Starting phenix.real_space_refine
on Sat Apr 26 18:12:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gzx_51736/04_2025/9gzx_51736.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gzx_51736/04_2025/9gzx_51736.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gzx_51736/04_2025/9gzx_51736.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gzx_51736/04_2025/9gzx_51736.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gzx_51736/04_2025/9gzx_51736.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gzx_51736/04_2025/9gzx_51736.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    1854      2.51       5
     N     546      2.21       5
     O     606      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3006
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 212
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 212
          Classifications: {'peptide': 28}
          Link IDs: {'TRANS': 27}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 179
          Classifications: {'peptide': 24}
          Link IDs: {'TRANS': 23}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {'NH2': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 108
          Classifications: {'peptide': 15}
          Link IDs: {'TRANS': 14}
  Restraints were copied for chains:
    E, H, K, N, Q, F, I, L, O, R, D, G, J, M, P
  Time building chain proxies: 1.75, per 1000 atoms: 0.58
  Number of scatterers: 3006
  At special positions: 0
  Unit cell: (92.38, 75.99, 49.17, 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     606      8.00
     N     546      7.00
     C    1854      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: 0.76
  Conformation dependent library (CDL) restraints added in 338.1 milliseconds
  

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  744

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 7 sheets defined
      0.0% alpha, 53.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13
    Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 22
    Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 33
      removed outlier: 6.482A  pdb=" N   LEU A  27 " --> pdb=" O   SER D  28 " (cutoff:3.500A)
      removed outlier: 8.020A  pdb=" N   THR D  30 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   SER A  29 " --> pdb=" O   THR D  30 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   VAL D  32 " --> pdb=" O   SER A  29 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   ASN A  31 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   LEU D  27 " --> pdb=" O   SER G  28 " (cutoff:3.500A)
      removed outlier: 8.012A  pdb=" N   THR G  30 " --> pdb=" O   LEU D  27 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   SER D  29 " --> pdb=" O   THR G  30 " (cutoff:3.500A)
      removed outlier: 7.986A  pdb=" N   VAL G  32 " --> pdb=" O   SER D  29 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   ASN D  31 " --> pdb=" O   VAL G  32 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   LEU G  27 " --> pdb=" O   SER J  28 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   THR J  30 " --> pdb=" O   LEU G  27 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   SER G  29 " --> pdb=" O   THR J  30 " (cutoff:3.500A)
      removed outlier: 7.983A  pdb=" N   VAL J  32 " --> pdb=" O   SER G  29 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   ASN G  31 " --> pdb=" O   VAL J  32 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   LEU J  27 " --> pdb=" O   SER M  28 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   THR M  30 " --> pdb=" O   LEU J  27 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   SER J  29 " --> pdb=" O   THR M  30 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   VAL M  32 " --> pdb=" O   SER J  29 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   ASN J  31 " --> pdb=" O   VAL M  32 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   LEU M  27 " --> pdb=" O   SER P  28 " (cutoff:3.500A)
      removed outlier: 8.012A  pdb=" N   THR P  30 " --> pdb=" O   LEU M  27 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   SER M  29 " --> pdb=" O   THR P  30 " (cutoff:3.500A)
      removed outlier: 7.986A  pdb=" N   VAL P  32 " --> pdb=" O   SER M  29 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   ASN M  31 " --> pdb=" O   VAL P  32 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 22
    Processing sheet with id=AA5, first strand: chain 'B' and resid 26 through 33
      removed outlier: 6.547A  pdb=" N   LEU B  27 " --> pdb=" O   SER E  28 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   THR E  30 " --> pdb=" O   LEU B  27 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   SER B  29 " --> pdb=" O   THR E  30 " (cutoff:3.500A)
