Starting phenix.real_space_refine
on Tue Mar  3 19:09:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ugo_64142/03_2026/9ugo_64142.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ugo_64142/03_2026/9ugo_64142.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ugo_64142/03_2026/9ugo_64142.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ugo_64142/03_2026/9ugo_64142.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ugo_64142/03_2026/9ugo_64142.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ugo_64142/03_2026/9ugo_64142.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      54      5.16       5
     C    5115      2.51       5
     N    1359      2.21       5
     O    1551      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8079
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1647
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1647
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 202}
    Chain: "B"
      Number of atoms: 1633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1633
          Classifications: {'peptide': 222}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 13, 'TRANS': 208}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 8
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 758
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 89}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "E"
      Number of atoms: 758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 758
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 89}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 1645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1645
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 202}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 1638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1638
          Classifications: {'peptide': 222}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 13, 'TRANS': 208}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.89, per 1000 atoms: 0.23
  Number of scatterers: 8079
  At special positions: 0
  Unit cell: (158.175, 84.645, 117.99, 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      54     16.00
     O    1551      8.00
     N    1359      7.00
     C    5115      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=13, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  23 " - pdb=" SG  CYS A  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 135 " - pdb=" SG  CYS A 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 215 " - pdb=" SG  CYS B 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 153 " - pdb=" SG  CYS B 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 107 " - pdb=" SG  CYS C 138 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 139 " - pdb=" SG  CYS E 139 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 107 " - pdb=" SG  CYS E 138 " distance=2.05
    Simple disulfide: pdb=" SG  CYS D  23 " - pdb=" SG  CYS D  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 135 " - pdb=" SG  CYS D 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 215 " - pdb=" SG  CYS F 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 153 " - pdb=" SG  CYS F 209 " distance=2.03

  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: 0.67
  Conformation dependent library (CDL) restraints added in 285.8 milliseconds
  

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1964

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 21 sheets defined
      11.9% alpha, 22.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 122 through 129
      removed outlier: 4.002A  pdb=" N   GLY A 129 " --> pdb=" O   GLN A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 188
    Processing helix  chain 'B' and resid 106 through 110
      removed outlier: 3.524A  pdb=" N   GLY B 109 " --> pdb=" O   GLY B 106 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLU B 110 " --> pdb=" O   SER B 107 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 106 through 110'
    Processing helix  chain 'B' and resid 169 through 171
      No H-bonds generated for 'chain 'B' and resid 169 through 171'
    Processing helix  chain 'C' and resid 74 through 101
      removed outlier: 3.504A  pdb=" N   ILE C  86 " --> pdb=" O   ILE C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 156 through 169
    Processing helix  chain 'E' and resid 74 through 101
      removed outlier: 3.504A  pdb=" N   ILE E  86 " --> pdb=" O   ILE E  82 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 156 through 169
    Processing helix  chain 'D' and resid 122 through 128
    Processing helix  chain 'D' and resid 184 through 189
    Processing helix  chain 'F' and resid 106 through 110
      removed outlier: 4.166A  pdb=" N   GLU F 110 " --> pdb=" O   SER F 107 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 169 through 171
      No H-bonds generated for 'chain 'F' and resid 169 through 171'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13
      removed outlier: 6.651A  pdb=" N   TRP A  35 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 117 through 119
      removed outlier: 3.855A  pdb=" N   VAL A 134 " --> pdb=" O   PHE A 119 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 151
      removed outlier: 3.677A  pdb=" N   LYS A 146 " --> pdb=" O   THR A 198 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   TYR A 193 " --> pdb=" O   PHE A 210 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   VAL A 197 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   VAL A 206 " --> pdb=" O   VAL A 197 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 17 through 18
    Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 47
    Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 51
    Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 71
      removed outlier: 3.746A  pdb=" N   THR B  71 " --> pdb=" O   TYR B  80 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 133 through 137
      removed outlier: 3.581A  pdb=" N   GLY B 152 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ALA B 149 " --> pdb=" O   VAL B 197 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ASP B 157 " --> pdb=" O   TYR B 189 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   TYR B 189 " --> pdb=" O   ASP B 157 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 133 through 137
      removed outlier: 3.581A  pdb=" N   GLY B 152 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ALA B 149 " --> pdb=" O   VAL B 197 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ASP B 157 " --> pdb=" O   TYR B 189 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   TYR B 189 " --> pdb=" O   ASP B 157 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 164 through 167
      removed outlier: 3.589A  pdb=" N   LYS B 222 " --> pdb=" O   CYS B 209 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL B 211 " --> pdb=" O   VAL B 220 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 19 through 20
    Processing sheet with id=AB3, first strand: chain 'D' and resid 45 through 49
      removed outlier: 6.722A  pdb=" N   TRP D  35 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 117 through 119
      removed outlier: 3.814A  pdb=" N   VAL D 134 " --> pdb=" O   PHE D 119 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL D 133 " --> pdb=" O   LEU D 180 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 146 through 151
      removed outlier: 3.833A  pdb=" N   LYS D 146 " --> pdb=" O   THR D 198 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   TYR D 193 " --> pdb=" O   PHE D 210 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL D 197 " --> pdb=" O   VAL D 206 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   VAL D 206 " --> pdb=" O   VAL D 197 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 17 through 18
    Processing sheet with id=AB7, first strand: chain 'F' and resid 45 through 47
      removed outlier: 3.571A  pdb=" N   VAL F  97 " --> pdb=" O   ASN F  35 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL F  93 " --> pdb=" O   GLN F  39 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 50 through 51
    Processing sheet with id=AB9, first strand: chain 'F' and resid 70 through 71
      removed outlier: 3.867A  pdb=" N   THR F  71 " --> pdb=" O   TYR F  80 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 133 through 137
      removed outlier: 3.916A  pdb=" N   GLY F 152 " --> pdb=" O   LEU F 137 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   TYR F 189 " --> pdb=" O   ASP F 157 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   HIS F 177 " --> pdb=" O   VAL F 194 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 133 through 137
      removed outlier: 3.916A  pdb=" N   GLY F 152 " --> pdb=" O   LEU F 137 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   TYR F 189 " --> pdb=" O   ASP F 157 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER F 190 " --> pdb=" O   VAL F 182 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 166 through 167
      removed outlier: 3.771A  pdb=" N   ASN F 210 " --> pdb=" O   SER F 166 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LYS F 222 " --> pdb=" O   CYS F 209 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL F 211 " --> pdb=" O   VAL F 220 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   VAL F 220 " --> pdb=" O   VAL F 211 " (cutoff:3.500A)

    241 hydrogen bonds defined for protein.
