Starting phenix.real_space_refine
on Mon Feb 10 22:12:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ovk_17218/02_2025/8ovk_17218.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ovk_17218/02_2025/8ovk_17218.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ovk_17218/02_2025/8ovk_17218.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ovk_17218/02_2025/8ovk_17218.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ovk_17218/02_2025/8ovk_17218.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ovk_17218/02_2025/8ovk_17218.cif"
  }
  resolution = 2.88
  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=   0.001 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      10      5.16       5
     C    1940      2.51       5
     N     530      2.21       5
     O     580      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3060
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 306
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 306
          Classifications: {'peptide': 40}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 39}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 1.68, per 1000 atoms: 0.55
  Number of scatterers: 3060
  At special positions: 0
  Unit cell: (100.8, 124.95, 39.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      10     16.00
     O     580      8.00
     N     530      7.00
     C    1940      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.73
  Conformation dependent library (CDL) restraints added in 362.0 milliseconds
  

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  680

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 47.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13
    Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 24
      removed outlier: 6.224A  pdb=" N   LYS A  16 " --> pdb=" O   LEU C  17 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   PHE C  19 " --> pdb=" O   LYS A  16 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   VAL A  18 " --> pdb=" O   PHE C  19 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ALA C  21 " --> pdb=" O   VAL A  18 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   PHE A  20 " --> pdb=" O   ALA C  21 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   ASP C  23 " --> pdb=" O   PHE A  20 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   GLU A  22 " --> pdb=" O   ASP C  23 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   LYS C  16 " --> pdb=" O   LEU E  17 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   PHE E  19 " --> pdb=" O   LYS C  16 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   VAL C  18 " --> pdb=" O   PHE E  19 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ALA E  21 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   PHE C  20 " --> pdb=" O   ALA E  21 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   ASP E  23 " --> pdb=" O   PHE C  20 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   GLU C  22 " --> pdb=" O   ASP E  23 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   LYS E  16 " --> pdb=" O   LEU G  17 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   PHE G  19 " --> pdb=" O   LYS E  16 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   VAL E  18 " --> pdb=" O   PHE G  19 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ALA G  21 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   PHE E  20 " --> pdb=" O   ALA G  21 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   ASP G  23 " --> pdb=" O   PHE E  20 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   GLU E  22 " --> pdb=" O   ASP G  23 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   LYS G  16 " --> pdb=" O   LEU I  17 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   PHE I  19 " --> pdb=" O   LYS G  16 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   VAL G  18 " --> pdb=" O   PHE I  19 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   ALA I  21 " --> pdb=" O   VAL G  18 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   PHE G  20 " --> pdb=" O   ALA I  21 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   ASP I  23 " --> pdb=" O   PHE G  20 " (cutoff:3.500A)
      removed outlier: 8.450A  pdb=" N   GLU G  22 " --> pdb=" O   ASP I  23 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 39
      removed outlier: 6.785A  pdb=" N   ILE C  32 " --> pdb=" O   ILE A  31 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   GLY A  33 " --> pdb=" O   ILE C  32 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   VAL A  39 " --> pdb=" O   GLY C  38 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ILE E  32 " --> pdb=" O   ILE C  31 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   GLY C  33 " --> pdb=" O   ILE E  32 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   VAL C  39 " --> pdb=" O   GLY E  38 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ILE G  32 " --> pdb=" O   ILE E  31 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   GLY E  33 " --> pdb=" O   ILE G  32 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   VAL E  39 " --> pdb=" O   GLY G  38 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ILE I  32 " --> pdb=" O   ILE G  31 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   GLY G  33 " --> pdb=" O   ILE I  32 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   VAL G  39 " --> pdb=" O   GLY I  38 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 13
    Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 24
      removed outlier: 6.225A  pdb=" N   LYS B  16 " --> pdb=" O   LEU D  17 " (cutoff:3.500A)
      removed outlier: 7.614A  pdb=" N   PHE D  19 " --> pdb=" O   LYS B  16 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   VAL B  18 " --> pdb=" O   PHE D  19 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ALA D  21 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   PHE B  20 " --> pdb=" O   ALA D  21 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   ASP D  23 " --> pdb=" O   PHE B  20 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   GLU B  22 " --> pdb=" O   ASP D  23 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   LYS D  16 " --> pdb=" O   LEU F  17 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   PHE F  19 " --> pdb=" O   LYS D  16 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   VAL D  18 " --> pdb=" O   PHE F  19 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ALA F  21 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   PHE D  20 " --> pdb=" O   ALA F  21 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   ASP F  23 " --> pdb=" O   PHE D  20 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   GLU D  22 " --> pdb=" O   ASP F  23 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   LYS F  16 " --> pdb=" O   LEU H  17 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   PHE H  19 " --> pdb=" O   LYS F  16 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   VAL F  18 " --> pdb=" O   PHE H  19 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ALA H  21 " --> pdb=" O   VAL F  18 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   PHE F  20 " --> pdb=" O   ALA H  21 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   ASP H  23 " --> pdb=" O   PHE F  20 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   GLU F  22 " --> pdb=" O   ASP H  23 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   LYS H  16 " --> pdb=" O   LEU J  17 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   PHE J  19 " --> pdb=" O   LYS H  16 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   VAL H  18 " --> pdb=" O   PHE J  19 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ALA J  21 " --> pdb=" O   VAL H  18 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   PHE H  20 " --> pdb=" O   ALA J  21 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   ASP J  23 " --> pdb=" O   PHE H  20 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   GLU H  22 " --> pdb=" O   ASP J  23 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 39
      removed outlier: 6.785A  pdb=" N   ILE D  32 " --> pdb=" O   ILE B  31 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   GLY B  33 " --> pdb=" O   ILE D  32 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   VAL B  39 " --> pdb=" O   GLY D  38 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ILE F  32 " --> pdb=" O   ILE D  31 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   GLY D  33 " --> pdb=" O   ILE F  32 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   VAL D  39 " --> pdb=" O   GLY F  38 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ILE H  32 " --> pdb=" O   ILE F  31 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   GLY F  33 " --> pdb=" O   ILE H  32 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   VAL F  39 " --> pdb=" O   GLY H  38 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ILE J  32 " --> pdb=" O   ILE H  31 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   GLY H  33 " --> pdb=" O   ILE J  32 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   VAL H  39 " --> pdb=" O   GLY J  38 " (cutoff:3.500A)

    64 hydrogen bonds defined for protein.