      removed outlier: 8.054A  pdb=" N   VAL E  32 " --> pdb=" O   SER B  29 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   ASN B  31 " --> pdb=" O   VAL E  32 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   LEU E  27 " --> pdb=" O   SER H  28 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   THR H  30 " --> pdb=" O   LEU E  27 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   SER E  29 " --> pdb=" O   THR H  30 " (cutoff:3.500A)
      removed outlier: 8.004A  pdb=" N   VAL H  32 " --> pdb=" O   SER E  29 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   ASN E  31 " --> pdb=" O   VAL H  32 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   LEU H  27 " --> pdb=" O   SER K  28 " (cutoff:3.500A)
      removed outlier: 8.040A  pdb=" N   THR K  30 " --> pdb=" O   LEU H  27 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   SER H  29 " --> pdb=" O   THR K  30 " (cutoff:3.500A)
      removed outlier: 8.050A  pdb=" N   VAL K  32 " --> pdb=" O   SER H  29 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   ASN H  31 " --> pdb=" O   VAL K  32 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   LEU K  27 " --> pdb=" O   SER N  28 " (cutoff:3.500A)
      removed outlier: 7.984A  pdb=" N   THR N  30 " --> pdb=" O   LEU K  27 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   SER K  29 " --> pdb=" O   THR N  30 " (cutoff:3.500A)
      removed outlier: 7.998A  pdb=" N   VAL N  32 " --> pdb=" O   SER K  29 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ASN K  31 " --> pdb=" O   VAL N  32 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   LEU N  27 " --> pdb=" O   SER Q  28 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   THR Q  30 " --> pdb=" O   LEU N  27 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   SER N  29 " --> pdb=" O   THR Q  30 " (cutoff:3.500A)
      removed outlier: 8.041A  pdb=" N   VAL Q  32 " --> pdb=" O   SER N  29 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ASN N  31 " --> pdb=" O   VAL Q  32 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 17 through 20
      removed outlier: 6.320A  pdb=" N   VAL C  17 " --> pdb=" O   HIS F  18 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   SER F  20 " --> pdb=" O   VAL C  17 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   SER C  19 " --> pdb=" O   SER F  20 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   VAL F  17 " --> pdb=" O   HIS I  18 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   SER I  20 " --> pdb=" O   VAL F  17 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   SER F  19 " --> pdb=" O   SER I  20 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   VAL I  17 " --> pdb=" O   HIS L  18 " (cutoff:3.500A)
      removed outlier: 8.062A  pdb=" N   SER L  20 " --> pdb=" O   VAL I  17 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   SER I  19 " --> pdb=" O   SER L  20 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   VAL L  17 " --> pdb=" O   HIS O  18 " (cutoff:3.500A)
      removed outlier: 7.848A  pdb=" N   SER O  20 " --> pdb=" O   VAL L  17 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   SER L  19 " --> pdb=" O   SER O  20 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   VAL O  17 " --> pdb=" O   HIS R  18 " (cutoff:3.500A)
      removed outlier: 8.020A  pdb=" N   SER R  20 " --> pdb=" O   VAL O  17 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   SER O  19 " --> pdb=" O   SER R  20 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 25 through 29
      removed outlier: 6.483A  pdb=" N   ILE C  26 " --> pdb=" O   LEU F  27 " (cutoff:3.500A)
      removed outlier: 8.006A  pdb=" N   SER F  29 " --> pdb=" O   ILE C  26 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   SER C  28 " --> pdb=" O   SER F  29 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ILE F  26 " --> pdb=" O   LEU I  27 " (cutoff:3.500A)
      removed outlier: 7.967A  pdb=" N   SER I  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   SER F  28 " --> pdb=" O   SER I  29 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ILE I  26 " --> pdb=" O   LEU L  27 " (cutoff:3.500A)
      removed outlier: 7.684A  pdb=" N   SER L  29 " --> pdb=" O   ILE I  26 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   SER I  28 " --> pdb=" O   SER L  29 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ILE L  26 " --> pdb=" O   LEU O  27 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   SER O  29 " --> pdb=" O   ILE L  26 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   SER L  28 " --> pdb=" O   SER O  29 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   ILE O  26 " --> pdb=" O   LEU R  27 " (cutoff:3.500A)
      removed outlier: 8.116A  pdb=" N   SER R  29 " --> pdb=" O   ILE O  26 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   SER O  28 " --> pdb=" O   SER R  29 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7

    75 hydrogen bonds defined for protein.
    225 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: 0.66