    606 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: 1.09

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2509
        1.34 -     1.46: 1552
        1.46 -     1.58: 4152
        1.58 -     1.70: 0
        1.70 -     1.82: 68
  Bond restraints: 8281
  Sorted by residual:
  bond pdb=" N   CYS C 137 "
       pdb=" CA  CYS C 137 "
    ideal  model  delta    sigma   weight residual
    1.455  1.501 -0.047 1.26e-02 6.30e+03 1.38e+01
  bond pdb=" N   ILE C 150 "
       pdb=" CA  ILE C 150 "
    ideal  model  delta    sigma   weight residual
    1.461  1.506 -0.045 1.23e-02 6.61e+03 1.34e+01
  bond pdb=" N   ILE E 150 "
       pdb=" CA  ILE E 150 "
    ideal  model  delta    sigma   weight residual
    1.461  1.506 -0.044 1.23e-02 6.61e+03 1.30e+01
  bond pdb=" N   THR C 123 "
       pdb=" CA  THR C 123 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.00e-02 1.00e+04 9.15e+00
  bond pdb=" N   CYS C 147 "
       pdb=" CA  CYS C 147 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.16e-02 7.43e+03 8.75e+00
  ... (remaining 8276 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 10916
        1.92 -     3.83: 287
        3.83 -     5.75: 51
        5.75 -     7.67: 10
        7.67 -     9.58: 4
  Bond angle restraints: 11268
  Sorted by residual:
  angle pdb=" O   GLY E 119 "
        pdb=" C   GLY E 119 "
        pdb=" N   PRO E 120 "
      ideal   model   delta    sigma   weight residual
     121.07  119.08    1.99 3.60e-01 7.72e+00 3.06e+01
  angle pdb=" CA  CYS C 149 "
        pdb=" C   CYS C 149 "
        pdb=" O   CYS C 149 "
      ideal   model   delta    sigma   weight residual
     120.51  112.67    7.84 1.43e+00 4.89e-01 3.01e+01
  angle pdb=" C   CYS E 149 "
        pdb=" N   ILE E 150 "
        pdb=" CA  ILE E 150 "
      ideal   model   delta    sigma   weight residual
     122.13  131.71   -9.58 1.85e+00 2.92e-01 2.68e+01
  angle pdb=" CA  CYS C 147 "
        pdb=" C   CYS C 147 "
        pdb=" O   CYS C 147 "
      ideal   model   delta    sigma   weight residual
     121.07  115.94    5.13 1.10e+00 8.26e-01 2.17e+01
  angle pdb=" N   ILE C 150 "
        pdb=" CA  ILE C 150 "
        pdb=" CB  ILE C 150 "
      ideal   model   delta    sigma   weight residual
     111.21  117.35   -6.14 1.40e+00 5.10e-01 1.92e+01
  ... (remaining 11263 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 4445
       17.90 -    35.80: 391
       35.80 -    53.70: 78
       53.70 -    71.60: 22
       71.60 -    89.50: 13
  Dihedral angle restraints: 4949
    sinusoidal: 1883
      harmonic: 3066
  Sorted by residual:
  dihedral pdb=" CB  CYS F  22 "
           pdb=" SG  CYS F  22 "
           pdb=" SG  CYS F  96 "
           pdb=" CB  CYS F  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -174.28   88.28     1      1.00e+01 1.00e-02 9.31e+01
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  96 "
           pdb=" CB  CYS B  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -173.35   87.35     1      1.00e+01 1.00e-02 9.16e+01
  dihedral pdb=" CB  CYS A  23 "
           pdb=" SG  CYS A  23 "
           pdb=" SG  CYS A  88 "
           pdb=" CB  CYS A  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -172.80   86.80     1      1.00e+01 1.00e-02 9.06e+01
  ... (remaining 4946 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1016
       0.052 -    0.103: 178
       0.103 -    0.155: 64
       0.155 -    0.207: 4
       0.207 -    0.259: 3
  Chirality restraints: 1265
  Sorted by residual:
  chirality pdb=" CB  ILE C 150 "
            pdb=" CA  ILE C 150 "
            pdb=" CG1 ILE C 150 "
            pdb=" CG2 ILE C 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" CB  ILE E 150 "
            pdb=" CA  ILE E 150 "
            pdb=" CG1 ILE E 150 "
            pdb=" CG2 ILE E 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CA  CYS E 138 "
            pdb=" N   CYS E 138 "
            pdb=" C   CYS E 138 "
            pdb=" CB  CYS E 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.45e+00
  ... (remaining 1262 not shown)

  Planarity restraints: 1438
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 141 "   -0.068 5.00e-02 4.00e+02   1.04e-01 1.73e+01
        pdb=" N   PRO C 142 "    0.180 5.00e-02 4.00e+02
        pdb=" CA  PRO C 142 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO C 142 "   -0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 141 "   -0.068 5.00e-02 4.00e+02   1.04e-01 1.72e+01
        pdb=" N   PRO E 142 "    0.179 5.00e-02 4.00e+02
        pdb=" CA  PRO E 142 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO E 142 "   -0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A  95 "    0.065 5.00e-02 4.00e+02   9.85e-02 1.55e+01
        pdb=" N   PRO A  96 "   -0.170 5.00e-02 4.00e+02
        pdb=" CA  PRO A  96 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO A  96 "    0.056 5.00e-02 4.00e+02
  ... (remaining 1435 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1329
        2.77 -     3.30: 7437
        3.30 -     3.84: 12716
        3.84 -     4.37: 14062
        4.37 -     4.90: 24332
  Nonbonded interactions: 59876
  Sorted by model distance:
  nonbonded pdb=" O   GLN A 125 "
            pdb=" OG  SER A 128 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   GLN D 125 "
            pdb=" OG  SER D 128 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OE2 GLU D 162 "
            pdb=" OG  SER D 178 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OD2 ASP A 152 "
            pdb=" ND1 HIS A 190 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" SG  CYS C 137 "
            pdb=" CB  CYS E 139 "
     model   vdw