    192 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: 0.71

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1003
        1.33 -     1.45: 538
        1.45 -     1.57: 1559
        1.57 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 3120
  Sorted by residual:
  bond pdb=" CA  GLN D  15 "
       pdb=" C   GLN D  15 "
    ideal  model  delta    sigma   weight residual
    1.523  1.485  0.038 1.28e-02 6.10e+03 8.65e+00
  bond pdb=" CA  GLN B  15 "
       pdb=" C   GLN B  15 "
    ideal  model  delta    sigma   weight residual
    1.523  1.485  0.037 1.28e-02 6.10e+03 8.51e+00
  bond pdb=" CA  GLN I  15 "
       pdb=" C   GLN I  15 "
    ideal  model  delta    sigma   weight residual
    1.523  1.486  0.037 1.28e-02 6.10e+03 8.45e+00
  bond pdb=" CA  GLN G  15 "
       pdb=" C   GLN G  15 "
    ideal  model  delta    sigma   weight residual
    1.523  1.486  0.037 1.28e-02 6.10e+03 8.44e+00
  bond pdb=" CA  GLN E  15 "
       pdb=" C   GLN E  15 "
    ideal  model  delta    sigma   weight residual
    1.523  1.486  0.037 1.28e-02 6.10e+03 8.43e+00
  ... (remaining 3115 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 2778
        1.45 -     2.90: 992
        2.90 -     4.36: 280
        4.36 -     5.81: 90
        5.81 -     7.26: 50
  Bond angle restraints: 4190
  Sorted by residual:
  angle pdb=" O   GLY H  29 "
        pdb=" C   GLY H  29 "
        pdb=" N   ALA H  30 "
      ideal   model   delta    sigma   weight residual
     123.59  119.55    4.04 8.70e-01 1.32e+00 2.16e+01
  angle pdb=" O   GLY E  29 "
        pdb=" C   GLY E  29 "
        pdb=" N   ALA E  30 "
      ideal   model   delta    sigma   weight residual
     123.59  119.58    4.01 8.70e-01 1.32e+00 2.12e+01
  angle pdb=" O   GLY C  29 "
        pdb=" C   GLY C  29 "
        pdb=" N   ALA C  30 "
      ideal   model   delta    sigma   weight residual
     123.59  119.58    4.01 8.70e-01 1.32e+00 2.12e+01
  angle pdb=" N   PHE D   4 "
        pdb=" CA  PHE D   4 "
        pdb=" C   PHE D   4 "
      ideal   model   delta    sigma   weight residual
     111.52  117.84   -6.32 1.40e+00 5.10e-01 2.04e+01
  angle pdb=" N   PHE J   4 "
        pdb=" CA  PHE J   4 "
        pdb=" C   PHE J   4 "
      ideal   model   delta    sigma   weight residual
     111.52  117.84   -6.32 1.40e+00 5.10e-01 2.04e+01
  ... (remaining 4185 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.03 -    10.60: 1390
       10.60 -    21.18: 193
       21.18 -    31.75: 97
       31.75 -    42.33: 50
       42.33 -    52.90: 20
  Dihedral angle restraints: 1750
    sinusoidal: 670
      harmonic: 1080
  Sorted by residual:
  dihedral pdb=" CA  LEU J  34 "
           pdb=" C   LEU J  34 "
           pdb=" N   MET J  35 "
           pdb=" CA  MET J  35 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.89   22.11     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  LEU A  34 "
           pdb=" C   LEU A  34 "
           pdb=" N   MET A  35 "
           pdb=" CA  MET A  35 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.93   22.07     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  LEU G  34 "
           pdb=" C   LEU G  34 "
           pdb=" N   MET G  35 "
           pdb=" CA  MET G  35 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.94   22.06     0      5.00e+00 4.00e-02 1.95e+01
  ... (remaining 1747 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 90
       0.046 -    0.092: 141
       0.092 -    0.137: 129
       0.137 -    0.183: 50
       0.183 -    0.229: 30
  Chirality restraints: 440
  Sorted by residual:
  chirality pdb=" CA  GLU C  11 "
            pdb=" N   GLU C  11 "
            pdb=" C   GLU C  11 "
            pdb=" CB  GLU C  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  GLU B  11 "
            pdb=" N   GLU B  11 "
            pdb=" C   GLU B  11 "
            pdb=" CB  GLU B  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  GLU G  11 "
            pdb=" N   GLU G  11 "
            pdb=" C   GLU G  11 "
            pdb=" CB  GLU G  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 437 not shown)

  Planarity restraints: 560
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H  10 "    0.062 2.00e-02 2.50e+03   3.56e-02 2.54e+01
        pdb=" CG  TYR H  10 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD1 TYR H  10 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD2 TYR H  10 "   -0.032 2.00e-02 2.50e+03
        pdb=" CE1 TYR H  10 "   -0.028 2.00e-02 2.50e+03
        pdb=" CE2 TYR H  10 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  TYR H  10 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR H  10 "    0.058 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  10 "    0.062 2.00e-02 2.50e+03   3.56e-02 2.53e+01
        pdb=" CG  TYR D  10 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  10 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  10 "   -0.032 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  10 "   -0.028 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  10 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  10 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR D  10 "    0.058 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  10 "   -0.061 2.00e-02 2.50e+03   3.55e-02 2.52e+01
        pdb=" CG  TYR A  10 "    0.012 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  10 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  10 "    0.032 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  10 "    0.028 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  10 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  10 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A  10 "   -0.058 2.00e-02 2.50e+03
  ... (remaining 557 not shown)

  Histogram of nonbonded interaction distances:
        2.39 -     2.89: 1120
        2.89 -     3.39: 2591
        3.39 -     3.89: 5434
        3.89 -     4.40: 6090
        4.40 -     4.90: 11642
  Nonbonded interactions: 26877
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG H   5 "
            pdb=" OD2 ASP J   7 "
     model   vdw
     2.386 3.120
  nonbonded pdb=" NH2 ARG A   5 "
            pdb=" OD2 ASP C   7 "
     model   vdw
     2.387 3.120
  nonbonded pdb=" NH2 ARG G   5 "
            pdb=" OD2 ASP I   7 "
     model   vdw
     2.387 3.120
  nonbonded pdb=" NH2 ARG D   5 "
            pdb=" OD2 ASP F   7 "
     model   vdw
     2.387 3.120
  nonbonded pdb=" NH2 ARG B   5 "
            pdb=" OD2 ASP D   7 "
     model   vdw
     2.387 3.120
  ... (remaining 26872 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 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.230
  Find NCS groups from input model:        0.060
  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:12.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
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      :  0.012   0.038   3120  Z= 0.812
