Starting phenix.real_space_refine
on Mon Feb 10 21:26:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vps_21316/02_2025/6vps_21316.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vps_21316/02_2025/6vps_21316.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vps_21316/02_2025/6vps_21316.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vps_21316/02_2025/6vps_21316.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vps_21316/02_2025/6vps_21316.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vps_21316/02_2025/6vps_21316.cif"
  }
  resolution = 2.6
  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=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    1611      2.51       5
     N     648      2.21       5
     O     477      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: 2736
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 304
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 31, 280
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
      Conformer: "B"
        Number of residues, atoms: 31, 280
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
          bond proxies already assigned to first conformer: 256
    Chain: "B"
      Number of atoms: 304
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 31, 280
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
      Conformer: "B"
        Number of residues, atoms: 31, 280
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
          bond proxies already assigned to first conformer: 256
    Chain: "C"
      Number of atoms: 304
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 31, 280
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
      Conformer: "B"
        Number of residues, atoms: 31, 280
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
          bond proxies already assigned to first conformer: 256
    Chain: "D"
      Number of atoms: 304
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 31, 280
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
      Conformer: "B"
        Number of residues, atoms: 31, 280
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
          bond proxies already assigned to first conformer: 256
    Chain: "E"
      Number of atoms: 304
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 31, 280
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
      Conformer: "B"
        Number of residues, atoms: 31, 280
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
          bond proxies already assigned to first conformer: 256
    Chain: "F"
      Number of atoms: 304
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 31, 280
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
      Conformer: "B"
        Number of residues, atoms: 31, 280
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
          bond proxies already assigned to first conformer: 256
    Chain: "G"
      Number of atoms: 304
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 31, 280
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
      Conformer: "B"
        Number of residues, atoms: 31, 280
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
          bond proxies already assigned to first conformer: 256
    Chain: "H"
      Number of atoms: 304
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 31, 280
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
      Conformer: "B"
        Number of residues, atoms: 31, 280
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
          bond proxies already assigned to first conformer: 256
    Chain: "I"
      Number of atoms: 304
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 31, 280
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
      Conformer: "B"
        Number of residues, atoms: 31, 280
          Classifications: {'peptide': 31}
          Link IDs: {'TRANS': 30}
          bond proxies already assigned to first conformer: 256
  Residues with excluded nonbonded symmetry interactions: 9
    residue:
      pdb=" N  AHIS A  36 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS A  36 " occ=0.50
    residue:
      pdb=" N  AHIS B  36 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS B  36 " occ=0.50
    residue:
      pdb=" N  AHIS C  36 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS C  36 " occ=0.50
    residue:
      pdb=" N  AHIS D  36 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS D  36 " occ=0.50
    residue:
      pdb=" N  AHIS E  36 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS E  36 " occ=0.50
    residue:
      pdb=" N  AHIS F  36 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS F  36 " occ=0.50
    residue:
      pdb=" N  AHIS G  36 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS G  36 " occ=0.50
    residue:
      pdb=" N  AHIS H  36 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS H  36 " occ=0.50
    residue:
      pdb=" N  AHIS I  36 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS I  36 " occ=0.50
  Time building chain proxies: 2.68, per 1000 atoms: 0.98
  Number of scatterers: 2736
  At special positions: 0
  Unit cell: (86.72, 88.888, 31.436, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     477      8.00
     N     648      7.00
     C    1611      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: 0.60
  Conformation dependent library (CDL) restraints added in 479.5 milliseconds
  

