Starting phenix.real_space_refine
on Thu Nov 14 00:50:26 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovk_17218/11_2024/8ovk_17218.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovk_17218/11_2024/8ovk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovk_17218/11_2024/8ovk_17218.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovk_17218/11_2024/8ovk_17218.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovk_17218/11_2024/8ovk_17218.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ovk_17218/11_2024/8ovk_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-5513/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: 1.49, per 1000 atoms: 0.49
  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: 0.65
  Conformation dependent library (CDL) restraints added in 399.3 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: 0.38
  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: 0.70

  Time building geometry restraints manager: 0.77 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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:             0.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.980
  Find NCS groups from input model:        0.110
  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:             0.010
  Load rotamer database and sin/cos tables:13.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.810
-------------------------------------------------------------------------------
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  : 0.346 
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: 1.1669
  time to fit residues: 198.2632
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  : 0.526 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
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  : 0.319 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6786 (pm20)
REVERT: A    5 ARG cc_start: 0.8442 (mtp180) cc_final: 0.6412 (pmt170)
REVERT: A   40 VAL cc_start: 0.8744 (m) cc_final: 0.8457 (p)
REVERT: B    3 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7032 (pm20)
REVERT: B    5 ARG cc_start: 0.8379 (mtp180) cc_final: 0.6360 (pmt170)
REVERT: B   22 GLU cc_start: 0.7671 (tt0) cc_final: 0.7104 (tt0)
REVERT: B   28 LYS cc_start: 0.8821 (mttm) cc_final: 0.8296 (mttt)
REVERT: C    3 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7311 (mm-30)
REVERT: C    5 ARG cc_start: 0.8340 (ttp80) cc_final: 0.7893 (ttt-90)
REVERT: C   22 GLU cc_start: 0.7444 (tt0) cc_final: 0.7241 (tt0)
REVERT: D    3 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7107 (mp0)
REVERT: D   28 LYS cc_start: 0.8800 (mttt) cc_final: 0.8591 (mttm)
REVERT: E    3 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7178 (mm-30)
REVERT: E    7 ASP cc_start: 0.8585 (p0) cc_final: 0.8311 (p0)
REVERT: E   28 LYS cc_start: 0.8747 (mttt) cc_final: 0.8462 (mttm)
REVERT: F    3 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7259 (mm-30)
REVERT: F    5 ARG cc_start: 0.8358 (mmm-85) cc_final: 0.8087 (tpt-90)
REVERT: F   28 LYS cc_start: 0.8726 (mttt) cc_final: 0.8512 (mtpt)
REVERT: G    3 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7235 (mm-30)
REVERT: G    5 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7804 (ttt-90)
REVERT: G    7 ASP cc_start: 0.8578 (p0) cc_final: 0.8322 (p0)
REVERT: G   28 LYS cc_start: 0.8846 (mttt) cc_final: 0.8587 (mttt)
REVERT: H    3 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7190 (mm-30)
REVERT: H    5 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7948 (ttt-90)
REVERT: H    7 ASP cc_start: 0.8618 (p0) cc_final: 0.8359 (p0)
REVERT: H   28 LYS cc_start: 0.8848 (mttt) cc_final: 0.8590 (mttm)
REVERT: I    3 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6956 (mm-30)
REVERT: I    5 ARG cc_start: 0.8030 (mtp180) cc_final: 0.6852 (tpm170)
REVERT: I   28 LYS cc_start: 0.8743 (mttm) cc_final: 0.8475 (mttm)
REVERT: J    5 ARG cc_start: 0.8118 (mtp180) cc_final: 0.6948 (tpm170)
  outliers start: 22
  outliers final: 4
  residues processed: 122
  average time/residue: 1.3719
  time to fit residues: 170.9759
Evaluate side-chains
  114 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 24 optimal weight:   20.0000
   chunk 10 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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
F  14 HIS
G  14 HIS
J   6 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   3120  Z= 0.315
  Angle     :  0.514   7.475   4190  Z= 0.277
  Chirality :  0.052   0.124    440
  Planarity :  0.002   0.012    560
  Dihedral  :  9.931  58.977    447