  Angle     :  1.803   7.261   4190  Z= 1.167
  Chirality :  0.109   0.229    440
  Planarity :  0.011   0.036    560
  Dihedral  : 14.992  52.904   1070
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers : 12.90 %
    Allowed  :  9.68 %
    Favored  : 77.42 %
  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: -1.83 (0.32), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.39 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  13 
 PHE   0.027   0.009   PHE B  19 
 TYR   0.062   0.030   TYR H  10 
 ARG   0.002   0.001   ARG I   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 156
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A    3 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6818 (pm20)
REVERT: A    5 ARG cc_start: 0.8391 (mtp180) cc_final: 0.6681 (pmt170)
REVERT: B    3 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7068 (pm20)
REVERT: B    5 ARG cc_start: 0.8356 (mtp180) cc_final: 0.6701 (pmt170)
REVERT: C    3 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7026 (mm-30)
REVERT: D    3 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6746 (mm-30)
REVERT: D   28 LYS cc_start: 0.8549 (mttt) cc_final: 0.8026 (mttm)
REVERT: E    3 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6813 (mp0)
REVERT: E   15 GLN cc_start: 0.8909 (tt0) cc_final: 0.8641 (tt0)
REVERT: F    3 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6865 (mm-30)
REVERT: G    3 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6991 (mm-30)
REVERT: H    3 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6670 (mm-30)
REVERT: H   15 GLN cc_start: 0.8933 (tt0) cc_final: 0.8684 (tt0)
REVERT: I    3 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6962 (mp0)
REVERT: I    5 ARG cc_start: 0.8259 (mtp180) cc_final: 0.6763 (tpm170)
REVERT: I   34 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8935 (mt)
REVERT: J    3 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7501 (mm-30)
REVERT: J    5 ARG cc_start: 0.8261 (mtp180) cc_final: 0.7012 (tpm170)
  outliers start: 40
  outliers final: 5
  residues processed: 166
  average time/residue: 1.1668
  time to fit residues: 198.1833
Evaluate side-chains
  135 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLU
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain C residue    3 GLU
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain D residue    3 GLU
Chi-restraints excluded: chain D residue   34 LEU
Chi-restraints excluded: chain E residue    3 GLU
Chi-restraints excluded: chain F residue    3 GLU
Chi-restraints excluded: chain G residue    3 GLU
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain H residue    3 GLU
Chi-restraints excluded: chain H residue    7 ASP
Chi-restraints excluded: chain H residue   34 LEU
Chi-restraints excluded: chain I residue    3 GLU
Chi-restraints excluded: chain I residue   34 LEU
Chi-restraints excluded: chain J residue    3 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 30 optimal weight:    0.6980
   chunk 16 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9990
   chunk 20 optimal weight:    7.9990
   chunk 31 optimal weight:    0.8980
   chunk 12 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    7.9990
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
D  27 ASN
F   6 HIS
F  15 GLN
F  27 ASN
G  27 ASN
H  27 ASN
I  27 ASN
J  27 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.126331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.098004 restraints weight = 3799.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 2.35
r_work: 0.3565 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3443 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8216
moved from start:          0.2961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3120  Z= 0.212
  Angle     :  0.528   8.219   4190  Z= 0.283
  Chirality :  0.052   0.125    440
  Planarity :  0.002   0.011    560
  Dihedral  : 10.830  59.979    462
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  7.10 %
    Allowed  : 25.16 %
    Favored  : 67.74 %
  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: -2.50 (0.29), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.22), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  14 
 PHE   0.009   0.001   PHE E  20 
 TYR   0.007   0.001   TYR G  10 
 ARG   0.007   0.001   ARG F   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.6768 (pm20)
REVERT: A    5 ARG cc_start: 0.8544 (mtp180) cc_final: 0.6360 (pmt170)
REVERT: A   40 VAL cc_start: 0.8811 (m) cc_final: 0.8467 (p)
REVERT: B    3 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.6936 (pm20)
REVERT: B    5 ARG cc_start: 0.8500 (mtp180) cc_final: 0.6260 (pmt170)
REVERT: B   22 GLU cc_start: 0.8296 (tt0) cc_final: 0.7695 (tt0)
REVERT: B   28 LYS cc_start: 0.8971 (mttm) cc_final: 0.8406 (mttt)
REVERT: C    3 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7304 (mm-30)
REVERT: C    5 ARG cc_start: 0.8377 (ttp80) cc_final: 0.7833 (ttt-90)
REVERT: C   22 GLU cc_start: 0.8100 (tt0) cc_final: 0.7838 (tt0)
REVERT: D    3 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7082 (mp0)
REVERT: D   28 LYS cc_start: 0.9009 (mttt) cc_final: 0.8741 (mttm)
REVERT: E    3 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7168 (mm-30)
REVERT: E    7 ASP cc_start: 0.8609 (p0) cc_final: 0.8290 (p0)
REVERT: E   28 LYS cc_start: 0.8936 (mttt) cc_final: 0.8606 (mttm)
REVERT: F    3 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7335 (mm-30)
REVERT: F    5 ARG cc_start: 0.8263 (mmm-85) cc_final: 0.7879 (tpt-90)
REVERT: F   28 LYS cc_start: 0.8893 (mttt) cc_final: 0.8627 (mtpt)
REVERT: G    3 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7185 (mm-30)
REVERT: G    5 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7653 (ttt-90)
REVERT: G    7 ASP cc_start: 0.8618 (p0) cc_final: 0.8349 (p0)
REVERT: G   28 LYS cc_start: 0.9039 (mttt) cc_final: 0.8759 (mttt)
REVERT: H    3 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7152 (mm-30)
REVERT: H    5 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7810 (ttt-90)
REVERT: H    7 ASP cc_start: 0.8593 (p0) cc_final: 0.8265 (p0)
REVERT: H   28 LYS cc_start: 0.9049 (mttt) cc_final: 0.8674 (mttm)
REVERT: I    3 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7040 (mm-30)
REVERT: I    5 ARG cc_start: 0.7959 (mtp180) cc_final: 0.6650 (tpm170)
REVERT: I   28 LYS cc_start: 0.8939 (mttm) cc_final: 0.8593 (mttm)
REVERT: J    3 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7534 (mm-30)
REVERT: J    5 ARG cc_start: 0.8005 (mtp180) cc_final: 0.6660 (tpm170)
  outliers start: 22
  outliers final: 4
  residues processed: 122
  average time/residue: 1.3380
  time to fit residues: 166.7154
Evaluate side-chains
  115 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLU
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain C residue    3 GLU