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  612

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 67.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 24 through 38
      removed outlier: 6.811A  pdb=" N   GLN A  37 " --> pdb=" O  AHIS D  36 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   GLN D  38 " --> pdb=" O   GLN A  37 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   LEU A  24 " --> pdb=" O   HIS E  25 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   GLN E  27 " --> pdb=" O   LEU A  24 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   GLN A  26 " --> pdb=" O   GLN E  27 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   HIS E  29 " --> pdb=" O   GLN A  26 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   GLN A  28 " --> pdb=" O   HIS E  29 " (cutoff:3.500A)
      removed outlier: 8.055A  pdb=" N   GLN E  31 " --> pdb=" O   GLN A  28 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   GLN A  30 " --> pdb=" O   GLN E  31 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   HIS E  33 " --> pdb=" O   GLN A  30 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   GLN A  32 " --> pdb=" O   HIS E  33 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   GLN E  35 " --> pdb=" O   GLN A  32 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   GLN A  34 " --> pdb=" O   GLN E  35 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   GLN E  37 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N  AHIS A  36 " --> pdb=" O   GLN E  37 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 44 through 51
      removed outlier: 6.145A  pdb=" N   GLN A  44 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   GLN D  47 " --> pdb=" O   GLN A  44 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   HIS A  46 " --> pdb=" O   GLN D  47 " (cutoff:3.500A)
      removed outlier: 8.422A  pdb=" N   GLN D  49 " --> pdb=" O   HIS A  46 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   HIS A  48 " --> pdb=" O   GLN D  49 " (cutoff:3.500A)
      removed outlier: 8.422A  pdb=" N   GLN D  51 " --> pdb=" O   HIS A  48 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   GLN A  50 " --> pdb=" O   GLN D  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 24 through 38
      removed outlier: 6.800A  pdb=" N   GLN B  37 " --> pdb=" O  AHIS F  36 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   GLN F  38 " --> pdb=" O   GLN B  37 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   LEU B  24 " --> pdb=" O   HIS G  25 " (cutoff:3.500A)
      removed outlier: 7.795A  pdb=" N   GLN G  27 " --> pdb=" O   LEU B  24 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   GLN B  26 " --> pdb=" O   GLN G  27 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   HIS G  29 " --> pdb=" O   GLN B  26 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   GLN B  28 " --> pdb=" O   HIS G  29 " (cutoff:3.500A)
      removed outlier: 8.060A  pdb=" N   GLN G  31 " --> pdb=" O   GLN B  28 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   GLN B  30 " --> pdb=" O   GLN G  31 " (cutoff:3.500A)
      removed outlier: 8.001A  pdb=" N   HIS G  33 " --> pdb=" O   GLN B  30 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   GLN B  32 " --> pdb=" O   HIS G  33 " (cutoff:3.500A)
      removed outlier: 8.175A  pdb=" N   GLN G  35 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   GLN B  34 " --> pdb=" O   GLN G  35 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   GLN G  37 " --> pdb=" O   GLN B  34 " (cutoff:3.500A)
      removed outlier: 7.681A  pdb=" N  AHIS B  36 " --> pdb=" O   GLN G  37 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'F' and resid 44 through 51
      removed outlier: 6.144A  pdb=" N   GLN B  44 " --> pdb=" O   LEU F  45 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   GLN F  47 " --> pdb=" O   GLN B  44 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   HIS B  46 " --> pdb=" O   GLN F  47 " (cutoff:3.500A)
      removed outlier: 8.238A  pdb=" N   GLN F  49 " --> pdb=" O   HIS B  46 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   HIS B  48 " --> pdb=" O   GLN F  49 " (cutoff:3.500A)
      removed outlier: 8.408A  pdb=" N   GLN F  51 " --> pdb=" O   HIS B  48 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   GLN B  50 " --> pdb=" O   GLN F  51 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 24 through 38
      removed outlier: 6.788A  pdb=" N   GLN C  37 " --> pdb=" O  AHIS H  36 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   GLN H  38 " --> pdb=" O   GLN C  37 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   LEU C  24 " --> pdb=" O   HIS I  25 " (cutoff:3.500A)
      removed outlier: 7.846A  pdb=" N   GLN I  27 " --> pdb=" O   LEU C  24 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   GLN C  26 " --> pdb=" O   GLN I  27 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   HIS I  29 " --> pdb=" O   GLN C  26 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   GLN C  28 " --> pdb=" O   HIS I  29 " (cutoff:3.500A)
      removed outlier: 8.071A  pdb=" N   GLN I  31 " --> pdb=" O   GLN C  28 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   GLN C  30 " --> pdb=" O   GLN I  31 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   HIS I  33 " --> pdb=" O   GLN C  30 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   GLN C  32 " --> pdb=" O   HIS I  33 " (cutoff:3.500A)
      removed outlier: 8.191A  pdb=" N   GLN I  35 " --> pdb=" O   GLN C  32 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   GLN C  34 " --> pdb=" O   GLN I  35 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   GLN I  37 " --> pdb=" O   GLN C  34 " (cutoff:3.500A)
      removed outlier: 7.686A  pdb=" N  AHIS C  36 " --> pdb=" O   GLN I  37 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 44 through 51
      removed outlier: 6.122A  pdb=" N   GLN C  44 " --> pdb=" O   LEU H  45 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   GLN H  47 " --> pdb=" O   GLN C  44 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   HIS C  46 " --> pdb=" O   GLN H  47 " (cutoff:3.500A)
      removed outlier: 8.249A  pdb=" N   GLN H  49 " --> pdb=" O   HIS C  46 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   HIS C  48 " --> pdb=" O   GLN H  49 " (cutoff:3.500A)
      removed outlier: 8.374A  pdb=" N   GLN H  51 " --> pdb=" O   HIS C  48 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   GLN C  50 " --> pdb=" O   GLN H  51 " (cutoff:3.500A)