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 480
        1.29 -     1.35: 534
        1.35 -     1.42: 384
        1.42 -     1.49: 467
        1.49 -     1.55: 1171
  Bond restraints: 3036
  Sorted by residual:
  bond pdb=" CG  LEU P  12 "
       pdb=" CD2 LEU P  12 "
    ideal  model  delta    sigma   weight residual
    1.521  1.446  0.075 3.30e-02 9.18e+02 5.21e+00
  bond pdb=" CG  LEU G  12 "
       pdb=" CD2 LEU G  12 "
    ideal  model  delta    sigma   weight residual
    1.521  1.446  0.075 3.30e-02 9.18e+02 5.21e+00
  bond pdb=" CG  LEU D  12 "
       pdb=" CD2 LEU D  12 "
    ideal  model  delta    sigma   weight residual
    1.521  1.446  0.075 3.30e-02 9.18e+02 5.19e+00
  bond pdb=" CG  LEU J  12 "
       pdb=" CD2 LEU J  12 "
    ideal  model  delta    sigma   weight residual
    1.521  1.446  0.075 3.30e-02 9.18e+02 5.19e+00
  bond pdb=" CG  LEU M  12 "
       pdb=" CD2 LEU M  12 "
    ideal  model  delta    sigma   weight residual
    1.521  1.446  0.075 3.30e-02 9.18e+02 5.18e+00
  ... (remaining 3031 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 3965
        2.28 -     4.56: 116
        4.56 -     6.84: 23
        6.84 -     9.13: 0
        9.13 -    11.41: 6
  Bond angle restraints: 4110
  Sorted by residual:
  angle pdb=" CB  LEU G  16 "
        pdb=" CG  LEU G  16 "
        pdb=" CD1 LEU G  16 "
      ideal   model   delta    sigma   weight residual
     110.70  122.11  -11.41 3.00e+00 1.11e-01 1.45e+01
  angle pdb=" CB  LEU D  16 "
        pdb=" CG  LEU D  16 "
        pdb=" CD1 LEU D  16 "
      ideal   model   delta    sigma   weight residual
     110.70  122.10  -11.40 3.00e+00 1.11e-01 1.44e+01
  angle pdb=" CB  LEU A  16 "
        pdb=" CG  LEU A  16 "
        pdb=" CD1 LEU A  16 "
      ideal   model   delta    sigma   weight residual
     110.70  122.09  -11.39 3.00e+00 1.11e-01 1.44e+01
  angle pdb=" CB  LEU P  16 "
        pdb=" CG  LEU P  16 "
        pdb=" CD1 LEU P  16 "
      ideal   model   delta    sigma   weight residual
     110.70  122.07  -11.37 3.00e+00 1.11e-01 1.44e+01
  angle pdb=" CB  LEU M  16 "
        pdb=" CG  LEU M  16 "
        pdb=" CD1 LEU M  16 "
      ideal   model   delta    sigma   weight residual
     110.70  122.06  -11.36 3.00e+00 1.11e-01 1.43e+01
  ... (remaining 4105 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.78: 1449
       10.78 -    21.56: 195
       21.56 -    32.35: 60
       32.35 -    43.13: 0
       43.13 -    53.91: 12
  Dihedral angle restraints: 1716
    sinusoidal: 576
      harmonic: 1140
  Sorted by residual:
  dihedral pdb=" N   GLN A  10 "
           pdb=" CA  GLN A  10 "
           pdb=" CB  GLN A  10 "
           pdb=" CG  GLN A  10 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -91.25   31.25     3      1.50e+01 4.44e-03 5.05e+00
  dihedral pdb=" N   GLN M  10 "
           pdb=" CA  GLN M  10 "
           pdb=" CB  GLN M  10 "
           pdb=" CG  GLN M  10 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -91.22   31.22     3      1.50e+01 4.44e-03 5.04e+00
  dihedral pdb=" N   GLN P  10 "
           pdb=" CA  GLN P  10 "
           pdb=" CB  GLN P  10 "
           pdb=" CG  GLN P  10 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -91.20   31.20     3      1.50e+01 4.44e-03 5.04e+00
  ... (remaining 1713 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.127: 462
       0.127 -    0.254: 12
       0.254 -    0.381: 12
       0.381 -    0.508: 0
       0.508 -    0.636: 6
  Chirality restraints: 492
  Sorted by residual:
  chirality pdb=" CG  LEU P  16 "
            pdb=" CB  LEU P  16 "
            pdb=" CD1 LEU P  16 "
            pdb=" CD2 LEU P  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.95   -0.64 2.00e-01 2.50e+01 1.01e+01
  chirality pdb=" CG  LEU A  16 "
            pdb=" CB  LEU A  16 "
            pdb=" CD1 LEU A  16 "
            pdb=" CD2 LEU A  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.96   -0.63 2.00e-01 2.50e+01 1.00e+01
  chirality pdb=" CG  LEU M  16 "
            pdb=" CB  LEU M  16 "
            pdb=" CD1 LEU M  16 "
            pdb=" CD2 LEU M  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.96   -0.63 2.00e-01 2.50e+01 1.00e+01
  ... (remaining 489 not shown)