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  7.10 %
    Allowed  : 25.81 %
    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: -2.57 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.95 (0.23), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS G  14 
 PHE   0.009   0.001   PHE D  20 
 TYR   0.005   0.001   TYR G  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
  123 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6762 (pm20)
REVERT: A    5 ARG cc_start: 0.8309 (mtp180) cc_final: 0.6354 (pmt170)
REVERT: B    3 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6832 (pm20)
REVERT: B    5 ARG cc_start: 0.8419 (mtp180) cc_final: 0.6361 (pmt170)
REVERT: B   28 LYS cc_start: 0.8820 (mttm) cc_final: 0.8449 (mttt)
REVERT: C    3 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7404 (mm-30)
REVERT: C    5 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7903 (ttt-90)
REVERT: D    3 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7132 (mm-30)
REVERT: D   23 ASP cc_start: 0.8688 (m-30) cc_final: 0.8364 (m-30)
REVERT: D   28 LYS cc_start: 0.9052 (mttt) cc_final: 0.8743 (mttm)
REVERT: E    3 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7205 (mm-30)
REVERT: E    5 ARG cc_start: 0.8477 (ttp80) cc_final: 0.7921 (tpt-90)
REVERT: E   28 LYS cc_start: 0.8819 (mttt) cc_final: 0.8564 (mttm)
REVERT: F    3 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7359 (mm-30)
REVERT: F   28 LYS cc_start: 0.8926 (mttt) cc_final: 0.8615 (mtpt)
REVERT: G    3 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7272 (mm-30)
REVERT: G    5 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7866 (ttt-90)
REVERT: G    7 ASP cc_start: 0.8508 (p0) cc_final: 0.8084 (p0)
REVERT: G   28 LYS cc_start: 0.9038 (mttt) cc_final: 0.8816 (mttt)
REVERT: H    3 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6998 (mm-30)
REVERT: H    5 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8072 (ttt-90)
REVERT: H   28 LYS cc_start: 0.8969 (mttt) cc_final: 0.8731 (mttm)
REVERT: I    3 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7220 (mp0)
REVERT: I    5 ARG cc_start: 0.8101 (mtp180) cc_final: 0.6885 (tpm170)
REVERT: I   28 LYS cc_start: 0.8910 (mttm) cc_final: 0.8649 (mttm)
REVERT: J    5 ARG cc_start: 0.8050 (mtp180) cc_final: 0.6928 (tpm170)
  outliers start: 22
  outliers final: 7
  residues processed: 113
  average time/residue: 1.4123
  time to fit residues: 162.9843
Evaluate side-chains
  116 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
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   32 ILE
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   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 H residue    3 GLU
Chi-restraints excluded: chain H residue    5 ARG
Chi-restraints excluded: chain I residue    3 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 17 optimal weight:    4.9990
   chunk 24 optimal weight:   20.0000
   chunk 36 optimal weight:    0.0030
   chunk 38 optimal weight:    0.1980
   chunk 19 optimal weight:    0.8980
   chunk 34 optimal weight:    7.9990
   chunk 10 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 21 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.8194

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

Flipped N/Q/H residues before XYZ refinement:
H  14 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.3973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3120  Z= 0.264
  Angle     :  0.470   6.759   4190  Z= 0.255
  Chirality :  0.051   0.125    440
  Planarity :  0.002   0.010    560
  Dihedral  :  9.785  58.102    447
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  7.42 %
    Allowed  : 25.48 %
    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: -2.70 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.05 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H  14 
 PHE   0.008   0.001   PHE D  20 
 TYR   0.006   0.001   TYR D  10 
 ARG   0.003   0.001   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: 23
    poor density    : 97
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.6627 (pm20)
REVERT: A    5 ARG cc_start: 0.8368 (mtp180) cc_final: 0.6351 (pmt170)
REVERT: B    3 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.6743 (pm20)
REVERT: B    5 ARG cc_start: 0.8494 (mtp180) cc_final: 0.6229 (pmt170)
REVERT: B   28 LYS cc_start: 0.8805 (mttm) cc_final: 0.8505 (mtpt)
REVERT: C    3 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7500 (mm-30)
REVERT: C    5 ARG cc_start: 0.8278 (ttp80) cc_final: 0.7806 (ttt-90)