    60 hydrogen bonds defined for protein.
    174 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: 0.54

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.21 -     1.28: 468
        1.28 -     1.35: 628
        1.35 -     1.42: 299
        1.42 -     1.49: 330
        1.49 -     1.55: 1119
  Bond restraints: 2844
  Sorted by residual:
  bond pdb=" CE1 HIS A  48 "
       pdb=" NE2 HIS A  48 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 9.26e+00
  bond pdb=" CE1 HIS F  48 "
       pdb=" NE2 HIS F  48 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 9.23e+00
  bond pdb=" CE1 HIS E  48 "
       pdb=" NE2 HIS E  48 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 8.79e+00
  bond pdb=" CE1 HIS F  39 "
       pdb=" NE2 HIS F  39 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.27e+00
  bond pdb=" CE1 HIS C  48 "
       pdb=" NE2 HIS C  48 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.25e+00
  ... (remaining 2839 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 3356
        1.45 -     2.89: 377
        2.89 -     4.34: 102
        4.34 -     5.78: 17
        5.78 -     7.23: 9
  Bond angle restraints: 3861
  Sorted by residual:
  angle pdb=" C   GLN H  31 "
        pdb=" CA  GLN H  31 "
        pdb=" CB  GLN H  31 "
      ideal   model   delta    sigma   weight residual
     109.35  116.58   -7.23 1.98e+00 2.55e-01 1.33e+01
  angle pdb=" C   GLN C  31 "
        pdb=" CA  GLN C  31 "
        pdb=" CB  GLN C  31 "
      ideal   model   delta    sigma   weight residual
     109.35  116.15   -6.80 1.98e+00 2.55e-01 1.18e+01
  angle pdb=" C   GLN G  31 "
        pdb=" CA  GLN G  31 "
        pdb=" CB  GLN G  31 "
      ideal   model   delta    sigma   weight residual
     109.35  116.01   -6.66 1.98e+00 2.55e-01 1.13e+01
  angle pdb=" C   GLN F  31 "
        pdb=" CA  GLN F  31 "
        pdb=" CB  GLN F  31 "
      ideal   model   delta    sigma   weight residual
     109.35  115.93   -6.58 1.98e+00 2.55e-01 1.10e+01
  angle pdb=" C   GLN D  31 "
        pdb=" CA  GLN D  31 "
        pdb=" CB  GLN D  31 "
      ideal   model   delta    sigma   weight residual
     109.35  115.72   -6.37 1.98e+00 2.55e-01 1.03e+01
  ... (remaining 3856 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    15.66: 1331
       15.66 -    31.30: 252
       31.30 -    46.94: 84
       46.94 -    62.59: 41
       62.59 -    78.23: 11
  Dihedral angle restraints: 1719
    sinusoidal: 783
      harmonic: 936
  Sorted by residual:
  dihedral pdb=" C   GLN H  31 "
           pdb=" N   GLN H  31 "
           pdb=" CA  GLN H  31 "
           pdb=" CB  GLN H  31 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.19   11.59     0      2.50e+00 1.60e-01 2.15e+01
  dihedral pdb=" C   GLN G  31 "
           pdb=" N   GLN G  31 "
           pdb=" CA  GLN G  31 "
           pdb=" CB  GLN G  31 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.59   10.99     0      2.50e+00 1.60e-01 1.93e+01
  dihedral pdb=" C   GLN C  31 "
           pdb=" N   GLN C  31 "
           pdb=" CA  GLN C  31 "
           pdb=" CB  GLN C  31 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.50   10.90     0      2.50e+00 1.60e-01 1.90e+01
  ... (remaining 1716 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 209
       0.091 -    0.181: 94
       0.181 -    0.271: 12
       0.271 -    0.361: 0
       0.361 -    0.452: 18
  Chirality restraints: 333
  Sorted by residual:
  chirality pdb=" CA  GLN G  31 "
            pdb=" N   GLN G  31 "
            pdb=" C   GLN G  31 "
            pdb=" CB  GLN G  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.10e+00
  chirality pdb=" CA  GLN H  31 "
            pdb=" N   GLN H  31 "
            pdb=" C   GLN H  31 "
            pdb=" CB  GLN H  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.87e+00
  chirality pdb=" CA  GLN D  27 "
            pdb=" N   GLN D  27 "
            pdb=" C   GLN D  27 "
            pdb=" CB  GLN D  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.47e+00
  ... (remaining 330 not shown)

