Starting phenix.real_space_refine
on Mon Jun 16 14:30:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cl2_16710/06_2025/8cl2_16710.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cl2_16710/06_2025/8cl2_16710.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cl2_16710/06_2025/8cl2_16710.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cl2_16710/06_2025/8cl2_16710.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cl2_16710/06_2025/8cl2_16710.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cl2_16710/06_2025/8cl2_16710.cif"
  }
  resolution = 3.45
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.051
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 6995 atoms to isotropic.
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     115      5.16       5
     C    8400      2.51       5
     N    2285      2.21       5
     O    2535      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13335
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 67, 527
          Classifications: {'peptide': 67}
          Link IDs: {'PTRANS': 4, 'TRANS': 62}
    Chain: "C"
      Number of atoms: 514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 514
          Classifications: {'peptide': 65}
          Link IDs: {'PTRANS': 3, 'TRANS': 61}
    Chain: "A"
      Number of atoms: 1626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1626
          Classifications: {'peptide': 213}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 38
  Restraints were copied for chains:
    F, I, L, O, E, H, K, N, D, G, J, M
  Time building chain proxies: 5.96, per 1000 atoms: 0.45
  Number of scatterers: 13335
  At special positions: 0
  Unit cell: (159.96, 155.31, 93.93, 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     115     16.00
     O    2535      8.00
     N    2285      7.00
     C    8400      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.29
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3250

  Finding SS restraints...
    Secondary structure from input PDB file:
      100 helices and 5 sheets defined
      75.4% alpha, 1.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'B' and resid 160 through 175
      removed outlier: 3.855A  pdb=" N   ALA B 174 " --> pdb=" O   LYS B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 193
      removed outlier: 4.035A  pdb=" N   LEU B 190 " --> pdb=" O   THR B 186 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   VAL B 191 " --> pdb=" O   GLU B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 206
      removed outlier: 3.559A  pdb=" N   ALA B 204 " --> pdb=" O   THR B 200 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU B 205 " --> pdb=" O   ILE B 201 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLY B 206 " --> pdb=" O   LEU B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 219
    Processing helix  chain 'C' and resid 160 through 175
      removed outlier: 3.748A  pdb=" N   ALA C 174 " --> pdb=" O   LYS C 170 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 178 through 193
      removed outlier: 4.245A  pdb=" N   VAL C 191 " --> pdb=" O   GLU C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 195 through 204
      removed outlier: 3.807A  pdb=" N   ALA C 204 " --> pdb=" O   THR C 200 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 210 through 219
    Processing helix  chain 'A' and resid 16 through 30
      removed outlier: 3.576A  pdb=" N   LYS A  30 " --> pdb=" O   VAL A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 44
    Processing helix  chain 'A' and resid 48 through 57
    Processing helix  chain 'A' and resid 62 through 84
    Processing helix  chain 'A' and resid 100 through 105
    Processing helix  chain 'A' and resid 110 through 120
    Processing helix  chain 'A' and resid 125 through 145
      removed outlier: 4.027A  pdb=" N   ARG A 132 " --> pdb=" O   GLU A 128 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   TRP A 133 " --> pdb=" O   ILE A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 153
    Processing helix  chain 'A' and resid 160 through 175
      removed outlier: 3.564A  pdb=" N   ALA A 174 " --> pdb=" O   LYS A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 193
      removed outlier: 3.702A  pdb=" N   VAL A 191 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 205
      removed outlier: 3.724A  pdb=" N   LEU A 205 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 219
    Processing helix  chain 'D' and resid 160 through 175
      removed outlier: 3.855A  pdb=" N   ALA D 174 " --> pdb=" O   LYS D 170 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 178 through 193
      removed outlier: 4.036A  pdb=" N   LEU D 190 " --> pdb=" O   THR D 186 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   VAL D 191 " --> pdb=" O   GLU D 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 195 through 206