  Planarity restraints: 528
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H  15 "   -0.013 2.00e-02 2.50e+03   1.49e-02 3.89e+00
        pdb=" CG  PHE H  15 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE H  15 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE H  15 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 PHE H  15 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE H  15 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE H  15 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE Q  15 "   -0.013 2.00e-02 2.50e+03   1.48e-02 3.85e+00
        pdb=" CG  PHE Q  15 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE Q  15 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE Q  15 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE Q  15 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE Q  15 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE Q  15 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE N  15 "   -0.013 2.00e-02 2.50e+03   1.48e-02 3.81e+00
        pdb=" CG  PHE N  15 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE N  15 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE N  15 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE N  15 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE N  15 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE N  15 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 525 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 1524
        2.99 -     3.46: 2743
        3.46 -     3.94: 4713
        3.94 -     4.42: 5313
        4.42 -     4.90: 10080
  Nonbonded interactions: 24373
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A  10 "
            pdb=" OD1 ASN C  21 "
     model   vdw
     2.508 3.120
  nonbonded pdb=" N   NH2 N  38 "
            pdb=" O   TYR Q  37 "
     model   vdw
     2.614 3.120
  nonbonded pdb=" N   SER N  34 "
            pdb=" OG  SER N  34 "
     model   vdw
     2.663 2.496
  nonbonded pdb=" N   SER K  34 "
            pdb=" OG  SER K  34 "
     model   vdw
     2.663 2.496
  nonbonded pdb=" N   SER Q  34 "
            pdb=" OG  SER Q  34 "
     model   vdw
     2.663 2.496
  ... (remaining 24368 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'E'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'N'
  selection = chain 'Q'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'L'
  selection = chain 'O'
  selection = chain 'R'
}
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'J'
  selection = chain 'M'
  selection = chain 'P'
}

