Starting phenix.real_space_refine
on Fri May  9 15:46:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gzx_51736/05_2025/9gzx_51736.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gzx_51736/05_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_51736/05_2025/9gzx_51736.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gzx_51736/05_2025/9gzx_51736.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gzx_51736/05_2025/9gzx_51736.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gzx_51736/05_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-5687/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: 1.67, per 1000 atoms: 0.56
  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: 0.78
  Conformation dependent library (CDL) restraints added in 368.8 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: 0.46
  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: 0.69

  Time building geometry restraints manager: 0.90 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:             1.450
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.170
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.570
-------------------------------------------------------------------------------
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  : 0.312 
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: 0.0710
  time to fit residues: 5.4273
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  : 0.333 
-------------------------------------------------------------------------------
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:    3.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3668 r_free = 0.3668 target = 0.099411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.078021 restraints weight = 4834.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 2.07
r_work: 0.3179 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3079 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   3048  Z= 0.248
  Angle     :  0.845  11.418   4110  Z= 0.382
  Chirality :  0.052   0.238    492
  Planarity :  0.002   0.011    528
  Dihedral  :  4.640  22.867    411
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 1.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  :  8.33 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.57 (0.34), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.95 (0.26), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  18 
 PHE   0.026   0.002   PHE J  15 
 TYR   0.004   0.001   TYR Q  37 
 ARG   0.000   0.000   ARG D  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04882 (   75)
  hydrogen bonds       : angle       5.18652 (  225)
  covalent geometry    : bond        0.00567 ( 3036)
  covalent geometry    : angle       0.84532 ( 4110)
  Misc. bond           : bond        0.00171 (   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  : 0.349 
Fit side-chains
  outliers start: 16
  outliers final: 13
  residues processed: 40
  average time/residue: 0.0677
  time to fit residues: 4.1929
Evaluate side-chains
  32 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 19
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:    7.9990
   chunk 15 optimal weight:    9.9990
   chunk 4 optimal weight:    9.9990
   chunk 28 optimal weight:    4.9990
   chunk 5 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 14 optimal weight:   20.0000
   chunk 17 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   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  10 GLN
C  21 ASN
K  21 ASN
R  21 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.098889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.077614 restraints weight = 4766.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.09
r_work: 0.3168 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8617
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   3048  Z= 0.273
  Angle     :  0.774  11.093   4110  Z= 0.361
  Chirality :  0.048   0.206    492
  Planarity :  0.002   0.010    528
  Dihedral  :  4.663  19.801    403
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 1.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 10.63 %
    Favored  : 85.06 %
  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 (0.34), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.26), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  18 
 PHE   0.024   0.002   PHE J  15 
 TYR   0.004   0.001   TYR A  37 
 ARG   0.002   0.000   ARG P  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04913 (   75)
  hydrogen bonds       : angle       5.00912 (  225)
  covalent geometry    : bond        0.00608 ( 3036)
  covalent geometry    : angle       0.77444 ( 4110)
  Misc. bond           : bond        0.00195 (   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
  28 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 13
  time to evaluate  : 0.348 
Fit side-chains
  outliers start: 15
  outliers final: 14
  residues processed: 27
  average time/residue: 0.0618
  time to fit residues: 2.8413
Evaluate side-chains
  25 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 11
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    6.9990

-------------------------------------------------------------------------------
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
M  10 GLN
O  21 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.098280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.076522 restraints weight = 5158.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.17
r_work: 0.3111 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8682
moved from start:          0.3238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.054   3048  Z= 0.369
  Angle     :  0.795  10.428   4110  Z= 0.384
  Chirality :  0.048   0.129    492
  Planarity :  0.003   0.009    528
  Dihedral  :  5.183  26.319    403
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 1.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 12.07 %
    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: -3.06 (0.32), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (0.25), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS L  18 
 PHE   0.020   0.003   PHE N  15 
 TYR   0.009   0.002   TYR K  37 
 ARG   0.001   0.000   ARG M  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05164 (   75)
  hydrogen bonds       : angle       5.22644 (  225)
  covalent geometry    : bond        0.00806 ( 3036)
  covalent geometry    : angle       0.79472 ( 4110)
  Misc. bond           : bond        0.00234 (   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
  32 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 15
  time to evaluate  : 0.339 
Fit side-chains
  outliers start: 17
  outliers final: 15
  residues processed: 31
  average time/residue: 0.0552
  time to fit residues: 2.9251
Evaluate side-chains
  26 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 11
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
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   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   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:    4.9990
   chunk 19 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 10 optimal weight:   10.0000
   chunk 3 optimal weight:    7.9990
   chunk 18 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    4.5788