      removed outlier: 3.559A  pdb=" N   ALA D 204 " --> pdb=" O   THR D 200 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU D 205 " --> pdb=" O   ILE D 201 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLY D 206 " --> pdb=" O   LEU D 202 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 210 through 219
    Processing helix  chain 'E' and resid 160 through 175
      removed outlier: 3.749A  pdb=" N   ALA E 174 " --> pdb=" O   LYS E 170 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 178 through 193
      removed outlier: 4.245A  pdb=" N   VAL E 191 " --> pdb=" O   GLU E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 195 through 204
      removed outlier: 3.807A  pdb=" N   ALA E 204 " --> pdb=" O   THR E 200 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 210 through 219
    Processing helix  chain 'F' and resid 16 through 30
      removed outlier: 3.577A  pdb=" N   LYS F  30 " --> pdb=" O   VAL F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 35 through 44
    Processing helix  chain 'F' and resid 48 through 57
    Processing helix  chain 'F' and resid 62 through 84
    Processing helix  chain 'F' and resid 100 through 105
    Processing helix  chain 'F' and resid 110 through 120
    Processing helix  chain 'F' and resid 125 through 145
      removed outlier: 4.028A  pdb=" N   ARG F 132 " --> pdb=" O   GLU F 128 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   TRP F 133 " --> pdb=" O   ILE F 129 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 149 through 153
    Processing helix  chain 'F' and resid 160 through 175
      removed outlier: 3.565A  pdb=" N   ALA F 174 " --> pdb=" O   LYS F 170 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 178 through 193
      removed outlier: 3.702A  pdb=" N   VAL F 191 " --> pdb=" O   GLU F 187 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 195 through 205
      removed outlier: 3.724A  pdb=" N   LEU F 205 " --> pdb=" O   ILE F 201 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 210 through 219
    Processing helix  chain 'G' and resid 160 through 175
      removed outlier: 3.855A  pdb=" N   ALA G 174 " --> pdb=" O   LYS G 170 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 178 through 193
      removed outlier: 4.036A  pdb=" N   LEU G 190 " --> pdb=" O   THR G 186 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   VAL G 191 " --> pdb=" O   GLU G 187 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 195 through 206
      removed outlier: 3.559A  pdb=" N   ALA G 204 " --> pdb=" O   THR G 200 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU G 205 " --> pdb=" O   ILE G 201 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLY G 206 " --> pdb=" O   LEU G 202 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 210 through 219
    Processing helix  chain 'H' and resid 160 through 175
      removed outlier: 3.748A  pdb=" N   ALA H 174 " --> pdb=" O   LYS H 170 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 178 through 193
      removed outlier: 4.245A  pdb=" N   VAL H 191 " --> pdb=" O   GLU H 187 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 195 through 204
      removed outlier: 3.807A  pdb=" N   ALA H 204 " --> pdb=" O   THR H 200 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 210 through 219
    Processing helix  chain 'I' and resid 16 through 30
      removed outlier: 3.576A  pdb=" N   LYS I  30 " --> pdb=" O   VAL I  26 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 35 through 44
    Processing helix  chain 'I' and resid 48 through 57
    Processing helix  chain 'I' and resid 62 through 84
    Processing helix  chain 'I' and resid 100 through 105
    Processing helix  chain 'I' and resid 110 through 120
    Processing helix  chain 'I' and resid 125 through 145
      removed outlier: 4.028A  pdb=" N   ARG I 132 " --> pdb=" O   GLU I 128 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   TRP I 133 " --> pdb=" O   ILE I 129 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 149 through 153
    Processing helix  chain 'I' and resid 160 through 175
      removed outlier: 3.564A  pdb=" N   ALA I 174 " --> pdb=" O   LYS I 170 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 178 through 193
      removed outlier: 3.703A  pdb=" N   VAL I 191 " --> pdb=" O   GLU I 187 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 195 through 205
      removed outlier: 3.724A  pdb=" N   LEU I 205 " --> pdb=" O   ILE I 201 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 210 through 219
    Processing helix  chain 'J' and resid 160 through 175
      removed outlier: 3.855A  pdb=" N   ALA J 174 " --> pdb=" O   LYS J 170 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 178 through 193
      removed outlier: 4.035A  pdb=" N   LEU J 190 " --> pdb=" O   THR J 186 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   VAL J 191 " --> pdb=" O   GLU J 187 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 195 through 206