     2.344 3.800
  ... (remaining 59871 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' and (resid 1 through 55 or (resid 56 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 57 through 215))
  selection = chain 'D'
}
ncs_group {
  reference = (chain 'B' and (resid 8 through 196 or (resid 197 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 198 or (resid 199 through 202 and (name N or \ 
 name CA or name C or name O or name CB )) or resid 203 through 229))
  selection = (chain 'F' and (resid 8 through 199 or (resid 200 through 202 and (name N or nam \ 
e CA or name C or name O or name CB )) or resid 203 through 226 or (resid 227 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 228 through 229) \ 
)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.690
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
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      :  0.004   0.049   8294  Z= 0.236
  Angle     :  0.735   9.585  11294  Z= 0.421
  Chirality :  0.047   0.259   1265
  Planarity :  0.007   0.104   1438
  Dihedral  : 14.486  89.496   2946
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.38 %
    Allowed  :  9.07 %
    Favored  : 90.55 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  0.56 %
    Favored  : 97.88 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.27), residues: 1058
  helix: -0.05 (0.43), residues: 128
  sheet: -0.46 (0.30), residues: 348
  loop : -1.81 (0.27), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  24 
 TYR   0.022   0.001   TYR D  49 
 PHE   0.013   0.001   PHE A  97 
 TRP   0.008   0.001   TRP C 165 
 HIS   0.001   0.000   HIS D  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 8281)
  covalent geometry    : angle       0.73266 (11268)
  SS BOND              : bond        0.00563 (   13)
  SS BOND              : angle       1.31338 (   26)
  hydrogen bonds       : bond        0.26675 (  219)
  hydrogen bonds       : angle       9.46492 (  606)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 156
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A   90 GLN cc_start: 0.7689 (pp30) cc_final: 0.7357 (pp30)
REVERT: C  123 THR cc_start: 0.5489 (OUTLIER) cc_final: 0.4989 (p)
REVERT: E  147 CYS cc_start: 0.5185 (OUTLIER) cc_final: 0.4685 (p)
REVERT: D   29 VAL cc_start: 0.7833 (t) cc_final: 0.7365 (p)
  outliers start: 14
  outliers final: 6
  residues processed: 166
  average time/residue: 0.1089
  time to fit residues: 23.2977
Evaluate side-chains
  143 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 135
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain E residue  123 THR
Chi-restraints excluded: chain E residue  137 CYS
Chi-restraints excluded: chain E residue  147 CYS
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  150 ILE
Chi-restraints excluded: chain F residue   31 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    0.7980
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    5.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
E 146 ASN
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.189163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.173212 restraints weight = 11661.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.171694 restraints weight = 23954.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.162486 restraints weight = 26564.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.160612 restraints weight = 24740.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.159150 restraints weight = 20412.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8294  Z= 0.142
  Angle     :  0.680   9.776  11294  Z= 0.342
  Chirality :  0.047   0.333   1265
  Planarity :  0.007   0.075   1438
  Dihedral  :  6.329  87.209   1153
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  9.92 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  8.80 %
    Favored  : 89.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.50 (0.27), residues: 1058
  helix:  1.11 (0.44), residues: 128
  sheet: -0.48 (0.29), residues: 348
  loop : -1.87 (0.27), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  24 
 TYR   0.035   0.001   TYR A  49 
 PHE   0.014   0.001   PHE B  64 
 TRP   0.019   0.001   TRP C 165 
 HIS   0.003   0.001   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8281)
  covalent geometry    : angle       0.67871 (11268)
  SS BOND              : bond        0.00220 (   13)
  SS BOND              : angle       1.02470 (   26)
  hydrogen bonds       : bond        0.04794 (  219)
  hydrogen bonds       : angle       6.27808 (  606)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 149
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A   27 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7418 (pt0)
REVERT: A   90 GLN cc_start: 0.8243 (pp30) cc_final: 0.7657 (pp30)
REVERT: B  163 VAL cc_start: 0.7567 (t) cc_final: 0.7268 (t)
REVERT: E  147 CYS cc_start: 0.5402 (OUTLIER) cc_final: 0.4555 (p)
REVERT: D   29 VAL cc_start: 0.7867 (t) cc_final: 0.7431 (p)
REVERT: D   90 GLN cc_start: 0.8490 (pp30) cc_final: 0.8191 (pp30)
REVERT: D  109 ARG cc_start: 0.5288 (ptt180) cc_final: 0.5050 (ptt90)
  outliers start: 16
  outliers final: 8
  residues processed: 160
  average time/residue: 0.1119
  time to fit residues: 22.7812
Evaluate side-chains
  139 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain E residue  123 THR
Chi-restraints excluded: chain E residue  137 CYS
Chi-restraints excluded: chain E residue  147 CYS
Chi-restraints excluded: chain E residue  148 THR
Chi-restraints excluded: chain E residue  150 ILE
Chi-restraints excluded: chain E residue  170 PHE