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue    3 GLU
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain E residue    3 GLU
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain F residue    3 GLU
Chi-restraints excluded: chain F residue   40 VAL
Chi-restraints excluded: chain G residue    3 GLU
Chi-restraints excluded: chain G residue    5 ARG
Chi-restraints excluded: chain H residue    3 GLU
Chi-restraints excluded: chain H residue    5 ARG
Chi-restraints excluded: chain I residue    3 GLU
Chi-restraints excluded: chain J residue    3 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 17 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 10 optimal weight:    7.9990
   chunk 14 optimal weight:    8.9990
   chunk 28 optimal weight:   20.0000
   chunk 4 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 34 optimal weight:    8.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
B  14 HIS
C   6 HIS
C  14 HIS
D   6 HIS
D  14 HIS
D  15 GLN
E  14 HIS
F  14 HIS
G   6 HIS
G  14 HIS
H   6 HIS
H  14 HIS
J   6 HIS
J  14 HIS

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.115514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.086649 restraints weight = 3823.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 2.18
r_work: 0.3331 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.3671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.052   3120  Z= 0.588
  Angle     :  0.610   7.758   4190  Z= 0.330
  Chirality :  0.054   0.131    440
  Planarity :  0.002   0.014    560
  Dihedral  : 10.487  59.606    450
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  8.71 %
    Allowed  : 23.23 %
    Favored  : 68.06 %
  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: -2.51 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.90 (0.23), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS H  14 
 PHE   0.014   0.002   PHE D  20 
 TYR   0.007   0.001   TYR D  10 
 ARG   0.005   0.001   ARG F   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.6682 (pm20)
REVERT: A    5 ARG cc_start: 0.8405 (mtp180) cc_final: 0.6318 (pmt170)
REVERT: B    3 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.6772 (pm20)
REVERT: B    5 ARG cc_start: 0.8542 (mtp180) cc_final: 0.6266 (pmt170)
REVERT: B   28 LYS cc_start: 0.9087 (mttm) cc_final: 0.8630 (mttt)
REVERT: C    3 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7254 (mm-30)
REVERT: C    5 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7927 (ttt-90)
REVERT: D    3 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7348 (mm-30)
REVERT: D    5 ARG cc_start: 0.8190 (ttt-90) cc_final: 0.7823 (tpt-90)
REVERT: D    7 ASP cc_start: 0.8653 (p0) cc_final: 0.8441 (p0)
REVERT: D   28 LYS cc_start: 0.9231 (mttt) cc_final: 0.8942 (mttm)
REVERT: E    3 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7443 (mm-30)
REVERT: E    5 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7801 (tpt-90)
REVERT: E   28 LYS cc_start: 0.9093 (mttt) cc_final: 0.8830 (mttp)
REVERT: F    3 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7472 (mm-30)
REVERT: F    7 ASP cc_start: 0.8634 (p0) cc_final: 0.8410 (p0)
REVERT: G    3 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7002 (mm-30)
REVERT: G    5 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7671 (ttt-90)
REVERT: G    7 ASP cc_start: 0.8530 (p0) cc_final: 0.8180 (p0)
REVERT: G   28 LYS cc_start: 0.9283 (mttt) cc_final: 0.9017 (mttt)
REVERT: G   40 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8624 (t)
REVERT: H    3 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7178 (mm-30)
REVERT: H    5 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7925 (ttt-90)
REVERT: H   28 LYS cc_start: 0.9236 (mttt) cc_final: 0.8911 (mttm)
REVERT: I    3 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7195 (mm-30)
REVERT: I    5 ARG cc_start: 0.8031 (mtp180) cc_final: 0.6607 (tpm170)
REVERT: I   28 LYS cc_start: 0.9162 (mttm) cc_final: 0.8834 (mttm)
REVERT: J    3 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7954 (mm-30)
REVERT: J    5 ARG cc_start: 0.8048 (mtp180) cc_final: 0.6640 (tpm170)
  outliers start: 27
  outliers final: 7
  residues processed: 122
  average time/residue: 1.4430
  time to fit residues: 179.6743
Evaluate side-chains
  119 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLU
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain C residue    3 GLU
Chi-restraints excluded: chain C residue    5 ARG
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue    3 GLU
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain E residue    3 GLU
Chi-restraints excluded: chain E residue    5 ARG
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain F residue    3 GLU
Chi-restraints excluded: chain G residue    3 GLU
Chi-restraints excluded: chain G residue    5 ARG
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain H residue    3 GLU
Chi-restraints excluded: chain H residue    5 ARG
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain I residue    3 GLU
Chi-restraints excluded: chain J residue    3 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 24 optimal weight:   20.0000
   chunk 37 optimal weight:    2.9990
   chunk 20 optimal weight:   20.0000
   chunk 33 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 16 optimal weight:    8.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** D  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  15 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.117442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.090152 restraints weight = 3893.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.26
r_work: 0.3435 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.4175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3120  Z= 0.234
  Angle     :  0.493   7.646   4190  Z= 0.261
  Chirality :  0.052   0.127    440
  Planarity :  0.002   0.013    560
  Dihedral  : 10.248  59.693    450
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  8.06 %
    Allowed  : 23.87 %
    Favored  : 68.06 %
  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: -2.64 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.01 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS I  14 
 PHE   0.008   0.001   PHE D  20 
 TYR   0.005   0.001   TYR G  10 
 ARG   0.003   0.000   ARG F   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.6593 (pm20)
REVERT: A    5 ARG cc_start: 0.8423 (mtp180) cc_final: 0.6216 (pmt170)
REVERT: B    3 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.6618 (pm20)
REVERT: B   28 LYS cc_start: 0.8915 (mttt) cc_final: 0.8482 (mttt)
REVERT: C    3 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7599 (mm-30)
REVERT: C    5 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8049 (ttt-90)
REVERT: C   28 LYS cc_start: 0.9278 (mttt) cc_final: 0.8937 (mttp)
REVERT: D    3 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7325 (mm-30)