REVERT: C   28 LYS cc_start: 0.9119 (mttt) cc_final: 0.8817 (mttp)
REVERT: D    3 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7262 (mm-30)
REVERT: D   28 LYS cc_start: 0.9035 (mttt) cc_final: 0.8784 (mttm)
REVERT: E    3 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7330 (mm-30)
REVERT: E    5 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8021 (tpt-90)
REVERT: E    7 ASP cc_start: 0.8524 (p0) cc_final: 0.8297 (p0)
REVERT: E   28 LYS cc_start: 0.8804 (mttt) cc_final: 0.8490 (mttm)
REVERT: F    3 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7395 (mm-30)
REVERT: F   28 LYS cc_start: 0.8927 (mttt) cc_final: 0.8699 (mttm)
REVERT: G    3 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7300 (mm-30)
REVERT: G    5 ARG cc_start: 0.8319 (ttp80) cc_final: 0.8029 (ttt-90)
REVERT: G    7 ASP cc_start: 0.8526 (p0) cc_final: 0.8087 (p0)
REVERT: G   28 LYS cc_start: 0.9064 (mttt) cc_final: 0.8796 (mttt)
REVERT: H    3 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7219 (mm-30)
REVERT: H    5 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8212 (ttt-90)
REVERT: H   28 LYS cc_start: 0.9017 (mttt) cc_final: 0.8744 (mttm)
REVERT: I    3 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7093 (mm-30)
REVERT: I    5 ARG cc_start: 0.8033 (mtp180) cc_final: 0.6804 (tpm170)
REVERT: I   28 LYS cc_start: 0.8940 (mttm) cc_final: 0.8672 (mttm)
REVERT: J    5 ARG cc_start: 0.8071 (mtp180) cc_final: 0.6917 (tpm170)
  outliers start: 23
  outliers final: 4
  residues processed: 111
  average time/residue: 1.3980
  time to fit residues: 158.4375
Evaluate side-chains
  109 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
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 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 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
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 15 optimal weight:    7.9990
   chunk 32 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 9 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    8.9990
   overall best weight:    3.7386

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

Flipped N/Q/H residues before XYZ refinement:
E  14 HIS
G   6 HIS
H   6 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.4184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059   3120  Z= 0.463
  Angle     :  0.567   8.234   4190  Z= 0.299
  Chirality :  0.053   0.132    440
  Planarity :  0.002   0.014    560
  Dihedral  : 10.017  59.745    447
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  8.06 %
    Allowed  : 24.52 %
    Favored  : 67.42 %
  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: -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   0.004   0.001   HIS I  14 
 PHE   0.015   0.002   PHE B  20 
 TYR   0.012   0.002   TYR J  10 
 ARG   0.003   0.001   ARG H   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
  128 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
REVERT: A    3 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.6596 (pm20)
REVERT: A    5 ARG cc_start: 0.8346 (mtp180) cc_final: 0.6165 (pmt170)
REVERT: B    3 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.6638 (pm20)
REVERT: C    3 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7507 (mm-30)
REVERT: C    5 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7974 (ttt-90)
REVERT: C   32 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8962 (mt)
REVERT: D    3 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7394 (mm-30)
REVERT: D    5 ARG cc_start: 0.8226 (ttt-90) cc_final: 0.7900 (ttt180)
REVERT: E    3 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7423 (mm-30)
REVERT: E    5 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7960 (tpt-90)
REVERT: E   28 LYS cc_start: 0.8843 (mttt) cc_final: 0.8555 (mttp)
REVERT: F    3 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7568 (mm-30)
REVERT: F   40 VAL cc_start: 0.8706 (m) cc_final: 0.8453 (p)
REVERT: G    3 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7232 (mm-30)
REVERT: G    5 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7841 (ttt-90)
REVERT: G    7 ASP cc_start: 0.8486 (p0) cc_final: 0.8100 (p0)
REVERT: G   28 LYS cc_start: 0.9057 (mttt) cc_final: 0.8692 (mttp)
REVERT: G   32 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8853 (mt)
REVERT: H    3 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7314 (mm-30)
REVERT: H    5 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8192 (ttt-90)
REVERT: H   28 LYS cc_start: 0.9037 (mttt) cc_final: 0.8756 (mttm)