      removed outlier: 3.559A  pdb=" N   ALA J 204 " --> pdb=" O   THR J 200 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU J 205 " --> pdb=" O   ILE J 201 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLY J 206 " --> pdb=" O   LEU J 202 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 210 through 219
    Processing helix  chain 'K' and resid 160 through 175
      removed outlier: 3.748A  pdb=" N   ALA K 174 " --> pdb=" O   LYS K 170 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 178 through 193
      removed outlier: 4.246A  pdb=" N   VAL K 191 " --> pdb=" O   GLU K 187 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 195 through 204
      removed outlier: 3.807A  pdb=" N   ALA K 204 " --> pdb=" O   THR K 200 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 210 through 219
    Processing helix  chain 'L' and resid 16 through 30
      removed outlier: 3.576A  pdb=" N   LYS L  30 " --> pdb=" O   VAL L  26 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 35 through 44
    Processing helix  chain 'L' and resid 48 through 57
    Processing helix  chain 'L' and resid 62 through 84
    Processing helix  chain 'L' and resid 100 through 105
    Processing helix  chain 'L' and resid 110 through 120
    Processing helix  chain 'L' and resid 125 through 145
      removed outlier: 4.027A  pdb=" N   ARG L 132 " --> pdb=" O   GLU L 128 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   TRP L 133 " --> pdb=" O   ILE L 129 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 149 through 153
    Processing helix  chain 'L' and resid 160 through 175
      removed outlier: 3.565A  pdb=" N   ALA L 174 " --> pdb=" O   LYS L 170 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 178 through 193
      removed outlier: 3.703A  pdb=" N   VAL L 191 " --> pdb=" O   GLU L 187 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 195 through 205
      removed outlier: 3.724A  pdb=" N   LEU L 205 " --> pdb=" O   ILE L 201 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 210 through 219
    Processing helix  chain 'M' and resid 160 through 175
      removed outlier: 3.855A  pdb=" N   ALA M 174 " --> pdb=" O   LYS M 170 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 178 through 193
      removed outlier: 4.036A  pdb=" N   LEU M 190 " --> pdb=" O   THR M 186 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   VAL M 191 " --> pdb=" O   GLU M 187 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 195 through 206
      removed outlier: 3.559A  pdb=" N   ALA M 204 " --> pdb=" O   THR M 200 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU M 205 " --> pdb=" O   ILE M 201 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLY M 206 " --> pdb=" O   LEU M 202 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 210 through 219
    Processing helix  chain 'N' and resid 160 through 175
      removed outlier: 3.748A  pdb=" N   ALA N 174 " --> pdb=" O   LYS N 170 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 178 through 193
      removed outlier: 4.245A  pdb=" N   VAL N 191 " --> pdb=" O   GLU N 187 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 195 through 204
      removed outlier: 3.807A  pdb=" N   ALA N 204 " --> pdb=" O   THR N 200 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 210 through 219
    Processing helix  chain 'O' and resid 16 through 30
      removed outlier: 3.576A  pdb=" N   LYS O  30 " --> pdb=" O   VAL O  26 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 35 through 44
    Processing helix  chain 'O' and resid 48 through 57
    Processing helix  chain 'O' and resid 62 through 84
    Processing helix  chain 'O' and resid 100 through 105
    Processing helix  chain 'O' and resid 110 through 120
    Processing helix  chain 'O' and resid 125 through 145
      removed outlier: 4.027A  pdb=" N   ARG O 132 " --> pdb=" O   GLU O 128 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   TRP O 133 " --> pdb=" O   ILE O 129 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 149 through 153
    Processing helix  chain 'O' and resid 160 through 175
      removed outlier: 3.565A  pdb=" N   ALA O 174 " --> pdb=" O   LYS O 170 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 178 through 193
      removed outlier: 3.703A  pdb=" N   VAL O 191 " --> pdb=" O   GLU O 187 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 195 through 205
      removed outlier: 3.724A  pdb=" N   LEU O 205 " --> pdb=" O   ILE O 201 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 210 through 219
    Processing sheet with id=1, first strand: chain 'A' and resid 2 through 4
    Processing sheet with id=2, first strand: chain 'F' and resid 2 through 4
    Processing sheet with id=3, first strand: chain 'I' and resid 2 through 4
    Processing sheet with id=4, first strand: chain 'L' and resid 2 through 4
    Processing sheet with id=5, first strand: chain 'O' and resid 2 through 4

    840 hydrogen bonds defined for protein.