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain F residue  123 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 100 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 12 optimal weight:    8.9990
   chunk 11 optimal weight:   10.0000
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 138 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.181905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.164948 restraints weight = 11672.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.162721 restraints weight = 25938.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.150533 restraints weight = 28425.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.147545 restraints weight = 27168.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.146957 restraints weight = 18225.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8294  Z= 0.182
  Angle     :  0.694   9.299  11294  Z= 0.354
  Chirality :  0.046   0.185   1265
  Planarity :  0.007   0.077   1438
  Dihedral  :  6.286  85.537   1151
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 10.40 %
    Favored  : 89.41 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.69 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.55 (0.26), residues: 1058
  helix:  1.32 (0.43), residues: 124
  sheet: -0.61 (0.29), residues: 344
  loop : -1.87 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 169 
 TYR   0.039   0.002   TYR A  49 
 PHE   0.015   0.002   PHE B  64 
 TRP   0.023   0.002   TRP E 165 
 HIS   0.004   0.001   HIS D  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 8281)
  covalent geometry    : angle       0.69155 (11268)
  SS BOND              : bond        0.00257 (   13)
  SS BOND              : angle       1.46704 (   26)
  hydrogen bonds       : bond        0.04553 (  219)
  hydrogen bonds       : angle       5.83993 (  606)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 GLN cc_start: 0.8668 (pp30) cc_final: 0.7988 (pp30)
REVERT: D   29 VAL cc_start: 0.8076 (t) cc_final: 0.7657 (p)
REVERT: D   31 ASN cc_start: 0.7653 (t0) cc_final: 0.7428 (t0)
REVERT: D   90 GLN cc_start: 0.8666 (pp30) cc_final: 0.8385 (pp30)
REVERT: F   43 GLN cc_start: 0.8679 (mp10) cc_final: 0.8247 (mp10)
  outliers start: 18
  outliers final: 13
  residues processed: 151
  average time/residue: 0.1262
  time to fit residues: 24.0318
Evaluate side-chains
  145 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  212 ASN
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain E residue  123 THR
Chi-restraints excluded: chain E residue  137 CYS
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain F residue  114 ASP
Chi-restraints excluded: chain F residue  120 THR
Chi-restraints excluded: chain F residue  123 ILE
Chi-restraints excluded: chain F residue  155 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 39 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 66 optimal weight:    7.9990
   chunk 95 optimal weight:   30.0000
   chunk 85 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 71 optimal weight:    5.9990
   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  37 GLN
A 138 ASN
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  37 GLN
** D  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.177647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.155192 restraints weight = 11914.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.144640 restraints weight = 27677.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.139110 restraints weight = 24573.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.139115 restraints weight = 19916.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.138565 restraints weight = 17029.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   8294  Z= 0.210
  Angle     :  0.717   8.373  11294  Z= 0.370
  Chirality :  0.048   0.199   1265
  Planarity :  0.007   0.071   1438
  Dihedral  :  6.011  82.595   1147
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 11.53 %
    Favored  : 88.19 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.70 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.76 (0.26), residues: 1058
  helix:  1.15 (0.42), residues: 124
  sheet: -0.75 (0.30), residues: 314
  loop : -1.96 (0.25), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 169 
 TYR   0.042   0.002   TYR A  49 
 PHE   0.013   0.002   PHE D  62 
 TRP   0.025   0.002   TRP C 165 
 HIS   0.004   0.001   HIS D  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 ( 8281)
  covalent geometry    : angle       0.71474 (11268)
  SS BOND              : bond        0.00278 (   13)
  SS BOND              : angle       1.31222 (   26)
  hydrogen bonds       : bond        0.04396 (  219)
  hydrogen bonds       : angle       5.60432 (  606)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 129
  time to evaluate  : 0.310 
Fit side-chains
REVERT: E  121 CYS cc_start: 0.7638 (t) cc_final: 0.7302 (t)
REVERT: D   29 VAL cc_start: 0.8359 (t) cc_final: 0.7971 (p)
REVERT: D   31 ASN cc_start: 0.7979 (t0) cc_final: 0.7716 (t0)
REVERT: D   39 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8497 (mtmm)
REVERT: D   90 GLN cc_start: 0.8843 (pp30) cc_final: 0.8600 (pp30)
REVERT: D  109 ARG cc_start: 0.6311 (ptt180) cc_final: 0.6027 (ptt90)
REVERT: F   43 GLN cc_start: 0.8774 (mp10) cc_final: 0.8239 (mp10)
  outliers start: 24
  outliers final: 18
  residues processed: 146
  average time/residue: 0.1250
  time to fit residues: 23.1959
Evaluate side-chains
  146 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   32 TYR
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain E residue  123 THR