REVERT: I    3 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7632 (mm-30)
REVERT: I    5 ARG cc_start: 0.7959 (mtp180) cc_final: 0.6776 (tpm170)
REVERT: I   15 GLN cc_start: 0.8863 (tt0) cc_final: 0.8525 (tt0)
REVERT: I   28 LYS cc_start: 0.8988 (mttm) cc_final: 0.8689 (mttm)
  outliers start: 25
  outliers final: 6
  residues processed: 119
  average time/residue: 1.2608
  time to fit residues: 153.4628
Evaluate side-chains
  116 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
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   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    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 G residue   32 ILE
Chi-restraints excluded: chain G residue   39 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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   chunk 12 optimal weight:   20.0000
   chunk 20 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 28 optimal weight:   10.0000
   overall best weight:    1.5388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.4583

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     :  0.515   7.952   4190  Z= 0.263
  Chirality :  0.052   0.126    440
  Planarity :  0.002   0.013    560
  Dihedral  :  9.751  59.798    447
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Rotamer:
    Outliers :  8.39 %
    Allowed  : 25.81 %
    Favored  : 65.81 %
  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: -2.83 (0.31), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.15 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS I  14 
 PHE   0.017   0.001   PHE B  20 
 TYR   0.014   0.001   TYR J  10 
 ARG   0.002   0.000   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
  112 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 86
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.6611 (pm20)
REVERT: A    5 ARG cc_start: 0.8323 (mtp180) cc_final: 0.6175 (pmt170)
REVERT: B    3 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.6700 (pm20)
REVERT: B   28 LYS cc_start: 0.8825 (mttm) cc_final: 0.8620 (mttt)
REVERT: C    3 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7455 (mm-30)
REVERT: C    5 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7789 (ttt-90)
REVERT: C   23 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8511 (m-30)
REVERT: C   28 LYS cc_start: 0.9116 (mttt) cc_final: 0.8739 (mttp)
REVERT: D    3 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7608 (mm-30)
REVERT: D   28 LYS cc_start: 0.9007 (mttt) cc_final: 0.8752 (mttm)
REVERT: E    3 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7324 (mm-30)
REVERT: E    5 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8130 (tpt-90)
REVERT: E    7 ASP cc_start: 0.8458 (p0) cc_final: 0.8241 (p0)
REVERT: E   28 LYS cc_start: 0.8784 (mttt) cc_final: 0.8461 (mttp)
REVERT: F    3 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7513 (mm-30)
REVERT: F    7 ASP cc_start: 0.8501 (p0) cc_final: 0.8022 (p0)
REVERT: G    3 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7313 (mm-30)
REVERT: G    5 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7978 (ttt-90)
REVERT: G    7 ASP cc_start: 0.8501 (p0) cc_final: 0.8194 (p0)
REVERT: G   28 LYS cc_start: 0.9003 (mttt) cc_final: 0.8652 (mttp)
REVERT: H    3 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7287 (mm-30)
REVERT: H   28 LYS cc_start: 0.9015 (mttt) cc_final: 0.8713 (mttp)
REVERT: I    3 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6989 (mm-30)
REVERT: I    5 ARG cc_start: 0.7890 (mtp180) cc_final: 0.6782 (tpm170)
REVERT: I   15 GLN cc_start: 0.8815 (tt0) cc_final: 0.8554 (tt0)
REVERT: I   28 LYS cc_start: 0.8926 (mttm) cc_final: 0.8610 (mttm)
  outliers start: 26
  outliers final: 6
  residues processed: 103
  average time/residue: 1.2442
  time to fit residues: 131.3032
Evaluate side-chains
  104 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
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   23 ASP
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 F residue   32 ILE
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   39 VAL
Chi-restraints excluded: chain I residue    3 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 32 optimal weight:    8.9990
   chunk 38 optimal weight:    8.9990
   chunk 24 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 26 optimal weight:    8.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    4.3588

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

Flipped N/Q/H residues before XYZ refinement:
I   6 HIS
J  14 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