  Planarity restraints: 576
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  45 "    0.020 2.00e-02 2.50e+03   3.98e-02 1.58e+01
        pdb=" C   LEU A  45 "   -0.069 2.00e-02 2.50e+03
        pdb=" O   LEU A  45 "    0.026 2.00e-02 2.50e+03
        pdb=" N   HIS A  46 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU G  45 "   -0.019 2.00e-02 2.50e+03   3.86e-02 1.49e+01
        pdb=" C   LEU G  45 "    0.067 2.00e-02 2.50e+03
        pdb=" O   LEU G  45 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   HIS G  46 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E  45 "    0.019 2.00e-02 2.50e+03   3.86e-02 1.49e+01
        pdb=" C   LEU E  45 "   -0.067 2.00e-02 2.50e+03
        pdb=" O   LEU E  45 "    0.025 2.00e-02 2.50e+03
        pdb=" N   HIS E  46 "    0.023 2.00e-02 2.50e+03
  ... (remaining 573 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 1153
        2.98 -     3.46: 2478
        3.46 -     3.94: 5600
        3.94 -     4.42: 5649
        4.42 -     4.90: 10376
  Nonbonded interactions: 25256
  Sorted by model distance:
  nonbonded pdb=" CD2AHIS C  36 "
            pdb=" ND1AHIS H  36 "
     model   vdw
     2.501 3.340
  nonbonded pdb=" CD2AHIS B  36 "
            pdb=" ND1AHIS F  36 "
     model   vdw
     2.538 3.340
  nonbonded pdb=" CD2AHIS A  36 "
            pdb=" ND1AHIS D  36 "
     model   vdw
     2.565 3.340
  nonbonded pdb=" ND1AHIS C  36 "
            pdb=" CD2AHIS I  36 "
     model   vdw
     2.591 3.340
  nonbonded pdb=" OE1 GLN A  34 "
            pdb=" NE2 GLN E  34 "
     model   vdw
     2.599 3.120
  ... (remaining 25251 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: 0.02
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'
}

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=0.50 max=1.00 mean=0.92
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:             0.460
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     11.350
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
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      :  0.011   0.047   2844  Z= 0.788
  Angle     :  1.136   7.229   3861  Z= 0.683
  Chirality :  0.128   0.452    333
  Planarity :  0.012   0.040    576
  Dihedral  : 20.445  78.235   1107
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 19.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Cbeta Deviations :  3.27 %
  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: -3.61 (0.21), residues: 306
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.75 (0.16), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.024   0.007   HIS C  46 