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.099634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.077874 restraints weight = 5408.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 2.23
r_work: 0.3139 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8668
moved from start:          0.3357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3048  Z= 0.244
  Angle     :  0.691  10.064   4110  Z= 0.326
  Chirality :  0.045   0.121    492
  Planarity :  0.002   0.006    528
  Dihedral  :  4.535  21.011    403
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 0.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 13.51 %
    Favored  : 81.61 %
  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: -3.04 (0.33), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.25), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS L  18 
 PHE   0.014   0.002   PHE J  15 
 TYR   0.008   0.002   TYR K  37 
 ARG   0.000   0.000   ARG A  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04288 (   75)
  hydrogen bonds       : angle       4.89462 (  225)
  covalent geometry    : bond        0.00533 ( 3036)
  covalent geometry    : angle       0.69091 ( 4110)
  Misc. bond           : bond        0.00166 (   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
  31 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 14
  time to evaluate  : 0.334 
Fit side-chains
  outliers start: 17
  outliers final: 17
  residues processed: 30
  average time/residue: 0.0566
  time to fit residues: 2.9151
Evaluate side-chains
  30 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 13
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
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   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:    9.9990
   chunk 10 optimal weight:   20.0000
   chunk 23 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
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 = 0.3655 r_free = 0.3655 target = 0.100858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.078973 restraints weight = 5763.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.35
r_work: 0.3160 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8672
moved from start:          0.3366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3048  Z= 0.154
  Angle     :  0.626   9.343   4110  Z= 0.290
  Chirality :  0.044   0.118    492
  Planarity :  0.001   0.006    528
  Dihedral  :  4.007  15.824    403
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 0.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 12.07 %
    Favored  : 83.33 %
  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 (0.35), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.22 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS L  18 
 PHE   0.013   0.002   PHE J  15 
 TYR   0.007   0.001   TYR K  37 
 ARG   0.000   0.000   ARG D  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03644 (   75)
  hydrogen bonds       : angle       4.63250 (  225)
  covalent geometry    : bond        0.00336 ( 3036)
  covalent geometry    : angle       0.62589 ( 4110)
  Misc. bond           : bond        0.00106 (   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
  32 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 16
  time to evaluate  : 0.368 
Fit side-chains
  outliers start: 16
  outliers final: 16
  residues processed: 30
  average time/residue: 0.0575
  time to fit residues: 2.9317
Evaluate side-chains
  31 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 15
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
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   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   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:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 7 optimal weight:   20.0000
   chunk 1 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 23 optimal weight:    0.6980
   chunk 16 optimal weight:    9.9990
   chunk 24 optimal weight:   20.0000
   chunk 20 optimal weight:    8.9990
   chunk 9 optimal weight:    9.9990
   overall best weight:    6.3388

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

Flipped N/Q/H residues before XYZ refinement:
P  10 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.098976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.076894 restraints weight = 5486.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.26
r_work: 0.3140 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3039 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.3512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049   3048  Z= 0.334
  Angle     :  0.719  10.025   4110  Z= 0.351
  Chirality :  0.046   0.121    492
  Planarity :  0.002   0.008    528
  Dihedral  :  4.763  22.274    403
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 1.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 11.49 %
    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: -3.14 (0.34), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.39 (0.26), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS L  18 
 PHE   0.019   0.002   PHE J  15 
 TYR   0.014   0.002   TYR K  37 
 ARG   0.000   0.000   ARG P  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04796 (   75)
  hydrogen bonds       : angle       5.05331 (  225)
  covalent geometry    : bond        0.00722 ( 3036)
  covalent geometry    : angle       0.71881 ( 4110)
  Misc. bond           : bond        0.00232 (   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
  31 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 10
  time to evaluate  : 0.354 
Fit side-chains
  outliers start: 21
  outliers final: 19
  residues processed: 30
  average time/residue: 0.0604
  time to fit residues: 3.1172
Evaluate side-chains
  29 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 10
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
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   29 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:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   chunk 4 optimal weight:    9.9990
   chunk 25 optimal weight:    6.9990
   chunk 29 optimal weight:    9.9990
   chunk 7 optimal weight:    6.9990
   chunk 28 optimal weight:    0.0370
   chunk 17 optimal weight:   10.0000
   chunk 23 optimal weight:    0.0370
   overall best weight:    3.4142