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      :  0.008   0.048   3120  Z= 0.524
  Angle     :  0.569   7.042   4190  Z= 0.301
  Chirality :  0.053   0.132    440
  Planarity :  0.002   0.027    560
  Dihedral  : 10.020  59.787    447
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  8.06 %
    Allowed  : 26.13 %
    Favored  : 65.81 %
  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: -2.75 (0.32), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I  14 
 PHE   0.015   0.002   PHE B  20 
 TYR   0.013   0.002   TYR J  10 
 ARG   0.005   0.001   ARG D   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
  125 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 100
  time to evaluate  : 0.317 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.6359 (pm20)
REVERT: A    5 ARG cc_start: 0.8437 (mtp180) cc_final: 0.6192 (pmt170)
REVERT: B    3 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.6607 (pm20)
REVERT: B   28 LYS cc_start: 0.8896 (mttm) cc_final: 0.8662 (mttt)
REVERT: C    3 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7471 (mm-30)
REVERT: C    5 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7755 (ttt-90)
REVERT: C   23 ASP cc_start: 0.8735 (OUTLIER) cc_final: 0.8263 (m-30)
REVERT: C   28 LYS cc_start: 0.9125 (mttt) cc_final: 0.8655 (mttp)
REVERT: C   32 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8946 (mt)
REVERT: D    3 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7142 (mm-30)
REVERT: D    5 ARG cc_start: 0.8256 (tpt-90) cc_final: 0.7954 (tpt-90)
REVERT: D   28 LYS cc_start: 0.9092 (mttt) cc_final: 0.8841 (mttm)
REVERT: E    3 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7392 (mm-30)
REVERT: E    5 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8034 (tpt-90)
REVERT: E   15 GLN cc_start: 0.9048 (tt0) cc_final: 0.8770 (tt0)
REVERT: E   28 LYS cc_start: 0.8842 (mttt) cc_final: 0.8499 (mttm)
REVERT: F    3 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7519 (mm-30)
REVERT: G    3 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7212 (mm-30)
REVERT: G    5 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7779 (ttt-90)
REVERT: G    7 ASP cc_start: 0.8470 (p0) cc_final: 0.8139 (p0)
REVERT: G   28 LYS cc_start: 0.9049 (mttt) cc_final: 0.8701 (mttp)
REVERT: H    3 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7511 (mm-30)
REVERT: H   28 LYS cc_start: 0.8996 (mttt) cc_final: 0.8698 (mttm)
REVERT: I    3 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7777 (mm-30)
REVERT: I    5 ARG cc_start: 0.7990 (mtp180) cc_final: 0.6758 (tpm170)
REVERT: I   15 GLN cc_start: 0.8823 (tt0) cc_final: 0.8531 (tt0)
REVERT: I   28 LYS cc_start: 0.8969 (mttm) cc_final: 0.8665 (mttm)
  outliers start: 25
  outliers final: 8
  residues processed: 117
  average time/residue: 1.3721
  time to fit residues: 163.9356
Evaluate side-chains
  114 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
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   23 ASP
Chi-restraints excluded: chain C residue   32 ILE
Chi-restraints excluded: chain C residue   34 LEU
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   39 VAL
Chi-restraints excluded: chain H residue    3 GLU
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain I residue    3 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0020
   chunk 36 optimal weight:   10.0000
   chunk 33 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 28 optimal weight:   20.0000
   chunk 11 optimal weight:    0.9980
   chunk 32 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.6792

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.4946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   3120  Z= 0.151
  Angle     :  0.497   7.271   4190  Z= 0.255
  Chirality :  0.052   0.126    440
  Planarity :  0.002   0.018    560
  Dihedral  :  9.666  59.420    447
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 31.29 %
    Favored  : 63.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.95 (0.32), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.24 (0.24), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS I  14 
 PHE   0.015   0.001   PHE B  20 
 TYR   0.016   0.001   TYR J  10 
 ARG   0.003   0.000   ARG D   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
  99 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: A    3 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.6259 (pm20)
REVERT: B    3 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.6599 (pm20)
REVERT: C    3 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7532 (mm-30)