REVERT: D   28 LYS cc_start: 0.9175 (mttt) cc_final: 0.8833 (mttm)
REVERT: E    3 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7361 (mm-30)
REVERT: E    5 ARG cc_start: 0.8409 (ttp80) cc_final: 0.7799 (tpt-90)
REVERT: E   28 LYS cc_start: 0.9067 (mttt) cc_final: 0.8747 (mttp)
REVERT: F    3 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7526 (mm-30)
REVERT: F   28 LYS cc_start: 0.8991 (mttm) cc_final: 0.8782 (mttt)
REVERT: F   40 VAL cc_start: 0.8694 (m) cc_final: 0.8414 (p)
REVERT: G    3 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7027 (mm-30)
REVERT: G    5 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7736 (ttt-90)
REVERT: G    7 ASP cc_start: 0.8521 (p0) cc_final: 0.8083 (p0)
REVERT: G   28 LYS cc_start: 0.9166 (mttt) cc_final: 0.8737 (mttp)
REVERT: G   40 VAL cc_start: 0.8822 (m) cc_final: 0.8512 (t)
REVERT: H    3 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7270 (mm-30)
REVERT: H    5 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8062 (ttt-90)
REVERT: H   28 LYS cc_start: 0.9180 (mttt) cc_final: 0.8794 (mttp)
REVERT: I    3 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7211 (mm-30)
REVERT: I    5 ARG cc_start: 0.7849 (mtp180) cc_final: 0.6579 (tpm170)
REVERT: I   28 LYS cc_start: 0.9134 (mttm) cc_final: 0.8814 (mttm)
REVERT: J    3 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7740 (mm-30)
REVERT: J    5 ARG cc_start: 0.7982 (mtp180) cc_final: 0.6595 (tpm170)
  outliers start: 25
  outliers final: 6
  residues processed: 111
  average time/residue: 1.3212
  time to fit residues: 149.9389
Evaluate side-chains
  109 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLU
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain C residue    3 GLU
Chi-restraints excluded: chain C residue    5 ARG
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue    3 GLU
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain E residue    3 GLU
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain F residue    3 GLU
Chi-restraints excluded: chain F residue   32 ILE
Chi-restraints excluded: chain G residue    3 GLU
Chi-restraints excluded: chain H residue    3 GLU
Chi-restraints excluded: chain H residue    5 ARG
Chi-restraints excluded: chain I residue    3 GLU
Chi-restraints excluded: chain J residue    3 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 28 optimal weight:   20.0000
   chunk 32 optimal weight:    0.1980
   chunk 15 optimal weight:    6.9990
   chunk 8 optimal weight:   20.0000
   chunk 39 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 29 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 2 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.116786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.089913 restraints weight = 3883.000|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 2.24
r_work: 0.3442 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3322 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.4319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3120  Z= 0.221
  Angle     :  0.473   7.328   4190  Z= 0.250
  Chirality :  0.051   0.125    440
  Planarity :  0.001   0.010    560
  Dihedral  :  9.915  59.633    450
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  7.74 %
    Allowed  : 26.13 %
    Favored  : 66.13 %
  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: -2.65 (0.32), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.01 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  14 
 PHE   0.008   0.001   PHE D  20 
 TYR   0.015   0.001   TYR J  10 
 ARG   0.003   0.000   ARG F   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.6643 (pm20)
REVERT: A    5 ARG cc_start: 0.8435 (mtp180) cc_final: 0.6205 (pmt170)
REVERT: B    3 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.6562 (pm20)
REVERT: B   28 LYS cc_start: 0.8745 (mttt) cc_final: 0.8369 (mttt)
REVERT: C    3 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7565 (mm-30)
REVERT: C   28 LYS cc_start: 0.9271 (mttt) cc_final: 0.8916 (mttp)
REVERT: D    3 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7471 (mm-30)
REVERT: D    5 ARG cc_start: 0.8143 (ttt-90) cc_final: 0.7767 (ttt180)
REVERT: D   28 LYS cc_start: 0.9194 (mttt) cc_final: 0.8903 (mttm)
REVERT: E    3 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7296 (mm-30)
REVERT: E    5 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8093 (tpt-90)
REVERT: E   28 LYS cc_start: 0.8998 (mttt) cc_final: 0.8655 (mttp)
REVERT: F    3 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7435 (mm-30)
REVERT: F   40 VAL cc_start: 0.8599 (m) cc_final: 0.8293 (p)
REVERT: G    3 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7134 (mm-30)
REVERT: G    5 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7837 (ttt-90)
REVERT: G    7 ASP cc_start: 0.8531 (p0) cc_final: 0.8121 (p0)
REVERT: G   28 LYS cc_start: 0.9131 (mttt) cc_final: 0.8691 (mttp)
REVERT: G   40 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8468 (t)
REVERT: H    3 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7192 (mm-30)
REVERT: H    5 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8209 (ttt-90)
REVERT: H   28 LYS cc_start: 0.9173 (mttt) cc_final: 0.8814 (mttm)
REVERT: I    3 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7102 (mm-30)
REVERT: I    5 ARG cc_start: 0.7818 (mtp180) cc_final: 0.6622 (tpm170)
REVERT: I   15 GLN cc_start: 0.8997 (tt0) cc_final: 0.8720 (tt0)
REVERT: I   28 LYS cc_start: 0.9154 (mttm) cc_final: 0.8799 (mttm)
REVERT: J    3 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7716 (mm-30)
REVERT: J    5 ARG cc_start: 0.7942 (mtp180) cc_final: 0.6606 (tpm170)
  outliers start: 24
  outliers final: 6
  residues processed: 100
  average time/residue: 1.3022
  time to fit residues: 133.1189
Evaluate side-chains
  105 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLU
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain C residue    3 GLU
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue    3 GLU
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain E residue    3 GLU
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain F residue    3 GLU
Chi-restraints excluded: chain F residue   32 ILE
Chi-restraints excluded: chain G residue    3 GLU
Chi-restraints excluded: chain G residue    5 ARG
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain H residue    3 GLU
Chi-restraints excluded: chain H residue    5 ARG
Chi-restraints excluded: chain I residue    3 GLU
Chi-restraints excluded: chain J residue    3 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 16 optimal weight:    7.9990
   chunk 31 optimal weight:    6.9990
   chunk 35 optimal weight:    0.8980
   chunk 12 optimal weight:    9.9990
   chunk 11 optimal weight:    6.9990