    2490 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: 3.39

  Time building geometry restraints manager: 3.75 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: 4410
        1.34 -     1.46: 1422
        1.46 -     1.57: 7563
        1.57 -     1.69: 0
        1.69 -     1.81: 200
  Bond restraints: 13595
  Sorted by residual:
  bond pdb=" CB  PRO I   1 "
       pdb=" CG  PRO I   1 "
    ideal  model  delta    sigma   weight residual
    1.492  1.572 -0.080 5.00e-02 4.00e+02 2.58e+00
  bond pdb=" CB  PRO O   1 "
       pdb=" CG  PRO O   1 "
    ideal  model  delta    sigma   weight residual
    1.492  1.572 -0.080 5.00e-02 4.00e+02 2.57e+00
  bond pdb=" CB  PRO F   1 "
       pdb=" CG  PRO F   1 "
    ideal  model  delta    sigma   weight residual
    1.492  1.572 -0.080 5.00e-02 4.00e+02 2.57e+00
  bond pdb=" CB  PRO L   1 "
       pdb=" CG  PRO L   1 "
    ideal  model  delta    sigma   weight residual
    1.492  1.572 -0.080 5.00e-02 4.00e+02 2.57e+00
  bond pdb=" CB  PRO A   1 "
       pdb=" CG  PRO A   1 "
    ideal  model  delta    sigma   weight residual
    1.492  1.572 -0.080 5.00e-02 4.00e+02 2.56e+00
  ... (remaining 13590 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 15646
        1.03 -     2.06: 2240
        2.06 -     3.09: 384
        3.09 -     4.12: 140
        4.12 -     5.14: 30
  Bond angle restraints: 18440
  Sorted by residual:
  angle pdb=" N   ALA O 177 "
        pdb=" CA  ALA O 177 "
        pdb=" C   ALA O 177 "
      ideal   model   delta    sigma   weight residual
     110.24  114.10   -3.86 1.47e+00 4.63e-01 6.89e+00
  angle pdb=" N   ALA A 177 "
        pdb=" CA  ALA A 177 "
        pdb=" C   ALA A 177 "
      ideal   model   delta    sigma   weight residual
     110.24  114.08   -3.84 1.47e+00 4.63e-01 6.84e+00
  angle pdb=" N   ALA I 177 "
        pdb=" CA  ALA I 177 "
        pdb=" C   ALA I 177 "
      ideal   model   delta    sigma   weight residual
     110.24  114.08   -3.84 1.47e+00 4.63e-01 6.84e+00
  angle pdb=" N   ALA F 177 "
        pdb=" CA  ALA F 177 "
        pdb=" C   ALA F 177 "
      ideal   model   delta    sigma   weight residual
     110.24  114.08   -3.84 1.47e+00 4.63e-01 6.81e+00
  angle pdb=" N   ALA L 177 "
        pdb=" CA  ALA L 177 "
        pdb=" C   ALA L 177 "
      ideal   model   delta    sigma   weight residual
     110.24  114.07   -3.83 1.47e+00 4.63e-01 6.78e+00
  ... (remaining 18435 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.68: 7740
       15.68 -    31.37: 450
       31.37 -    47.05: 120
       47.05 -    62.74: 30
       62.74 -    78.42: 20
  Dihedral angle restraints: 8360
    sinusoidal: 3365
      harmonic: 4995
  Sorted by residual:
  dihedral pdb=" CA  GLU H 175 "
           pdb=" C   GLU H 175 "
           pdb=" N   GLN H 176 "
           pdb=" CA  GLN H 176 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.43  -29.57     0      5.00e+00 4.00e-02 3.50e+01
  dihedral pdb=" CA  GLU E 175 "
           pdb=" C   GLU E 175 "
           pdb=" N   GLN E 176 "
           pdb=" CA  GLN E 176 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.44  -29.56     0      5.00e+00 4.00e-02 3.50e+01
  dihedral pdb=" CA  GLU C 175 "