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

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

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.307 
Fit side-chains
REVERT: F   52 LEU cc_start: 0.9142 (mp) cc_final: 0.8853 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 1.5417
  time to fit residues: 34.8671
Evaluate side-chains
  13 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A  29 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  33 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  29 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
B  33 HIS    A
** B  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  36 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
B  38 GLN
** C  29 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  33 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN
** D  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  36 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
D  38 GLN
E  27 GLN
** E  29 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  33 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  36 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
G  25 HIS
** G  29 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
G  33 HIS    A
** G  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  36 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
H  38 GLN
I  27 GLN
** I  29 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  33 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
I  42 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.115838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.093113 restraints weight = 35444.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 3.71
r_work: 0.3168 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3155
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3155 r_free = 0.3155    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   2844  Z= 0.148
  Angle     :  0.435   5.490   3861  Z= 0.246
  Chirality :  0.033   0.087    333
  Planarity :  0.002   0.006    576
  Dihedral  :  4.366  11.724    324
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  7.84 %
    Favored  : 91.50 %
  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: -3.61 (0.21), residues: 306
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.75 (0.16), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS A  39 

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

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

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 0.281 
Fit side-chains
REVERT: C   35 GLN cc_start: 0.8562 (tt0) cc_final: 0.8298 (tt0)
REVERT: F   52 LEU cc_start: 0.9131 (mp) cc_final: 0.8775 (mt)
  outliers start: 2
  outliers final: 0
  residues processed: 36
  average time/residue: 1.6824
  time to fit residues: 61.8003
Evaluate side-chains
  26 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 2 optimal weight:    8.9990
   chunk 25 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A  29 HIS    A
A  33 HIS    B
** A  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
B  27 GLN
B  29 HIS    A
B  33 HIS    B
** B  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
C  33 HIS    A
C  35 GLN
C  36 HIS    A
D  31 GLN
** D  36 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
D  38 GLN
E  29 HIS    A
E  31 GLN
** E  33 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 HIS
G  27 GLN
G  29 HIS    A
** G  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
H  36 HIS    B
** I  29 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
I  33 HIS    A
I  36 HIS    A
** I  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.114650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.092345 restraints weight = 32630.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 3.69
r_work: 0.3191 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3162
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3162 r_free = 0.3162    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3160
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2844  Z= 0.179
  Angle     :  0.427   5.530   3861  Z= 0.240
  Chirality :  0.031   0.080    333
  Planarity :  0.001   0.005    576
  Dihedral  :  3.820   9.485    324
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  9.80 %
    Favored  : 88.24 %
  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: -3.72 (0.21), residues: 306
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.83 (0.16), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  46 

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

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

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.283 
Fit side-chains
REVERT: F   52 LEU cc_start: 0.9121 (mp) cc_final: 0.8763 (mt)
  outliers start: 6
  outliers final: 1
  residues processed: 33
  average time/residue: 1.8789
  time to fit residues: 63.2625
Evaluate side-chains
  27 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 26
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   27 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 18 optimal weight:    9.9990
   chunk 25 optimal weight:    0.8980
   chunk 3 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 4 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
A  27 GLN
** A  33 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 HIS
** B  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
B  48 HIS
C  27 GLN
** C  29 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  36 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
C  48 HIS
** D  36 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
E  27 GLN
** E  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  33 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
E  40 GLN
E  48 HIS
** F  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  27 GLN
** G  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
H  38 GLN
** I  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
I  40 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.103867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.084817 restraints weight = 42689.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 3.44
r_work: 0.3094 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3058
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3058 r_free = 0.3058    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3057 r_free = 0.3057    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3057
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.030   2844  Z= 0.392
  Angle     :  0.503   5.514   3861  Z= 0.281
  Chirality :  0.034   0.087    333
  Planarity :  0.002   0.006    576
  Dihedral  :  4.226   9.493    324
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  :  9.48 %
    Favored  : 88.24 %
  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: -3.78 (0.20), residues: 306
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.16), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS C  46 

