chunk 12 optimal weight:    6.9990
   chunk 4 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.7786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.131726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.096297 restraints weight = 3171.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3884 rms_B_bonded: 2.93
r_work: 0.3767 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.3629 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.4535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   2598  Z= 0.181
  Angle     :  0.629   4.503   3510  Z= 0.346
  Chirality :  0.050   0.129    456
  Planarity :  0.002   0.012    438
  Dihedral  :  6.311  23.344    372
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 18.06 %
    Favored  : 81.94 %
  Rotamer:
    Outliers :  7.58 %
    Allowed  : 16.67 %
    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 are not related in a simple way.
  whole: -3.43 (0.37), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.60 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR D  39 
 PHE   0.006   0.001   PHE D  94 
 HIS   0.004   0.003   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 2598)
  covalent geometry    : angle       0.62931 ( 3510)
  hydrogen bonds       : bond        0.02444 (   16)
  hydrogen bonds       : angle       3.74261 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 32
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 LEU cc_start: 0.5301 (OUTLIER) cc_final: 0.4929 (tt)
REVERT: A   57 GLU cc_start: 0.7750 (mp0) cc_final: 0.7078 (mp0)
REVERT: A   58 LYS cc_start: 0.7617 (ptpt) cc_final: 0.7194 (ptpt)
REVERT: B   38 LEU cc_start: 0.4155 (OUTLIER) cc_final: 0.3398 (tt)
REVERT: D   58 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.7027 (ptpt)
REVERT: D   92 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8481 (p)
REVERT: E   38 LEU cc_start: 0.4165 (OUTLIER) cc_final: 0.3689 (tt)
REVERT: E   57 GLU cc_start: 0.8087 (mp0) cc_final: 0.7573 (mp0)
REVERT: F   38 LEU cc_start: 0.4582 (OUTLIER) cc_final: 0.3779 (tt)
  outliers start: 20
  outliers final: 10
  residues processed: 48
  average time/residue: 0.0956
  time to fit residues: 5.2136
Evaluate side-chains
  48 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 32
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   65 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0980
   overall best weight:    1.1582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.134138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.098116 restraints weight = 3097.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 2.96
r_work: 0.3795 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3652 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.4551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2598  Z= 0.134
  Angle     :  0.606   4.235   3510  Z= 0.333
  Chirality :  0.049   0.128    456
  Planarity :  0.002   0.012    438
  Dihedral  :  6.094  22.686    372
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.83 %
    Favored  : 84.17 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 20.08 %
    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 are not related in a simple way.
  whole: -3.29 (0.39), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.50 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR B  39 
 PHE   0.006   0.001   PHE D  94 
 HIS   0.003   0.002   HIS E  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 2598)
  covalent geometry    : angle       0.60614 ( 3510)
  hydrogen bonds       : bond        0.01944 (   16)
  hydrogen bonds       : angle       3.65971 (   48)

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

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

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  720 Ramachandran restraints generated.
    360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 30
  time to evaluate  : 0.058 
Fit side-chains
REVERT: A   38 LEU cc_start: 0.5048 (OUTLIER) cc_final: 0.4543 (tt)
REVERT: A   57 GLU cc_start: 0.7728 (mp0) cc_final: 0.7149 (mp0)
REVERT: B   38 LEU cc_start: 0.4556 (OUTLIER) cc_final: 0.3653 (tt)
REVERT: B   97 LYS cc_start: 0.8222 (mttt) cc_final: 0.7952 (mttp)
REVERT: D   58 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6973 (ptpt)
REVERT: D   92 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8472 (p)
REVERT: E   38 LEU cc_start: 0.4096 (OUTLIER) cc_final: 0.3615 (tt)
REVERT: E   57 GLU cc_start: 0.7961 (mp0) cc_final: 0.7408 (mp0)
REVERT: F   38 LEU cc_start: 0.4417 (OUTLIER) cc_final: 0.3524 (tt)
  outliers start: 14
  outliers final: 8
  residues processed: 43
  average time/residue: 0.0900
  time to fit residues: 4.4122
Evaluate side-chains
  44 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 30
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   92 THR
Chi-restraints excluded: chain C residue   38 LEU
Chi-restraints excluded: chain C residue   65 ASN
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   59 THR
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   92 THR
Chi-restraints excluded: chain E residue   38 LEU
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain F residue   38 LEU
Chi-restraints excluded: chain F residue   59 THR
Chi-restraints excluded: chain F residue   65 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 15 optimal weight:    8.9990
   chunk 5 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 21 optimal weight:    0.3980
   chunk 12 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    1.7584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.131875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.096571 restraints weight = 3153.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3902 rms_B_bonded: 2.93
r_work: 0.3772 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3628 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.4663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2598  Z= 0.187
  Angle     :  0.666   5.356   3510  Z= 0.367
  Chirality :  0.050   0.127    456
  Planarity :  0.002   0.012    438
  Dihedral  :  6.365  23.203    372
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 19.17 %
    Favored  : 80.83 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 19.32 %
    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 are not related in a simple way.
  whole: -3.43 (0.38), residues: 360
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.61 (0.29), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR D  39 
 PHE   0.005   0.001   PHE D  94 
 HIS   0.004   0.003   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 2598)
  covalent geometry    : angle       0.66647 ( 3510)
  hydrogen bonds       : bond        0.02296 (   16)
  hydrogen bonds       : angle       3.72177 (   48)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 854.02 seconds
wall clock time: 15 minutes 15.48 seconds (915.48 seconds total)