           pdb=" C   GLU C 175 "
           pdb=" N   GLN C 176 "
           pdb=" CA  GLN C 176 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.45  -29.55     0      5.00e+00 4.00e-02 3.49e+01
  ... (remaining 8357 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1129
       0.033 -    0.065: 610
       0.065 -    0.098: 226
       0.098 -    0.131: 97
       0.131 -    0.164: 23
  Chirality restraints: 2085
  Sorted by residual:
  chirality pdb=" CA  LYS I  30 "
            pdb=" N   LYS I  30 "
            pdb=" C   LYS I  30 "
            pdb=" CB  LYS I  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.70e-01
  chirality pdb=" CA  LYS A  30 "
            pdb=" N   LYS A  30 "
            pdb=" C   LYS A  30 "
            pdb=" CB  LYS A  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.60e-01
  chirality pdb=" CA  LYS L  30 "
            pdb=" N   LYS L  30 "
            pdb=" C   LYS L  30 "
            pdb=" CB  LYS L  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.51e-01
  ... (remaining 2082 not shown)

  Planarity restraints: 2390
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR L 186 "    0.024 2.00e-02 2.50e+03   4.74e-02 2.25e+01
        pdb=" C   THR L 186 "   -0.082 2.00e-02 2.50e+03
        pdb=" O   THR L 186 "    0.031 2.00e-02 2.50e+03
        pdb=" N   GLU L 187 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR I 186 "    0.024 2.00e-02 2.50e+03   4.74e-02 2.24e+01
        pdb=" C   THR I 186 "   -0.082 2.00e-02 2.50e+03
        pdb=" O   THR I 186 "    0.031 2.00e-02 2.50e+03
        pdb=" N   GLU I 187 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 186 "   -0.024 2.00e-02 2.50e+03   4.74e-02 2.24e+01
        pdb=" C   THR A 186 "    0.082 2.00e-02 2.50e+03
        pdb=" O   THR A 186 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   GLU A 187 "   -0.028 2.00e-02 2.50e+03
  ... (remaining 2387 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 788
        2.73 -     3.28: 14664
        3.28 -     3.82: 21424
        3.82 -     4.36: 26734
        4.36 -     4.90: 43361
  Nonbonded interactions: 106971
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG I 173 "
            pdb=" OE1 GLU L  28 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" NH1 ARG F 173 "
            pdb=" OE1 GLU I  28 "
     model   vdw
     2.193 3.120
  nonbonded pdb=" NH1 ARG A 173 "
            pdb=" OE1 GLU F  28 "
     model   vdw
     2.193 3.120
  nonbonded pdb=" OE1 GLU A  28 "
            pdb=" NH1 ARG O 173 "
     model   vdw
     2.193 3.120
  nonbonded pdb=" NH1 ARG L 173 "
            pdb=" OE1 GLU O  28 "
     model   vdw
     2.193 3.120
  ... (remaining 106966 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: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'L'
  selection = chain 'O'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'N'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'J'
  selection = chain 'M'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.110
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     28.360
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
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   0.080  13595  Z= 0.227