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

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

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 26
  time to evaluate  : 0.298 
Fit side-chains
REVERT: F   52 LEU cc_start: 0.9102 (mp) cc_final: 0.8764 (mt)
  outliers start: 7
  outliers final: 1
  residues processed: 31
  average time/residue: 1.6945
  time to fit residues: 53.7717
Evaluate side-chains
  26 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 25
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   27 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 12 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9990
   chunk 3 optimal weight:   10.0000
   chunk 1 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  25 HIS
A  36 HIS    A
A  48 HIS
** B  35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
C  29 HIS    A
D  36 HIS    B
E  27 GLN
** E  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  33 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
E  36 HIS    A
** G  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  25 HIS
H  33 HIS    B
H  38 GLN
I  31 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.105577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.086966 restraints weight = 43513.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 3.43
r_work: 0.3150 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3140
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3140 r_free = 0.3140    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3140
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2844  Z= 0.247
  Angle     :  0.443   5.012   3861  Z= 0.249
  Chirality :  0.031   0.087    333
  Planarity :  0.001   0.006    576
  Dihedral  :  3.947   9.431    324
  Min Nonbonded Distance : 2.657

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 10.78 %
    Favored  : 87.58 %
  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: -3.78 (0.20), residues: 306
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.87 (0.16), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A  46 

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

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

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 25
  time to evaluate  : 0.282 
Fit side-chains
REVERT: F   27 GLN cc_start: 0.8611 (pt0) cc_final: 0.8352 (mt0)
REVERT: F   52 LEU cc_start: 0.9103 (mp) cc_final: 0.8736 (mt)
  outliers start: 5
  outliers final: 1
  residues processed: 29
  average time/residue: 1.7455
  time to fit residues: 51.7277
Evaluate side-chains
  25 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue   27 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 17 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  38 GLN
** B  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
C  27 GLN
E  27 GLN
** E  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  33 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  38 GLN
** I  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
I  48 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.103163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.084001 restraints weight = 36819.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 3.39
r_work: 0.3108 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3092
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3092
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.032   2844  Z= 0.467
  Angle     :  0.532   7.354   3861  Z= 0.294
  Chirality :  0.035   0.095    333
  Planarity :  0.002   0.007    576
  Dihedral  :  4.357  10.504    324
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 10.13 %
    Favored  : 87.25 %
  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: -3.82 (0.21), residues: 306
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.90 (0.16), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS C  46 

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

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

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 24
  time to evaluate  : 0.288 
Fit side-chains
REVERT: F   27 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8363 (mt0)
REVERT: F   52 LEU cc_start: 0.9116 (mp) cc_final: 0.8762 (mt)
  outliers start: 8
  outliers final: 2
  residues processed: 28
  average time/residue: 1.6572
  time to fit residues: 47.5075
Evaluate side-chains
  27 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain G residue   27 GLN
Chi-restraints excluded: chain H residue   27 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  33 HIS    A
** E  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  38 GLN
I  31 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.105027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.086100 restraints weight = 38611.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 3.40
r_work: 0.3138 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3136
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3136
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   2844  Z= 0.297
  Angle     :  0.468   6.436   3861  Z= 0.259
  Chirality :  0.032   0.111    333
  Planarity :  0.002   0.006    576
  Dihedral  :  4.104  10.865    324
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 11.44 %
    Favored  : 86.93 %
  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: -3.85 (0.20), residues: 306
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.93 (0.16), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C  46 

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

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

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 25
  time to evaluate  : 0.311 
Fit side-chains
REVERT: F   27 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8335 (mt0)
REVERT: F   52 LEU cc_start: 0.9113 (mp) cc_final: 0.8753 (mt)
  outliers start: 5
  outliers final: 3
  residues processed: 27
  average time/residue: 1.5834
  time to fit residues: 43.7608
Evaluate side-chains
  29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain G residue   27 GLN
Chi-restraints excluded: chain H residue   27 GLN
Chi-restraints excluded: chain I residue   31 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    1.9990
   chunk 15 optimal weight:    9.9990
   chunk 2 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   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  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
E  27 GLN
** E  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
F  48 HIS
** G  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  38 GLN
I  31 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.106160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.087345 restraints weight = 41825.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 3.42
r_work: 0.3159 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3150
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3150
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.2852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2844  Z= 0.241
  Angle     :  0.445   6.063   3861  Z= 0.247
  Chirality :  0.031   0.104    333
  Planarity :  0.001   0.006    576
  Dihedral  :  3.940  10.917    324
  Min Nonbonded Distance : 2.660