   chunk 36 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I   6 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.112459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.084719 restraints weight = 4014.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 2.26
r_work: 0.3323 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.4501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   3120  Z= 0.440
  Angle     :  0.527   6.820   4190  Z= 0.284
  Chirality :  0.052   0.129    440
  Planarity :  0.002   0.011    560
  Dihedral  : 10.204  59.845    450
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  7.74 %
    Allowed  : 25.16 %
    Favored  : 67.10 %
  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: -2.66 (0.32), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I  14 
 PHE   0.011   0.002   PHE D  20 
 TYR   0.014   0.002   TYR J  10 
 ARG   0.003   0.001   ARG H   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.6437 (pm20)
REVERT: A    5 ARG cc_start: 0.8475 (mtp180) cc_final: 0.6071 (pmt170)
REVERT: B    3 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.6554 (pm20)
REVERT: B   28 LYS cc_start: 0.8914 (mttt) cc_final: 0.8441 (mttt)
REVERT: C    3 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7411 (mm-30)
REVERT: C   28 LYS cc_start: 0.9276 (mttt) cc_final: 0.8908 (mttp)
REVERT: C   32 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8897 (mt)
REVERT: D    3 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7319 (mm-30)
REVERT: D    5 ARG cc_start: 0.8182 (ttt-90) cc_final: 0.7816 (ttt180)
REVERT: D   28 LYS cc_start: 0.9203 (mttt) cc_final: 0.8896 (mttm)
REVERT: E    3 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7329 (mm-30)
REVERT: E    5 ARG cc_start: 0.8427 (ttp80) cc_final: 0.7948 (tpt-90)
REVERT: E   28 LYS cc_start: 0.9006 (mttt) cc_final: 0.8659 (mttp)
REVERT: F    3 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7508 (mm-30)
REVERT: F   28 LYS cc_start: 0.9118 (mttm) cc_final: 0.8798 (mttp)
REVERT: F   40 VAL cc_start: 0.8662 (m) cc_final: 0.8424 (p)
REVERT: G    3 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7165 (mm-30)
REVERT: G    5 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7718 (ttt-90)
REVERT: G    7 ASP cc_start: 0.8501 (p0) cc_final: 0.8185 (p0)
REVERT: G   28 LYS cc_start: 0.9237 (mttt) cc_final: 0.8829 (mttp)
REVERT: H    3 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7323 (mm-30)
REVERT: H    5 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8156 (ttt-90)
REVERT: H   28 LYS cc_start: 0.9183 (mttt) cc_final: 0.8818 (mttp)
REVERT: I    3 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7763 (mm-30)
REVERT: I    5 ARG cc_start: 0.7880 (mtp180) cc_final: 0.6563 (tpm170)
REVERT: I   15 GLN cc_start: 0.9036 (tt0) cc_final: 0.8616 (tt0)
REVERT: I   28 LYS cc_start: 0.9166 (mttm) cc_final: 0.8835 (mttp)
REVERT: J    3 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7924 (mm-30)
  outliers start: 24
  outliers final: 7
  residues processed: 113
  average time/residue: 1.3343
  time to fit residues: 154.0490
Evaluate side-chains
  111 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLU
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain C residue    3 GLU
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue    3 GLU
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain E residue    3 GLU
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain F residue    3 GLU
Chi-restraints excluded: chain G residue    3 GLU
Chi-restraints excluded: chain G residue    5 ARG
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain H residue    3 GLU
Chi-restraints excluded: chain H residue    5 ARG
Chi-restraints excluded: chain I residue    3 GLU
Chi-restraints excluded: chain J residue    3 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 28 optimal weight:   20.0000
   chunk 15 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0570
   chunk 32 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.1904

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

Flipped N/Q/H residues before XYZ refinement:
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.116289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.089872 restraints weight = 3898.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 2.21
r_work: 0.3430 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3309 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.4616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3120  Z= 0.198
  Angle     :  0.479   7.218   4190  Z= 0.252
  Chirality :  0.051   0.125    440
  Planarity :  0.001   0.008    560
  Dihedral  :  9.866  59.034    450
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  7.74 %
    Allowed  : 28.06 %
    Favored  : 64.19 %
  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: -2.82 (0.32), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A  14 
 PHE   0.006   0.001   PHE D  20 
 TYR   0.016   0.001   TYR J  10 
 ARG   0.002   0.000   ARG F   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.6418 (pm20)
REVERT: A    5 ARG cc_start: 0.8436 (mtp180) cc_final: 0.5900 (ppt170)
REVERT: B    3 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.6579 (pm20)
REVERT: C    3 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7492 (mm-30)
REVERT: C    5 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7804 (ttt-90)
REVERT: C   28 LYS cc_start: 0.9265 (mttt) cc_final: 0.8794 (mttp)
REVERT: D    3 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7505 (mm-30)
REVERT: D    5 ARG cc_start: 0.8235 (ttt-90) cc_final: 0.7882 (tpt-90)
REVERT: D   28 LYS cc_start: 0.9191 (mttt) cc_final: 0.8807 (mttp)
REVERT: E    3 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7232 (mm-30)
REVERT: E    5 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8115 (tpt-90)
REVERT: E    7 ASP cc_start: 0.8439 (p0) cc_final: 0.8210 (p0)
REVERT: E   28 LYS cc_start: 0.8973 (mttt) cc_final: 0.8574 (mttp)
REVERT: F    3 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7519 (mm-30)
REVERT: F    7 ASP cc_start: 0.8508 (p0) cc_final: 0.8000 (p0)
REVERT: F   28 LYS cc_start: 0.9066 (mttm) cc_final: 0.8745 (mttp)
REVERT: F   40 VAL cc_start: 0.8596 (m) cc_final: 0.8395 (p)
REVERT: G    3 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7177 (mm-30)
REVERT: G    5 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7827 (ttt-90)
REVERT: G    7 ASP cc_start: 0.8496 (p0) cc_final: 0.8163 (p0)
REVERT: G   28 LYS cc_start: 0.9152 (mttt) cc_final: 0.8702 (mttp)
REVERT: G   40 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8338 (t)
REVERT: H    3 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7327 (mm-30)
REVERT: H   28 LYS cc_start: 0.9178 (mttt) cc_final: 0.8792 (mttp)
REVERT: I    3 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7100 (mm-30)
REVERT: I    5 ARG cc_start: 0.7733 (mtp180) cc_final: 0.6540 (tpm170)
REVERT: I   15 GLN cc_start: 0.8994 (tt0) cc_final: 0.8656 (tt0)