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:             1.440
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.160
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.740
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
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      :  0.010   0.104   3048  Z= 0.712
  Angle     :  1.042  11.406   4110  Z= 0.540
  Chirality :  0.102   0.636    492
  Planarity :  0.003   0.015    528
  Dihedral  : 11.519  53.909    972
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 15.52 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.36), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.53 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS I  18 
 PHE   0.035   0.004   PHE H  15 
 TYR   0.012   0.003   TYR P  37 
 ARG   0.002   0.001   ARG J  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11367 (   75)
  hydrogen bonds       : angle       7.20303 (  225)
  covalent geometry    : bond        0.00792 ( 3036)
  covalent geometry    : angle       1.04244 ( 4110)
  Misc. bond           : bond        0.10338 (   12)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.332 
Fit side-chains
REVERT: C   30 THR cc_start: 0.5605 (OUTLIER) cc_final: 0.5280 (p)
REVERT: Q   15 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7701 (t80)
  outliers start: 12
  outliers final: 3
  residues processed: 52
  average time/residue: 0.0728
  time to fit residues: 5.5466
Evaluate side-chains
  29 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 PHE
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain H residue   15 PHE
Chi-restraints excluded: chain N residue   15 PHE
Chi-restraints excluded: chain Q residue   15 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 9 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 17 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  21 ASN
D  21 ASN
E  21 ASN
G  10 GLN
G  21 ASN
H  21 ASN
I  21 ASN
J  10 GLN
J  21 ASN
K  21 ASN
L  21 ASN
M  21 ASN
P  10 GLN
P  21 ASN
R  21 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.098987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.077712 restraints weight = 4849.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.07
r_work: 0.3166 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   3048  Z= 0.268
  Angle     :  0.857  11.450   4110  Z= 0.391
  Chirality :  0.052   0.238    492
  Planarity :  0.002   0.011    528
  Dihedral  :  4.800  24.239    411
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 1.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  :  9.48 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.59 (0.34), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.96 (0.26), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  18 
 PHE   0.026   0.003   PHE J  15 
 TYR   0.004   0.001   TYR B  37 
 ARG   0.000   0.000   ARG J  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04990 (   75)
  hydrogen bonds       : angle       5.23526 (  225)
  covalent geometry    : bond        0.00609 ( 3036)
  covalent geometry    : angle       0.85739 ( 4110)
  Misc. bond           : bond        0.00174 (   12)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 25
  time to evaluate  : 0.347 
Fit side-chains
  outliers start: 16
  outliers final: 13
  residues processed: 40
  average time/residue: 0.0674
  time to fit residues: 4.2393
Evaluate side-chains
  33 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 20
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue   34 SER
Chi-restraints excluded: chain P residue   34 SER
Chi-restraints excluded: chain Q residue   34 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 26 optimal weight:    0.4980
   chunk 2 optimal weight:   10.0000
   chunk 15 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 14 optimal weight:   20.0000
   chunk 17 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   overall best weight:    4.4988

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

Flipped N/Q/H residues before XYZ refinement:
A  10 GLN
C  21 ASN
R  21 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.099528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.078191 restraints weight = 4744.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 2.08
r_work: 0.3172 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.2667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3048  Z= 0.236
  Angle     :  0.751  10.944   4110  Z= 0.345
  Chirality :  0.047   0.204    492
  Planarity :  0.002   0.010    528
  Dihedral  :  4.453  17.720    403
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 0.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 11.21 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.77 (0.35), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.10 (0.26), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS R  18 
 PHE   0.023   0.002   PHE J  15 
 TYR   0.004   0.001   TYR G  37 
 ARG   0.001   0.000   ARG A  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04641 (   75)
  hydrogen bonds       : angle       4.92585 (  225)
  covalent geometry    : bond        0.00528 ( 3036)
  covalent geometry    : angle       0.75116 ( 4110)
  Misc. bond           : bond        0.00166 (   12)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 17
  time to evaluate  : 0.352 
Fit side-chains
  outliers start: 15
  outliers final: 14
  residues processed: 31
  average time/residue: 0.0607
  time to fit residues: 3.1349
Evaluate side-chains
  30 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 16
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue   34 SER
Chi-restraints excluded: chain P residue   34 SER
Chi-restraints excluded: chain Q residue   34 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 20 optimal weight:   10.0000
   chunk 13 optimal weight:    0.0670
   chunk 26 optimal weight:    0.6980
   chunk 19 optimal weight:   20.0000
   chunk 5 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 28 optimal weight:    9.9990
   chunk 12 optimal weight:    7.9990
   chunk 16 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    4.9524