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 11.76 %
    Favored  : 86.60 %
  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: -3.84 (0.20), residues: 306
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.15), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A  39 

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

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

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 24
  time to evaluate  : 0.307 
Fit side-chains
REVERT: F   27 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8334 (mt0)
REVERT: F   52 LEU cc_start: 0.9111 (mp) cc_final: 0.8749 (mt)
  outliers start: 5
  outliers final: 2
  residues processed: 27
  average time/residue: 1.6416
  time to fit residues: 45.3888
Evaluate side-chains
  26 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 23
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain H residue   27 GLN
Chi-restraints excluded: chain I residue   31 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 17 optimal weight:    0.4980
   chunk 9 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 10 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:    8.9990
   chunk 16 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    1.8988

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

Flipped N/Q/H residues before XYZ refinement:
** B  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
E  27 GLN
** E  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  38 GLN
I  31 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.106804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.088171 restraints weight = 37863.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 3.38
r_work: 0.3165 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3160
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3160 r_free = 0.3160    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3160
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2844  Z= 0.213
  Angle     :  0.434   6.044   3861  Z= 0.241
  Chirality :  0.031   0.105    333
  Planarity :  0.001   0.006    576
  Dihedral  :  3.840  10.785    324
  Min Nonbonded Distance : 2.664

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 12.09 %
    Favored  : 86.60 %
  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: -3.85 (0.20), residues: 306
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.93 (0.15), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A  39 

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

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

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.311 
Fit side-chains
REVERT: F   27 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8337 (mt0)
REVERT: F   52 LEU cc_start: 0.9108 (mp) cc_final: 0.8741 (mt)
  outliers start: 4
  outliers final: 2
  residues processed: 28
  average time/residue: 1.6807
  time to fit residues: 48.1958
Evaluate side-chains
  28 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   27 GLN
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain H residue   35 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 2 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** B  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
E  27 GLN
** E  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.105827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.086998 restraints weight = 41564.400|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 3.44
r_work: 0.3138 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3128
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.2854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.020   2844  Z= 0.277
  Angle     :  0.452   5.979   3861  Z= 0.251
  Chirality :  0.031   0.100    333
  Planarity :  0.001   0.006    576
  Dihedral  :  3.910  10.702    324
  Min Nonbonded Distance : 2.659

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 12.09 %
    Favored  : 86.60 %
  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: -3.85 (0.20), residues: 306
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.15), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C  46 

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

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

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  612 Ramachandran restraints generated.
    306 Oldfield, 0 Emsley, 306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.317 
Fit side-chains
REVERT: F   27 GLN cc_start: 0.8541 (OUTLIER) cc_final: 0.8327 (mt0)
REVERT: F   52 LEU cc_start: 0.9112 (mp) cc_final: 0.8742 (mt)
  outliers start: 4
  outliers final: 1
  residues processed: 26
  average time/residue: 1.6494
  time to fit residues: 43.9429
Evaluate side-chains
  26 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   27 GLN
Chi-restraints excluded: chain H residue   27 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 10 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 18 optimal weight:    9.9990
   chunk 11 optimal weight:    0.0980
   chunk 1 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    2.8188

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

Flipped N/Q/H residues before XYZ refinement:
** B  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
E  27 GLN
** E  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  33 HIS    B ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  36 HIS    A ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.105343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.086426 restraints weight = 39534.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 3.40
r_work: 0.3120 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3128
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3128 r_free = 0.3128    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3127 r_free = 0.3127    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3127
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   2844  Z= 0.298
  Angle     :  0.461   6.096   3861  Z= 0.256
  Chirality :  0.031   0.099    333
  Planarity :  0.002   0.006    576
  Dihedral  :  3.981  10.608    324
  Min Nonbonded Distance : 2.656

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 12.09 %
    Favored  : 86.60 %
  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: -3.84 (0.20), residues: 306
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.16), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C  46 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2289.01 seconds
wall clock time: 41 minutes 19.50 seconds (2479.50 seconds total)