Chi-restraints excluded: chain E residue  137 CYS
Chi-restraints excluded: chain D residue   39 LYS
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain F residue   32 TYR
Chi-restraints excluded: chain F residue  114 ASP
Chi-restraints excluded: chain F residue  120 THR
Chi-restraints excluded: chain F residue  123 ILE
Chi-restraints excluded: chain F residue  155 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 78 optimal weight:    1.9990
   chunk 100 optimal weight:    9.9990
   chunk 7 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 87 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 94 optimal weight:    7.9990
   chunk 56 optimal weight:   10.0000
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 HIS ** 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 = 0.4002 r_free = 0.4002 target = 0.175477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.151544 restraints weight = 11819.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.146817 restraints weight = 28441.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.140554 restraints weight = 19606.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.139505 restraints weight = 24797.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.140445 restraints weight = 18110.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   8294  Z= 0.233
  Angle     :  0.735   8.266  11294  Z= 0.380
  Chirality :  0.048   0.197   1265
  Planarity :  0.007   0.063   1438
  Dihedral  :  6.135  78.863   1147
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 13.04 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 17.71 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.94 (0.26), residues: 1058
  helix:  0.96 (0.43), residues: 124
  sheet: -0.82 (0.30), residues: 312
  loop : -2.11 (0.25), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  18 
 TYR   0.037   0.002   TYR A  49 
 PHE   0.018   0.002   PHE B  64 
 TRP   0.022   0.002   TRP C 165 
 HIS   0.005   0.001   HIS D  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00557 ( 8281)
  covalent geometry    : angle       0.73297 (11268)
  SS BOND              : bond        0.00340 (   13)
  SS BOND              : angle       1.24763 (   26)
  hydrogen bonds       : bond        0.04398 (  219)
  hydrogen bonds       : angle       5.50576 (  606)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A   31 ASN cc_start: 0.7583 (t0) cc_final: 0.7258 (t0)
REVERT: A   54 ARG cc_start: 0.8151 (ptt180) cc_final: 0.7911 (ptt180)
REVERT: B   48 MET cc_start: 0.8232 (mmm) cc_final: 0.7564 (mtp)
REVERT: E  121 CYS cc_start: 0.7441 (t) cc_final: 0.7130 (t)
REVERT: D   31 ASN cc_start: 0.8092 (t0) cc_final: 0.7811 (t0)
REVERT: D   39 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8741 (mtmm)
REVERT: D   90 GLN cc_start: 0.8908 (pp30) cc_final: 0.8633 (pp30)
REVERT: F   43 GLN cc_start: 0.8780 (mp10) cc_final: 0.8235 (mp10)
REVERT: F   80 TYR cc_start: 0.7267 (m-10) cc_final: 0.6900 (m-10)
  outliers start: 26
  outliers final: 22
  residues processed: 140
  average time/residue: 0.1273
  time to fit residues: 22.4750
Evaluate side-chains
  141 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   53 THR
Chi-restraints excluded: chain B residue   32 TYR
Chi-restraints excluded: chain B residue  114 ASP
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain E residue  123 THR
Chi-restraints excluded: chain E residue  133 MET
Chi-restraints excluded: chain E residue  137 CYS
Chi-restraints excluded: chain D residue   39 LYS
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain F residue   32 TYR
Chi-restraints excluded: chain F residue  114 ASP
Chi-restraints excluded: chain F residue  120 THR
Chi-restraints excluded: chain F residue  123 ILE
Chi-restraints excluded: chain F residue  154 LEU
Chi-restraints excluded: chain F residue  155 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 70 optimal weight:    0.6980
   chunk 16 optimal weight:    7.9990
   chunk 88 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0370
   chunk 26 optimal weight:    0.9990
   chunk 98 optimal weight:    2.9990
   chunk 91 optimal weight:    0.5980
   chunk 47 optimal weight:    8.9990
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 HIS ** 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 = 0.4056 r_free = 0.4056 target = 0.180526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.162981 restraints weight = 11750.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.160648 restraints weight = 24204.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.157670 restraints weight = 26928.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.155905 restraints weight = 32639.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.155605 restraints weight = 30931.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.2996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8294  Z= 0.123
  Angle     :  0.672   8.429  11294  Z= 0.340
  Chirality :  0.046   0.157   1265
  Planarity :  0.006   0.061   1438
  Dihedral  :  5.736  76.062   1147
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  9.55 %
    Favored  : 90.17 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 20.27 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.27), residues: 1058
  helix:  1.70 (0.45), residues: 124
  sheet: -0.63 (0.29), residues: 348
  loop : -2.04 (0.26), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 109 
 TYR   0.030   0.001   TYR A  49 
 PHE   0.009   0.001   PHE F  64 
 TRP   0.012   0.001   TRP C 165 
 HIS   0.002   0.001   HIS D  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 8281)