  Angle     :  0.824   5.144  18440  Z= 0.497
  Chirality :  0.048   0.164   2085
  Planarity :  0.009   0.086   2390
  Dihedral  : 12.071  78.424   5110
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.18), residues: 1685
  helix: -0.79 (0.13), residues: 1145
  sheet: -2.23 (0.57), residues: 45
  loop :  0.82 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.004   TRP O 117 
 HIS   0.007   0.003   HIS A  12 
 PHE   0.024   0.003   PHE A  40 
 TYR   0.014   0.004   TYR O 169 
 ARG   0.011   0.002   ARG L  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12089 (  840)
  hydrogen bonds       : angle       6.27745 ( 2490)
  covalent geometry    : bond        0.00447 (13595)
  covalent geometry    : angle       0.82357 (18440)

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

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

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  681 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 681
  time to evaluate  : 1.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  170 LYS cc_start: 0.8710 (tttm) cc_final: 0.8427 (tppt)
REVERT: C  166 ASP cc_start: 0.7844 (m-30) cc_final: 0.7479 (m-30)
REVERT: C  183 ASN cc_start: 0.8349 (m-40) cc_final: 0.8040 (m-40)
REVERT: C  213 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7483 (mt-10)
REVERT: A   41 SER cc_start: 0.9001 (t) cc_final: 0.8262 (p)
REVERT: A  117 TRP cc_start: 0.8103 (m-10) cc_final: 0.7749 (m-90)
REVERT: A  167 ARG cc_start: 0.7978 (mtp180) cc_final: 0.7727 (mtm-85)
REVERT: A  183 ASN cc_start: 0.8615 (m-40) cc_final: 0.8405 (m-40)
REVERT: A  192 GLN cc_start: 0.8591 (tp40) cc_final: 0.8216 (tm-30)
REVERT: D  159 GLU cc_start: 0.8502 (tt0) cc_final: 0.8102 (tt0)
REVERT: D  170 LYS cc_start: 0.8690 (tttm) cc_final: 0.8471 (tppt)
REVERT: E  166 ASP cc_start: 0.7870 (m-30) cc_final: 0.7594 (m-30)
REVERT: E  168 PHE cc_start: 0.8949 (t80) cc_final: 0.8661 (t80)
REVERT: E  213 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7498 (mt-10)
REVERT: F   39 MET cc_start: 0.8466 (mtt) cc_final: 0.8230 (mtm)
REVERT: F   41 SER cc_start: 0.9200 (t) cc_final: 0.8547 (p)
REVERT: F   70 LYS cc_start: 0.8720 (mmmm) cc_final: 0.8518 (mptt)
REVERT: F  192 GLN cc_start: 0.8575 (tp40) cc_final: 0.8171 (tm-30)
REVERT: G  170 LYS cc_start: 0.8634 (tttm) cc_final: 0.8417 (tppt)
REVERT: I   41 SER cc_start: 0.9176 (t) cc_final: 0.8552 (p)
REVERT: I   68 MET cc_start: 0.8790 (mtp) cc_final: 0.8313 (mtp)
REVERT: I  183 ASN cc_start: 0.8494 (m-40) cc_final: 0.8254 (m-40)
REVERT: I  192 GLN cc_start: 0.8506 (tp40) cc_final: 0.8209 (tm-30)
REVERT: J  159 GLU cc_start: 0.8524 (tt0) cc_final: 0.8207 (tt0)
REVERT: J  170 LYS cc_start: 0.8632 (tttm) cc_final: 0.8365 (tppt)
REVERT: K  182 LYS cc_start: 0.8494 (mttt) cc_final: 0.8166 (mttp)
REVERT: K  183 ASN cc_start: 0.8337 (m-40) cc_final: 0.7921 (m-40)
REVERT: K  192 GLN cc_start: 0.8343 (mt0) cc_final: 0.8085 (tt0)
REVERT: K  213 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7486 (mt-10)
REVERT: L   25 LYS cc_start: 0.8326 (mttt) cc_final: 0.8102 (mtmt)
REVERT: L   41 SER cc_start: 0.9112 (t) cc_final: 0.8401 (p)
REVERT: L  183 ASN cc_start: 0.8512 (m-40) cc_final: 0.8091 (m-40)