REVERT: C    5 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7886 (ttt-90)
REVERT: C   23 ASP cc_start: 0.8739 (OUTLIER) cc_final: 0.8509 (m-30)
REVERT: C   28 LYS cc_start: 0.9111 (mttt) cc_final: 0.8718 (mttp)
REVERT: D    3 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7604 (mm-30)
REVERT: E    3 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7237 (mm-30)
REVERT: E   28 LYS cc_start: 0.8631 (mttt) cc_final: 0.8300 (mttm)
REVERT: F    3 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7571 (mm-30)
REVERT: G    3 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7302 (mm-30)
REVERT: G    7 ASP cc_start: 0.8449 (p0) cc_final: 0.8132 (p0)
REVERT: G   28 LYS cc_start: 0.8964 (mttt) cc_final: 0.8621 (mttp)
REVERT: H    3 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7392 (mm-30)
REVERT: H   28 LYS cc_start: 0.8994 (mttt) cc_final: 0.8703 (mttm)
REVERT: I    3 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7040 (mm-30)
REVERT: I    5 ARG cc_start: 0.7883 (mtp180) cc_final: 0.6759 (tpm170)
REVERT: I   15 GLN cc_start: 0.8773 (tt0) cc_final: 0.8526 (tt0)
REVERT: I   28 LYS cc_start: 0.8944 (mttm) cc_final: 0.8646 (mttm)
  outliers start: 15
  outliers final: 1
  residues processed: 96
  average time/residue: 1.2856
  time to fit residues: 126.3712
Evaluate side-chains
  91 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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    5 ARG
Chi-restraints excluded: chain C residue   23 ASP
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 F residue    3 GLU
Chi-restraints excluded: chain G residue    3 GLU
Chi-restraints excluded: chain H residue    3 GLU
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 37 optimal weight:    4.9990
   chunk 23 optimal weight:    6.9990
   chunk 18 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 39 optimal weight:    7.9990
   chunk 36 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   chunk 3 optimal weight:    4.9990
   chunk 24 optimal weight:   20.0000
   chunk 19 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0970
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.4860

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= 0.216
  Angle     :  0.515   7.097   4190  Z= 0.262
  Chirality :  0.052   0.127    440
  Planarity :  0.002   0.015    560
  Dihedral  :  9.610  58.832    447
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 31.94 %
    Favored  : 63.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.95 (0.33), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.24 (0.25), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  14 
 PHE   0.013   0.001   PHE B  20 
 TYR   0.015   0.001   TYR J  10 
 ARG   0.004   0.000   ARG D   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
  99 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A    3 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.6286 (pm20)
REVERT: A    5 ARG cc_start: 0.8451 (mtp180) cc_final: 0.5933 (ppt170)
REVERT: B    3 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.6555 (pm20)
REVERT: C    3 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7635 (mm-30)
REVERT: C    5 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7837 (ttt-90)
REVERT: C    7 ASP cc_start: 0.8397 (p0) cc_final: 0.8153 (p0)
REVERT: C   23 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8534 (m-30)
REVERT: C   28 LYS cc_start: 0.9120 (mttt) cc_final: 0.8782 (mttp)
REVERT: D    3 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7665 (mm-30)
REVERT: D   28 LYS cc_start: 0.8982 (mttt) cc_final: 0.8664 (mttp)
REVERT: E    3 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7246 (mm-30)
REVERT: E   28 LYS cc_start: 0.8662 (mttt) cc_final: 0.8329 (mttm)
REVERT: F    3 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7518 (mm-30)
REVERT: F   28 LYS cc_start: 0.8844 (mttt) cc_final: 0.8607 (mttp)
REVERT: G    3 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7213 (mm-30)
REVERT: G   28 LYS cc_start: 0.8973 (mttt) cc_final: 0.8640 (mttp)
REVERT: H   28 LYS cc_start: 0.8984 (mttt) cc_final: 0.8684 (mttp)
REVERT: I    3 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7567 (mm-30)
REVERT: I    5 ARG cc_start: 0.7968 (mtp180) cc_final: 0.6805 (tpm170)
REVERT: I   15 GLN cc_start: 0.8829 (tt0) cc_final: 0.8615 (tt0)
REVERT: I   28 LYS cc_start: 0.8925 (mttm) cc_final: 0.8566 (mttp)
REVERT: J    5 ARG cc_start: 0.8008 (mtp180) cc_final: 0.6783 (tpm170)
  outliers start: 13
  outliers final: 0
  residues processed: 97