-------------------------------------------------------------------------------
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 = 0.100464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.078451 restraints weight = 5542.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.29
r_work: 0.3177 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
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      :  0.004   0.030   3048  Z= 0.185
  Angle     :  0.640   9.367   4110  Z= 0.300
  Chirality :  0.044   0.119    492
  Planarity :  0.002   0.007    528
  Dihedral  :  4.194  17.626    403
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 0.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 12.07 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.04 (0.35), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  18 
 PHE   0.017   0.002   PHE J  15 
 TYR   0.009   0.001   TYR K  37 
 ARG   0.000   0.000   ARG J  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03885 (   75)
  hydrogen bonds       : angle       4.78739 (  225)
  covalent geometry    : bond        0.00406 ( 3036)
  covalent geometry    : angle       0.63990 ( 4110)
  Misc. bond           : bond        0.00128 (   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
  33 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 15
  time to evaluate  : 0.305 
Fit side-chains
  outliers start: 18
  outliers final: 18
  residues processed: 31
  average time/residue: 0.0588
  time to fit residues: 3.0380
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  : 0.313 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 30
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 9 optimal weight:   20.0000
   chunk 8 optimal weight:    2.9990
   chunk 2 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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 = 0.3634 r_free = 0.3634 target = 0.100026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.077565 restraints weight = 6218.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.41
r_work: 0.3152 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start:          0.3525

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= 0.243
  Angle     :  0.669   9.576   4110  Z= 0.318
  Chirality :  0.045   0.118    492
  Planarity :  0.002   0.007    528
  Dihedral  :  4.422  20.279    403
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 1.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 11.49 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.12 (0.35), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.37 (0.26), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS L  18 
 PHE   0.016   0.002   PHE J  15 
 TYR   0.010   0.002   TYR K  37 
 ARG   0.000   0.000   ARG P  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04296 (   75)
  hydrogen bonds       : angle       4.90983 (  225)
  covalent geometry    : bond        0.00529 ( 3036)
  covalent geometry    : angle       0.66858 ( 4110)
  Misc. bond           : bond        0.00173 (   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
  32 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 12
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   11 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7912 (mtp85)
  outliers start: 20
  outliers final: 19
  residues processed: 32
  average time/residue: 0.0914
  time to fit residues: 4.2209
Evaluate side-chains
  31 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 11
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
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 3 optimal weight:    7.9990
   chunk 25 optimal weight:    0.0870
   chunk 17 optimal weight:   20.0000
   chunk 24 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 28 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 11 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    3.8164

-------------------------------------------------------------------------------
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 = 0.100229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.078170 restraints weight = 5596.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.30
r_work: 0.3172 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.3520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3048  Z= 0.205
  Angle     :  0.646   9.386   4110  Z= 0.304
  Chirality :  0.045   0.118    492
  Planarity :  0.002   0.007    528
  Dihedral  :  4.212  18.098    403
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 0.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 11.49 %
    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: -3.07 (0.35), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  18 
 PHE   0.016   0.002   PHE J  15 
 TYR   0.009   0.002   TYR K  37 
 ARG   0.000   0.000   ARG G  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04005 (   75)
  hydrogen bonds       : angle       4.83754 (  225)
  covalent geometry    : bond        0.00448 ( 3036)
  covalent geometry    : angle       0.64593 ( 4110)
  Misc. bond           : bond        0.00142 (   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
  33 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 14
  time to evaluate  : 0.312 
Fit side-chains
  outliers start: 19
  outliers final: 19
  residues processed: 32
  average time/residue: 0.0563
  time to fit residues: 3.0334
Evaluate side-chains
  33 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 14
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
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   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:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 28 optimal weight:    0.5980
   chunk 22 optimal weight:    9.9990
   chunk 25 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 19 optimal weight:   20.0000
   chunk 15 optimal weight:   10.0000
   chunk 4 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    4.1188

-------------------------------------------------------------------------------
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 = 0.3650 r_free = 0.3650 target = 0.103149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.081235 restraints weight = 5180.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 2.15
r_work: 0.3154 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8707
moved from start:          0.3542

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= 0.220
  Angle     :  0.652   9.437   4110  Z= 0.309
  Chirality :  0.045   0.118    492
  Planarity :  0.002   0.007    528
  Dihedral  :  4.276  18.461    403
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 0.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  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: -3.11 (0.35), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.36 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS L  18 
 PHE   0.016   0.002   PHE J  15 
 TYR   0.010   0.002   TYR K  37 
 ARG   0.000   0.000   ARG D  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04124 (   75)
  hydrogen bonds       : angle       4.86297 (  225)
  covalent geometry    : bond        0.00480 ( 3036)
  covalent geometry    : angle       0.65196 ( 4110)
  Misc. bond           : bond        0.00154 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1783.67 seconds
wall clock time: 31 minutes 32.24 seconds (1892.24 seconds total)