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

Flipped N/Q/H residues before XYZ refinement:
D  10 GLN
F  21 ASN
K  21 ASN
M  10 GLN
O  21 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.099472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.078019 restraints weight = 4874.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 2.10
r_work: 0.3173 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3076 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.3117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   3048  Z= 0.265
  Angle     :  0.717   9.736   4110  Z= 0.340
  Chirality :  0.045   0.122    492
  Planarity :  0.002   0.007    528
  Dihedral  :  4.610  19.740    403
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 1.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 10.92 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.95 (0.33), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.24 (0.25), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS L  18 
 PHE   0.016   0.002   PHE J  15 
 TYR   0.007   0.002   TYR G  37 
 ARG   0.001   0.000   ARG G  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04562 (   75)
  hydrogen bonds       : angle       5.00240 (  225)
  covalent geometry    : bond        0.00582 ( 3036)
  covalent geometry    : angle       0.71733 ( 4110)
  Misc. bond           : bond        0.00196 (   12)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 13
  time to evaluate  : 0.338 
Fit side-chains
  outliers start: 18
  outliers final: 17
  residues processed: 30
  average time/residue: 0.0589
  time to fit residues: 3.0177
Evaluate side-chains
  29 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 12
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain H residue   28 SER
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue   34 SER
Chi-restraints excluded: chain P residue   27 LEU
Chi-restraints excluded: chain P residue   34 SER
Chi-restraints excluded: chain Q residue   29 SER
Chi-restraints excluded: chain Q residue   34 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 23 optimal weight:    0.1980
   chunk 17 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 10 optimal weight:    0.6980
   chunk 3 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   overall best weight:    2.7786

-------------------------------------------------------------------------------
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 = 0.3666 r_free = 0.3666 target = 0.101166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.079750 restraints weight = 5126.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 2.16
r_work: 0.3204 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.3171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3048  Z= 0.149
  Angle     :  0.624   9.376   4110  Z= 0.289
  Chirality :  0.044   0.120    492
  Planarity :  0.001   0.006    528
  Dihedral  :  3.972  15.650    403
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 0.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 10.92 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.35), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS R  18 
 PHE   0.014   0.002   PHE J  15 
 TYR   0.005   0.001   TYR K  37 
 ARG   0.000   0.000   ARG G  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03630 (   75)
  hydrogen bonds       : angle       4.58450 (  225)
  covalent geometry    : bond        0.00327 ( 3036)
  covalent geometry    : angle       0.62448 ( 4110)
  Misc. bond           : bond        0.00107 (   12)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 20
  time to evaluate  : 0.343 
Fit side-chains
  outliers start: 16
  outliers final: 15
  residues processed: 35
  average time/residue: 0.0619
  time to fit residues: 3.5378
Evaluate side-chains
  32 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 17
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain K residue   29 SER
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue   34 SER
Chi-restraints excluded: chain N residue   36 THR
Chi-restraints excluded: chain P residue   27 LEU
Chi-restraints excluded: chain P residue   34 SER
Chi-restraints excluded: chain Q residue   34 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 24 optimal weight:   20.0000
   chunk 10 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 20 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9980
   chunk 3 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   overall best weight:    4.3988

-------------------------------------------------------------------------------
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 = 0.3645 r_free = 0.3645 target = 0.099852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.078020 restraints weight = 5367.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.23
r_work: 0.3179 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.3321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3048  Z= 0.235
  Angle     :  0.659   9.588   4110  Z= 0.315
  Chirality :  0.045   0.120    492
  Planarity :  0.002   0.008    528
  Dihedral  :  4.296  17.141    402
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 0.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 10.92 %
    Favored  : 83.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.92 (0.34), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.22 (0.26), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS L  18 
 PHE   0.018   0.002   PHE J  15 
 TYR   0.010   0.002   TYR K  37 
 ARG   0.000   0.000   ARG J  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04298 (   75)
  hydrogen bonds       : angle       4.86636 (  225)
  covalent geometry    : bond        0.00512 ( 3036)
  covalent geometry    : angle       0.65928 ( 4110)
  Misc. bond           : bond        0.00168 (   12)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 17
  time to evaluate  : 0.314 
Fit side-chains
  outliers start: 18
  outliers final: 18
  residues processed: 34
  average time/residue: 0.0567
  time to fit residues: 3.2003
Evaluate side-chains
  33 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 15
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain H residue   28 SER
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain J residue   34 SER
Chi-restraints excluded: chain K residue   29 SER
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue   34 SER
Chi-restraints excluded: chain N residue   36 THR
Chi-restraints excluded: chain P residue   27 LEU
Chi-restraints excluded: chain P residue   34 SER
Chi-restraints excluded: chain Q residue   29 SER
Chi-restraints excluded: chain Q residue   34 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 7 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 27 optimal weight:   10.0000
   chunk 23 optimal weight:    0.4980
   chunk 16 optimal weight:    7.9990
   chunk 24 optimal weight:   20.0000
   chunk 20 optimal weight:    2.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    4.8988