  covalent geometry    : angle       0.67004 (11268)
  SS BOND              : bond        0.00259 (   13)
  SS BOND              : angle       1.35578 (   26)
  hydrogen bonds       : bond        0.03236 (  219)
  hydrogen bonds       : angle       5.19037 (  606)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.283 
Fit side-chains
REVERT: A   27 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7383 (pt0)
REVERT: A   31 ASN cc_start: 0.7405 (t0) cc_final: 0.7088 (t0)
REVERT: A   90 GLN cc_start: 0.8880 (pp30) cc_final: 0.8197 (pp30)
REVERT: B   48 MET cc_start: 0.8249 (mmm) cc_final: 0.7731 (mtp)
REVERT: E  121 CYS cc_start: 0.7157 (t) cc_final: 0.6856 (t)
REVERT: D   31 ASN cc_start: 0.7867 (t0) cc_final: 0.7609 (t0)
REVERT: D   39 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8666 (mtmm)
REVERT: D   90 GLN cc_start: 0.8664 (pp30) cc_final: 0.8349 (pp30)
REVERT: D  104 LYS cc_start: 0.7964 (tttm) cc_final: 0.7764 (tptt)
REVERT: F   43 GLN cc_start: 0.8628 (mp10) cc_final: 0.8184 (mp10)
  outliers start: 18
  outliers final: 12
  residues processed: 143
  average time/residue: 0.1333
  time to fit residues: 23.7853
Evaluate side-chains
  132 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain D residue   39 LYS
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain D residue  147 VAL
Chi-restraints excluded: chain F residue  123 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 32 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9990
   chunk 96 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 76 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 HIS ** 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 = 0.4066 r_free = 0.4066 target = 0.181570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.163844 restraints weight = 11688.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.162104 restraints weight = 22559.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.161174 restraints weight = 24028.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.159886 restraints weight = 20871.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.159222 restraints weight = 22835.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start:          0.3105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8294  Z= 0.138
  Angle     :  0.712   9.218  11294  Z= 0.353
  Chirality :  0.046   0.158   1265
  Planarity :  0.006   0.060   1438
  Dihedral  :  5.417  72.912   1145
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 10.96 %
    Favored  : 88.85 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 21.38 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.27), residues: 1058
  helix:  1.72 (0.45), residues: 124
  sheet: -0.64 (0.29), residues: 354
  loop : -1.98 (0.27), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  18 
 TYR   0.029   0.001   TYR A  49 
 PHE   0.027   0.001   PHE D 140 
 TRP   0.016   0.001   TRP C 165 
 HIS   0.003   0.001   HIS D  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8281)
  covalent geometry    : angle       0.71041 (11268)
  SS BOND              : bond        0.00247 (   13)
  SS BOND              : angle       1.15221 (   26)
  hydrogen bonds       : bond        0.03326 (  219)
  hydrogen bonds       : angle       5.05120 (  606)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A   27 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7386 (pt0)
REVERT: A   31 ASN cc_start: 0.7417 (t0) cc_final: 0.7089 (t0)
REVERT: A   90 GLN cc_start: 0.8920 (pp30) cc_final: 0.8207 (pp30)
REVERT: E  121 CYS cc_start: 0.7098 (t) cc_final: 0.6842 (t)
REVERT: D   29 VAL cc_start: 0.8267 (t) cc_final: 0.7924 (p)
REVERT: D   31 ASN cc_start: 0.7865 (t0) cc_final: 0.7647 (t0)
REVERT: D   39 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8331 (mtmm)
REVERT: D   90 GLN cc_start: 0.8682 (pp30) cc_final: 0.8443 (pp30)
REVERT: F   43 GLN cc_start: 0.8636 (mp10) cc_final: 0.8197 (mp10)
REVERT: F   48 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.6800 (mpp)
  outliers start: 17
  outliers final: 11
  residues processed: 134
  average time/residue: 0.1224
  time to fit residues: 20.8248
Evaluate side-chains
  128 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain D residue   39 LYS
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain F residue   48 MET
Chi-restraints excluded: chain F residue  123 ILE
Chi-restraints excluded: chain F residue  154 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 102 optimal weight:    7.9990
   chunk 69 optimal weight:    3.9990
   chunk 95 optimal weight:    0.7980
   chunk 103 optimal weight:    5.9990
   chunk 93 optimal weight:    6.9990
   chunk 6 optimal weight:   10.0000
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 200 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 = 0.4030 r_free = 0.4030 target = 0.177833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.159467 restraints weight = 11727.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.157742 restraints weight = 27632.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.147509 restraints weight = 27492.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.142714 restraints weight = 24541.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.141784 restraints weight = 19936.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.3289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8294  Z= 0.167
  Angle     :  0.706   9.321  11294  Z= 0.357
  Chirality :  0.047   0.173   1265
  Planarity :  0.007   0.062   1438
  Dihedral  :  5.475  67.739   1145
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 11.53 %