REVERT: I   28 LYS cc_start: 0.9158 (mttm) cc_final: 0.8794 (mttm)
REVERT: J    3 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7852 (mm-30)
  outliers start: 24
  outliers final: 6
  residues processed: 104
  average time/residue: 1.2986
  time to fit residues: 138.0703
Evaluate side-chains
  104 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLU
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain C residue    3 GLU
Chi-restraints excluded: chain C residue    5 ARG
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue    3 GLU
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain E residue    3 GLU
Chi-restraints excluded: chain E residue    5 ARG
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain F residue    3 GLU
Chi-restraints excluded: chain G residue    3 GLU
Chi-restraints excluded: chain G residue    5 ARG
Chi-restraints excluded: chain G residue   35 MET
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain H residue    3 GLU
Chi-restraints excluded: chain I residue    3 GLU
Chi-restraints excluded: chain J residue    3 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 6 optimal weight:    0.3980
   chunk 13 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9990
   chunk 36 optimal weight:   10.0000
   chunk 24 optimal weight:   20.0000
   chunk 31 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   chunk 23 optimal weight:    0.7980
   chunk 18 optimal weight:    7.9990
   chunk 5 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.117900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.091992 restraints weight = 3924.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 2.23
r_work: 0.3482 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3361 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.4843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3120  Z= 0.167
  Angle     :  0.489   6.894   4190  Z= 0.250
  Chirality :  0.051   0.125    440
  Planarity :  0.001   0.008    560
  Dihedral  :  9.547  57.658    450
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  6.13 %
    Allowed  : 30.32 %
    Favored  : 63.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.91 (0.32), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.21 (0.25), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  14 
 PHE   0.006   0.001   PHE A   4 
 TYR   0.017   0.002   TYR J  10 
 ARG   0.002   0.000   ARG F   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.6183 (pm20)
REVERT: A    5 ARG cc_start: 0.8510 (mtp180) cc_final: 0.5894 (ppt170)
REVERT: B    3 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.6559 (pm20)
REVERT: C    5 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7860 (ttt-90)
REVERT: C    7 ASP cc_start: 0.8422 (p0) cc_final: 0.8217 (p0)
REVERT: C   28 LYS cc_start: 0.9219 (mttt) cc_final: 0.8812 (mttp)
REVERT: D    3 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7450 (mm-30)
REVERT: D    5 ARG cc_start: 0.8282 (ttt-90) cc_final: 0.7960 (tpt-90)
REVERT: D    7 ASP cc_start: 0.8510 (p0) cc_final: 0.8271 (p0)
REVERT: D   28 LYS cc_start: 0.9158 (mttt) cc_final: 0.8791 (mttm)
REVERT: E    3 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7124 (mm-30)
REVERT: E    5 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8157 (tpt-90)
REVERT: E    7 ASP cc_start: 0.8487 (p0) cc_final: 0.8281 (p0)
REVERT: E   28 LYS cc_start: 0.8904 (mttt) cc_final: 0.8496 (mttm)
REVERT: F    3 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7559 (mm-30)
REVERT: F    7 ASP cc_start: 0.8451 (p0) cc_final: 0.7985 (p0)
REVERT: F   28 LYS cc_start: 0.9043 (mttm) cc_final: 0.8747 (mttp)
REVERT: G    3 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7180 (mm-30)
REVERT: G    5 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7866 (ttt-90)
REVERT: G    7 ASP cc_start: 0.8473 (p0) cc_final: 0.8068 (p0)
REVERT: G   28 LYS cc_start: 0.9161 (mttt) cc_final: 0.8737 (mttp)
REVERT: H   28 LYS cc_start: 0.9177 (mttt) cc_final: 0.8810 (mttp)
REVERT: I    3 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7075 (mm-30)
REVERT: I    5 ARG cc_start: 0.7764 (mtp180) cc_final: 0.6523 (tpm170)
REVERT: I   15 GLN cc_start: 0.8999 (tt0) cc_final: 0.8718 (tt0)
REVERT: I   28 LYS cc_start: 0.9127 (mttm) cc_final: 0.8722 (mttp)
REVERT: J    5 ARG cc_start: 0.7876 (mtp180) cc_final: 0.6553 (tpm170)
  outliers start: 19
  outliers final: 4
  residues processed: 99
  average time/residue: 1.3610
  time to fit residues: 137.6536
Evaluate side-chains
  96 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLU
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain C residue    5 ARG
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue    3 GLU
Chi-restraints excluded: chain E residue    3 GLU
Chi-restraints excluded: chain E residue    5 ARG
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain F residue    3 GLU
Chi-restraints excluded: chain G residue    3 GLU
Chi-restraints excluded: chain G residue    5 ARG
Chi-restraints excluded: chain I residue    3 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 28 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 20 optimal weight:    7.9990
   chunk 34 optimal weight:    7.9990
   chunk 32 optimal weight:   10.0000
   chunk 7 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 19 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    3.1986

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

Flipped N/Q/H residues before XYZ refinement:
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.111855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.085418 restraints weight = 3966.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 2.24
r_work: 0.3340 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.4730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   3120  Z= 0.404
  Angle     :  0.561   6.754   4190  Z= 0.293
  Chirality :  0.052   0.129    440
  Planarity :  0.002   0.014    560
  Dihedral  :  8.790  59.027    441
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  6.45 %
    Allowed  : 31.61 %
    Favored  : 61.94 %
  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: -2.86 (0.33), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.17 (0.25), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I  14 
 PHE   0.010   0.001   PHE B  20 
 TYR   0.014   0.002   TYR J  10 
 ARG   0.002   0.000   ARG G   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.385 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.6023 (pm20)
REVERT: A    5 ARG cc_start: 0.8479 (mtp180) cc_final: 0.6116 (pmt170)
REVERT: B    3 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.6487 (pm20)
REVERT: B   28 LYS cc_start: 0.9237 (mttt) cc_final: 0.8938 (mttt)
REVERT: C    5 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7523 (ttt180)
REVERT: C   28 LYS cc_start: 0.9265 (mttt) cc_final: 0.8909 (mttp)