-------------------------------------------------------------------------------
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 = 0.3631 r_free = 0.3631 target = 0.099609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.077694 restraints weight = 5206.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.22
r_work: 0.3137 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.3429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   3048  Z= 0.260
  Angle     :  0.673   9.576   4110  Z= 0.324
  Chirality :  0.045   0.120    492
  Planarity :  0.002   0.007    528
  Dihedral  :  4.381  16.910    402
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 0.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 11.21 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.34), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.28 (0.26), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS L  18 
 PHE   0.015   0.002   PHE J  15 
 TYR   0.011   0.002   TYR K  37 
 ARG   0.000   0.000   ARG J  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04360 (   75)
  hydrogen bonds       : angle       4.94712 (  225)
  covalent geometry    : bond        0.00566 ( 3036)
  covalent geometry    : angle       0.67346 ( 4110)
  Misc. bond           : bond        0.00182 (   12)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 15
  time to evaluate  : 0.343 
Fit side-chains
  outliers start: 20
  outliers final: 18
  residues processed: 34
  average time/residue: 0.0591
  time to fit residues: 3.3405
Evaluate side-chains
  32 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 14
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain H residue   28 SER
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue   36 THR
Chi-restraints excluded: chain K residue   29 SER
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue   34 SER
Chi-restraints excluded: chain N residue   36 THR
Chi-restraints excluded: chain P residue   27 LEU
Chi-restraints excluded: chain P residue   34 SER
Chi-restraints excluded: chain Q residue   34 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 0 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   chunk 4 optimal weight:    0.0010
   chunk 25 optimal weight:    8.9990
   chunk 29 optimal weight:    9.9990
   chunk 7 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    3.7994

-------------------------------------------------------------------------------
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 = 0.3645 r_free = 0.3645 target = 0.100448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.078299 restraints weight = 5575.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 2.30
r_work: 0.3176 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3048  Z= 0.204
  Angle     :  0.641   9.268   4110  Z= 0.303
  Chirality :  0.044   0.119    492
  Planarity :  0.002   0.006    528
  Dihedral  :  4.114  16.337    402
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 0.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 12.36 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.35), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  18 
 PHE   0.015   0.002   PHE J  15 
 TYR   0.009   0.002   TYR K  37 
 ARG   0.000   0.000   ARG J  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03974 (   75)
  hydrogen bonds       : angle       4.78393 (  225)
  covalent geometry    : bond        0.00446 ( 3036)
  covalent geometry    : angle       0.64122 ( 4110)
  Misc. bond           : bond        0.00141 (   12)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 16
  time to evaluate  : 0.347 
Fit side-chains
  outliers start: 18
  outliers final: 18
  residues processed: 32
  average time/residue: 0.0581
  time to fit residues: 3.1493
Evaluate side-chains
  34 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 16
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain H residue   28 SER
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue   36 THR
Chi-restraints excluded: chain K residue   29 SER
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue   34 SER
Chi-restraints excluded: chain P residue   27 LEU
Chi-restraints excluded: chain P residue   34 SER
Chi-restraints excluded: chain Q residue   29 SER
Chi-restraints excluded: chain Q residue   34 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 9 optimal weight:    9.9990
   chunk 8 optimal weight:    4.9990
   chunk 2 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 10 optimal weight:    3.9990
   chunk 26 optimal weight:    0.4980
   chunk 19 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    3.8988