    Favored  : 88.19 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 21.94 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.58 (0.27), residues: 1058
  helix:  1.52 (0.44), residues: 124
  sheet: -0.59 (0.29), residues: 358
  loop : -2.00 (0.27), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  18 
 TYR   0.029   0.002   TYR A  49 
 PHE   0.014   0.002   PHE D 140 
 TRP   0.023   0.001   TRP C 165 
 HIS   0.003   0.001   HIS D  92 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 8281)
  covalent geometry    : angle       0.70478 (11268)
  SS BOND              : bond        0.00279 (   13)
  SS BOND              : angle       1.10156 (   26)
  hydrogen bonds       : bond        0.03492 (  219)
  hydrogen bonds       : angle       5.05273 (  606)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A   31 ASN cc_start: 0.7614 (t0) cc_final: 0.7291 (t0)
REVERT: A   90 GLN cc_start: 0.8983 (pp30) cc_final: 0.8290 (pp30)
REVERT: B   62 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7543 (tt0)
REVERT: E  121 CYS cc_start: 0.7520 (t) cc_final: 0.7226 (t)
REVERT: D   29 VAL cc_start: 0.8337 (t) cc_final: 0.7993 (p)
REVERT: D   31 ASN cc_start: 0.8005 (t0) cc_final: 0.7761 (t0)
REVERT: D   39 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8422 (mtmm)
REVERT: D   90 GLN cc_start: 0.8673 (pp30) cc_final: 0.8412 (pp30)
REVERT: F   43 GLN cc_start: 0.8690 (mp10) cc_final: 0.8037 (mp10)
REVERT: F   48 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.6916 (mpp)
  outliers start: 19
  outliers final: 13
  residues processed: 127
  average time/residue: 0.1306
  time to fit residues: 20.9426
Evaluate side-chains
  128 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain E residue  137 CYS
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain D residue   39 LYS
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain F residue   48 MET
Chi-restraints excluded: chain F residue  123 ILE
Chi-restraints excluded: chain F residue  154 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 36 optimal weight:    6.9990
   chunk 94 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 56 optimal weight:   20.0000
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 HIS ** 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 = 0.4030 r_free = 0.4030 target = 0.177832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.159224 restraints weight = 11702.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.158468 restraints weight = 27956.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.147163 restraints weight = 26070.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.142075 restraints weight = 20591.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.141679 restraints weight = 18217.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.3433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8294  Z= 0.163
  Angle     :  0.717  11.057  11294  Z= 0.360
  Chirality :  0.047   0.168   1265
  Planarity :  0.007   0.060   1438
  Dihedral  :  5.429  61.823   1145
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 11.44 %
    Favored  : 88.28 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 21.83 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.27), residues: 1058
  helix:  1.53 (0.44), residues: 124
  sheet: -0.31 (0.31), residues: 320
  loop : -1.97 (0.25), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  18 
 TYR   0.029   0.002   TYR A  49 
 PHE   0.018   0.001   PHE B  64 
 TRP   0.018   0.001   TRP C 165 
 HIS   0.005   0.001   HIS D 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 8281)
  covalent geometry    : angle       0.71628 (11268)
  SS BOND              : bond        0.00280 (   13)
  SS BOND              : angle       0.98733 (   26)
  hydrogen bonds       : bond        0.03428 (  219)
  hydrogen bonds       : angle       5.04239 (  606)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A   27 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7522 (pt0)
REVERT: A   31 ASN cc_start: 0.7563 (t0) cc_final: 0.7251 (t0)
REVERT: A   90 GLN cc_start: 0.8984 (pp30) cc_final: 0.8308 (pp30)
REVERT: B   48 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7477 (mtp)
REVERT: B   62 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7624 (tt0)
REVERT: E  121 CYS cc_start: 0.7505 (t) cc_final: 0.7224 (t)
REVERT: D   29 VAL cc_start: 0.8336 (t) cc_final: 0.7988 (p)
REVERT: D   31 ASN cc_start: 0.7950 (t0) cc_final: 0.7734 (t0)
REVERT: D   39 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8417 (mtmm)
REVERT: D   90 GLN cc_start: 0.8709 (pp30) cc_final: 0.8441 (pp30)
REVERT: F   43 GLN cc_start: 0.8649 (mp10) cc_final: 0.8014 (mp10)
REVERT: F   48 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.6943 (mpp)
REVERT: F   80 TYR cc_start: 0.7217 (m-10) cc_final: 0.6867 (m-10)
  outliers start: 22
  outliers final: 14
  residues processed: 132
  average time/residue: 0.1267
  time to fit residues: 21.2855
Evaluate side-chains
  127 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   48 MET
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain D residue   39 LYS
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain F residue   48 MET
Chi-restraints excluded: chain F residue  123 ILE
Chi-restraints excluded: chain F residue  154 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 63 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 12 optimal weight:    0.2980
   chunk 18 optimal weight:    7.9990