  average time/residue: 1.2866
  time to fit residues: 127.6300
Evaluate side-chains
  92 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
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    5 ARG
Chi-restraints excluded: chain C residue   23 ASP
Chi-restraints excluded: chain D residue    3 GLU
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 I residue    3 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 5 optimal weight:    0.4980
   chunk 27 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    3.6988

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.4906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045   3120  Z= 0.463
  Angle     :  0.588   7.182   4190  Z= 0.307
  Chirality :  0.053   0.130    440
  Planarity :  0.002   0.021    560
  Dihedral  :  9.594  59.984    444
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 34.19 %
    Favored  : 62.58 %
  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: -2.87 (0.33), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.18 (0.25), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS F  13 
 PHE   0.014   0.002   PHE B  20 
 TYR   0.015   0.002   TYR J  10 
 ARG   0.004   0.001   ARG D   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
  99 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: A    3 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.6112 (pm20)
REVERT: A    5 ARG cc_start: 0.8408 (mtp180) cc_final: 0.6111 (pmt170)
REVERT: B    3 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.6564 (pm20)
REVERT: B   28 LYS cc_start: 0.9049 (mttt) cc_final: 0.8782 (mttp)
REVERT: C    3 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7788 (mm-30)
REVERT: C    5 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7620 (ttt-90)
REVERT: C   23 ASP cc_start: 0.8747 (OUTLIER) cc_final: 0.8326 (m-30)
REVERT: C   28 LYS cc_start: 0.9130 (mttt) cc_final: 0.8758 (mttp)
REVERT: C   40 VAL cc_start: 0.8762 (m) cc_final: 0.8479 (t)
REVERT: D    5 ARG cc_start: 0.8407 (tpt-90) cc_final: 0.7993 (tpt-90)
REVERT: E    3 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7362 (mm-30)
REVERT: E   28 LYS cc_start: 0.8768 (mttt) cc_final: 0.8409 (mttm)
REVERT: F    3 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7626 (mm-30)
REVERT: F    7 ASP cc_start: 0.8451 (p0) cc_final: 0.8198 (p0)
REVERT: F   28 LYS cc_start: 0.8974 (mttt) cc_final: 0.8733 (mttp)
REVERT: G    3 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7181 (mm-30)
REVERT: G   28 LYS cc_start: 0.8988 (mttt) cc_final: 0.8656 (mttp)
REVERT: H   28 LYS cc_start: 0.8969 (mttt) cc_final: 0.8682 (mttm)
REVERT: I    3 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7772 (mm-30)
REVERT: I    5 ARG cc_start: 0.8081 (mtp180) cc_final: 0.6772 (tpm170)
REVERT: I   28 LYS cc_start: 0.8960 (mttm) cc_final: 0.8647 (mttp)
  outliers start: 10
  outliers final: 0
  residues processed: 99
  average time/residue: 1.3439
  time to fit residues: 136.0461
Evaluate side-chains
  96 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
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    5 ARG
Chi-restraints excluded: chain C residue   23 ASP
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 I residue    3 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 36 optimal weight:    8.9990
   chunk 21 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 24 optimal weight:   20.0000
   chunk 23 optimal weight:    0.7980
   chunk 15 optimal weight:    0.4980
   chunk 14 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4001 r_free = 0.4001 target = 0.116177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.090508 restraints weight = 3875.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.24
r_work: 0.3448 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3328 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.5094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   3120  Z= 0.166
  Angle     :  0.546   7.854   4190  Z= 0.275
  Chirality :  0.053   0.126    440
  Planarity :  0.002   0.021    560
  Dihedral  :  9.027  59.015    441
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 36.13 %
    Favored  : 60.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.33), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.28 (0.25), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D   6 
 PHE   0.013   0.001   PHE B  20 
 TYR   0.016   0.002   TYR J  10 
 ARG   0.004   0.001   ARG E   5 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2474.88 seconds
wall clock time: 44 minutes 41.79 seconds (2681.79 seconds total)