-------------------------------------------------------------------------------
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 = 0.3641 r_free = 0.3641 target = 0.100322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.077890 restraints weight = 6208.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 2.41
r_work: 0.3162 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.3474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3048  Z= 0.209
  Angle     :  0.641   9.299   4110  Z= 0.304
  Chirality :  0.044   0.119    492
  Planarity :  0.002   0.006    528
  Dihedral  :  4.117  16.440    402
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 0.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 12.36 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.01 (0.35), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.29 (0.26), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS L  18 
 PHE   0.015   0.002   PHE J  15 
 TYR   0.009   0.002   TYR K  37 
 ARG   0.000   0.000   ARG J  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04060 (   75)
  hydrogen bonds       : angle       4.78113 (  225)
  covalent geometry    : bond        0.00456 ( 3036)
  covalent geometry    : angle       0.64098 ( 4110)
  Misc. bond           : bond        0.00145 (   12)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 15
  time to evaluate  : 0.318 
Fit side-chains
  outliers start: 18
  outliers final: 18
  residues processed: 32
  average time/residue: 0.0601
  time to fit residues: 3.2081
Evaluate side-chains
  33 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 15
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain H residue   28 SER
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain K residue   29 SER
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue   34 SER
Chi-restraints excluded: chain N residue   36 THR
Chi-restraints excluded: chain P residue   27 LEU
Chi-restraints excluded: chain P residue   34 SER
Chi-restraints excluded: chain Q residue   29 SER
Chi-restraints excluded: chain Q residue   34 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 25 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 24 optimal weight:    9.9990
   chunk 19 optimal weight:    9.9990
   chunk 28 optimal weight:    7.9990
   chunk 4 optimal weight:    0.0030
   chunk 12 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 11 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    3.9998

-------------------------------------------------------------------------------
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 = 0.3642 r_free = 0.3642 target = 0.100337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.078133 restraints weight = 5407.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 2.28
r_work: 0.3172 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.3519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3048  Z= 0.213
  Angle     :  0.642   9.263   4110  Z= 0.305
  Chirality :  0.044   0.118    492
  Planarity :  0.002   0.008    528
  Dihedral  :  4.124  16.402    402
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 0.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 11.78 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.03 (0.35), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.30 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS L  18 
 PHE   0.019   0.002   PHE P  15 
 TYR   0.009   0.002   TYR K  37 
 ARG   0.000   0.000   ARG P  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04060 (   75)
  hydrogen bonds       : angle       4.79791 (  225)
  covalent geometry    : bond        0.00466 ( 3036)
  covalent geometry    : angle       0.64166 ( 4110)
  Misc. bond           : bond        0.00149 (   12)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 15
  time to evaluate  : 0.517 
Fit side-chains
REVERT: A   11 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7913 (mtp85)
  outliers start: 20
  outliers final: 19
  residues processed: 34
  average time/residue: 0.0968
  time to fit residues: 4.8917
Evaluate side-chains
  35 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 15
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ARG
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain E residue   29 SER
Chi-restraints excluded: chain E residue   34 SER
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain H residue   28 SER
Chi-restraints excluded: chain H residue   34 SER
Chi-restraints excluded: chain H residue   36 THR
Chi-restraints excluded: chain K residue   29 SER
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain M residue   34 SER
Chi-restraints excluded: chain N residue   34 SER
Chi-restraints excluded: chain N residue   36 THR
Chi-restraints excluded: chain P residue   27 LEU
Chi-restraints excluded: chain P residue   34 SER
Chi-restraints excluded: chain Q residue   29 SER
Chi-restraints excluded: chain Q residue   34 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 27 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 22 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:   20.0000
   chunk 15 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0170
   overall best weight:    2.2024

-------------------------------------------------------------------------------
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 = 0.3667 r_free = 0.3667 target = 0.101693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.079738 restraints weight = 5467.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 2.28
r_work: 0.3205 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3106 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start:          0.3502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3048  Z= 0.124
  Angle     :  0.590   8.664   4110  Z= 0.274
  Chirality :  0.044   0.118    492
  Planarity :  0.001   0.007    528
  Dihedral  :  3.683  15.208    402
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 0.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 12.93 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.88 (0.36), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.18 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS O  18 
 PHE   0.015   0.001   PHE P  15 
 TYR   0.006   0.001   TYR K  37 
 ARG   0.000   0.000   ARG G  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03310 (   75)
  hydrogen bonds       : angle       4.46663 (  225)
  covalent geometry    : bond        0.00271 ( 3036)
  covalent geometry    : angle       0.59042 ( 4110)
  Misc. bond           : bond        0.00085 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1880.35 seconds
wall clock time: 33 minutes 0.32 seconds (1980.32 seconds total)