   chunk 99 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 39 optimal weight:    5.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 HIS ** 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 = 0.4023 r_free = 0.4023 target = 0.177302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.158922 restraints weight = 11770.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.156993 restraints weight = 25237.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.143537 restraints weight = 27918.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.140511 restraints weight = 24982.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.139729 restraints weight = 16656.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.3594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8294  Z= 0.179
  Angle     :  0.733  10.251  11294  Z= 0.369
  Chirality :  0.047   0.175   1265
  Planarity :  0.007   0.062   1438
  Dihedral  :  5.459  55.014   1145
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  : 11.15 %
    Favored  : 88.56 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 22.05 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.27), residues: 1058
  helix:  1.50 (0.44), residues: 124
  sheet: -0.38 (0.31), residues: 326
  loop : -1.99 (0.26), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D  18 
 TYR   0.028   0.002   TYR A  49 
 PHE   0.017   0.002   PHE B  64 
 TRP   0.019   0.001   TRP C 165 
 HIS   0.004   0.001   HIS D 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 8281)
  covalent geometry    : angle       0.73262 (11268)
  SS BOND              : bond        0.00315 (   13)
  SS BOND              : angle       1.01669 (   26)
  hydrogen bonds       : bond        0.03567 (  219)
  hydrogen bonds       : angle       4.94846 (  606)

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A   31 ASN cc_start: 0.7624 (t0) cc_final: 0.7323 (t0)
REVERT: A   54 ARG cc_start: 0.7884 (ptp-170) cc_final: 0.7601 (mtm180)
REVERT: A   90 GLN cc_start: 0.9020 (pp30) cc_final: 0.8332 (pp30)
REVERT: B   48 MET cc_start: 0.8133 (mmm) cc_final: 0.7569 (mtp)
REVERT: B   62 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7668 (tt0)
REVERT: E  121 CYS cc_start: 0.7483 (t) cc_final: 0.7242 (t)
REVERT: D   29 VAL cc_start: 0.8420 (t) cc_final: 0.8087 (p)
REVERT: D   31 ASN cc_start: 0.7974 (t0) cc_final: 0.7750 (t0)
REVERT: D   39 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8456 (mtmm)
REVERT: D   90 GLN cc_start: 0.8747 (pp30) cc_final: 0.8492 (pp30)
REVERT: F   43 GLN cc_start: 0.8671 (mp10) cc_final: 0.8019 (mp10)
REVERT: F   48 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.6946 (mpp)
REVERT: F   80 TYR cc_start: 0.7267 (m-10) cc_final: 0.6869 (m-10)
  outliers start: 21
  outliers final: 15
  residues processed: 137
  average time/residue: 0.1157
  time to fit residues: 20.1654
Evaluate side-chains
  134 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   52 SER
Chi-restraints excluded: chain A residue   58 ILE
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   51 ILE
Chi-restraints excluded: chain B residue  155 VAL
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain C residue  123 THR
Chi-restraints excluded: chain C residue  150 ILE
Chi-restraints excluded: chain D residue   21 LEU
Chi-restraints excluded: chain D residue   39 LYS
Chi-restraints excluded: chain D residue   78 LEU
Chi-restraints excluded: chain D residue  133 VAL
Chi-restraints excluded: chain F residue   48 MET
Chi-restraints excluded: chain F residue  123 ILE
Chi-restraints excluded: chain F residue  154 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 18 optimal weight:   20.0000
   chunk 27 optimal weight:    0.9990
   chunk 87 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   chunk 67 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9980
   chunk 100 optimal weight:    9.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** D  32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 HIS ** 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 = 0.4032 r_free = 0.4032 target = 0.178078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.159946 restraints weight = 11690.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.158317 restraints weight = 27439.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.149005 restraints weight = 25749.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.145000 restraints weight = 26697.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.144580 restraints weight = 21378.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.3630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8294  Z= 0.155
  Angle     :  0.722  10.525  11294  Z= 0.361
  Chirality :  0.046   0.166   1265
  Planarity :  0.007   0.061   1438
  Dihedral  :  5.340  50.117   1145
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  : 11.34 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 21.83 %
    Favored  : 75.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.27), residues: 1058
  helix:  1.85 (0.48), residues: 112
  sheet: -0.45 (0.30), residues: 326
  loop : -1.90 (0.25), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  18 
 TYR   0.027   0.002   TYR A  49 
 PHE   0.019   0.002   PHE B 135 
 TRP   0.015   0.001   TRP C 165 
 HIS   0.005   0.001   HIS D 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 8281)
  covalent geometry    : angle       0.72186 (11268)
  SS BOND              : bond        0.00243 (   13)
  SS BOND              : angle       0.91012 (   26)
  hydrogen bonds       : bond        0.03251 (  219)
  hydrogen bonds       : angle       4.88769 (  606)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1337.34 seconds
wall clock time: 23 minutes 50.24 seconds (1430.24 seconds total)