REVERT: D    3 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7581 (mm-30)
REVERT: D    5 ARG cc_start: 0.8286 (ttt-90) cc_final: 0.7907 (tpt-90)
REVERT: D   28 LYS cc_start: 0.9192 (mttt) cc_final: 0.8814 (mttp)
REVERT: E    3 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7194 (mm-30)
REVERT: E    5 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8102 (tpt-90)
REVERT: E    7 ASP cc_start: 0.8519 (p0) cc_final: 0.8260 (p0)
REVERT: E   28 LYS cc_start: 0.8917 (mttt) cc_final: 0.8498 (mttm)
REVERT: F    3 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7546 (mm-30)
REVERT: F    7 ASP cc_start: 0.8419 (p0) cc_final: 0.7971 (p0)
REVERT: F   28 LYS cc_start: 0.9211 (mttm) cc_final: 0.8912 (mttp)
REVERT: G    3 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7294 (mm-30)
REVERT: G    5 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7780 (ttt-90)
REVERT: G    7 ASP cc_start: 0.8520 (p0) cc_final: 0.8293 (p0)
REVERT: G   28 LYS cc_start: 0.9205 (mttt) cc_final: 0.8793 (mttp)
REVERT: G   40 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.8017 (t)
REVERT: H   28 LYS cc_start: 0.9171 (mttt) cc_final: 0.8794 (mttm)
REVERT: I    3 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7806 (mm-30)
REVERT: I    5 ARG cc_start: 0.7867 (mtp180) cc_final: 0.6535 (tpm170)
REVERT: I   28 LYS cc_start: 0.9180 (mttm) cc_final: 0.8828 (mttp)
  outliers start: 20
  outliers final: 6
  residues processed: 101
  average time/residue: 1.3507
  time to fit residues: 139.4500
Evaluate side-chains
  102 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLU
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain C residue    5 ARG
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue    3 GLU
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain E residue    3 GLU
Chi-restraints excluded: chain E residue    5 ARG
Chi-restraints excluded: chain E residue   40 VAL
Chi-restraints excluded: chain F residue    3 GLU
Chi-restraints excluded: chain G residue    3 GLU
Chi-restraints excluded: chain G residue    5 ARG
Chi-restraints excluded: chain G residue   40 VAL
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain I residue    3 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 26 optimal weight:    7.9990
   chunk 22 optimal weight:    0.3980
   chunk 18 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.116431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.090793 restraints weight = 3927.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.23
r_work: 0.3453 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.4953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3120  Z= 0.184
  Angle     :  0.521   6.651   4190  Z= 0.269
  Chirality :  0.052   0.125    440
  Planarity :  0.002   0.011    560
  Dihedral  :  8.611  58.384    441
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 33.23 %
    Favored  : 61.61 %
  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: -2.97 (0.33), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.26 (0.25), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  13 
 PHE   0.011   0.001   PHE A   4 
 TYR   0.017   0.001   TYR J  10 
 ARG   0.002   0.000   ARG F   5 

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.6059 (pm20)
REVERT: B    3 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.6377 (pm20)
REVERT: B   28 LYS cc_start: 0.9013 (mttt) cc_final: 0.8738 (mttp)
REVERT: C    5 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7869 (ttt-90)
REVERT: C   28 LYS cc_start: 0.9192 (mttt) cc_final: 0.8801 (mttp)
REVERT: D    3 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7522 (mm-30)
REVERT: D    5 ARG cc_start: 0.8312 (ttt-90) cc_final: 0.7983 (tpt-90)
REVERT: D   28 LYS cc_start: 0.9150 (mttt) cc_final: 0.8771 (mttp)
REVERT: E    3 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7238 (mm-30)
REVERT: E    5 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8147 (tpt-90)
REVERT: E   28 LYS cc_start: 0.8803 (mttt) cc_final: 0.8423 (mttm)
REVERT: F    3 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7551 (mm-30)
REVERT: F    7 ASP cc_start: 0.8358 (p0) cc_final: 0.7812 (p0)
REVERT: F   28 LYS cc_start: 0.9100 (mttm) cc_final: 0.8799 (mttp)
REVERT: G    3 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7361 (mm-30)
REVERT: G    5 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7905 (ttt-90)
REVERT: G    7 ASP cc_start: 0.8474 (p0) cc_final: 0.8135 (p0)
REVERT: G   28 LYS cc_start: 0.9153 (mttt) cc_final: 0.8730 (mttp)
REVERT: H   28 LYS cc_start: 0.9160 (mttt) cc_final: 0.8801 (mttp)
REVERT: I    3 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7732 (mm-30)
REVERT: I    5 ARG cc_start: 0.7807 (mtp180) cc_final: 0.6570 (tpm170)
REVERT: I   28 LYS cc_start: 0.9128 (mttm) cc_final: 0.8712 (mttp)
  outliers start: 16
  outliers final: 4
  residues processed: 97
  average time/residue: 1.2539
  time to fit residues: 124.5291
Evaluate side-chains
  99 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLU
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain B residue    3 GLU
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain C residue    5 ARG
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain D residue    3 GLU
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain E residue    3 GLU
Chi-restraints excluded: chain E residue    5 ARG
Chi-restraints excluded: chain F residue    3 GLU
Chi-restraints excluded: chain G residue    3 GLU
Chi-restraints excluded: chain G residue    5 ARG
Chi-restraints excluded: chain I residue    3 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 15 optimal weight:    0.7980
   chunk 13 optimal weight:    9.9990
   chunk 2 optimal weight:    3.9990
   chunk 28 optimal weight:    9.9990
   chunk 5 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
** B  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   6 HIS
** F  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.112741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.086359 restraints weight = 3988.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 2.24
r_work: 0.3363 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.4873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3120  Z= 0.359
  Angle     :  0.573   7.044   4190  Z= 0.295
  Chirality :  0.052   0.124    440
  Planarity :  0.002   0.013    560
  Dihedral  :  8.666  58.551    441
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 33.87 %
    Favored  : 61.61 %
  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: -2.93 (0.33), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.22 (0.25), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  13 
 PHE   0.010   0.001   PHE F   4 
 TYR   0.014   0.002   TYR J  10 
 ARG   0.001   0.000   ARG G   5 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3416.62 seconds
wall clock time: 60 minutes 47.58 seconds (3647.58 seconds total)