REVERT: L  192 GLN cc_start: 0.8518 (tp40) cc_final: 0.8110 (tm-30)
REVERT: L  195 ASN cc_start: 0.8522 (p0) cc_final: 0.8064 (p0)
REVERT: L  215 MET cc_start: 0.8794 (mtp) cc_final: 0.8589 (mtm)
REVERT: M  170 LYS cc_start: 0.8660 (tttm) cc_final: 0.8402 (tppt)
REVERT: N  213 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7530 (mt-10)
REVERT: O   39 MET cc_start: 0.8458 (mtt) cc_final: 0.8178 (mtp)
REVERT: O   41 SER cc_start: 0.9124 (t) cc_final: 0.8407 (p)
REVERT: O  117 TRP cc_start: 0.8111 (m-10) cc_final: 0.7518 (m-90)
REVERT: O  183 ASN cc_start: 0.8599 (m-40) cc_final: 0.8372 (m-40)
REVERT: O  192 GLN cc_start: 0.8636 (tp40) cc_final: 0.8299 (tm-30)
REVERT: O  214 MET cc_start: 0.9045 (mtp) cc_final: 0.8842 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 681
  average time/residue: 0.2970
  time to fit residues: 277.0556
Evaluate side-chains
  495 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 495
  time to evaluate  : 1.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 139 optimal weight:    0.3980
   chunk 125 optimal weight:    0.4980
   chunk 69 optimal weight:    0.6980
   chunk 42 optimal weight:    0.1980
   chunk 84 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 129 optimal weight:    0.8980
   chunk 50 optimal weight:    0.3980
   chunk 78 optimal weight:    0.0170
   chunk 96 optimal weight:    2.9990
   chunk 149 optimal weight:    0.9980
   overall best weight:    0.3018

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

Flipped N/Q/H residues before XYZ refinement:
** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 219 GLN
F  50 GLN
I 120 HIS
M 179 GLN
M 219 GLN
O  50 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.134799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.102714 restraints weight = 22850.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 2.54
r_work: 0.3178 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.3234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  13595  Z= 0.132
  Angle     :  0.607   9.531  18440  Z= 0.317
  Chirality :  0.041   0.154   2085
  Planarity :  0.005   0.038   2390
  Dihedral  :  5.061  25.112   1820
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.55 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.19), residues: 1685
  helix:  1.03 (0.14), residues: 1160
  sheet: -1.92 (0.64), residues: 45
  loop :  1.52 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP O 184 
 HIS   0.003   0.000   HIS I 120 
 PHE   0.013   0.001   PHE L  40 
 TYR   0.017   0.001   TYR H 164 
 ARG   0.005   0.000   ARG L  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04341 (  840)
  hydrogen bonds       : angle       4.31328 ( 2490)
  covalent geometry    : bond        0.00292 (13595)
  covalent geometry    : angle       0.60705 (18440)

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

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

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  594 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 565
  time to evaluate  : 2.533 
Fit side-chains
REVERT: B  175 GLU cc_start: 0.8630 (tp30) cc_final: 0.8315 (tp30)
REVERT: B  195 ASN cc_start: 0.7755 (t0) cc_final: 0.7249 (t0)
REVERT: C  166 ASP cc_start: 0.7924 (m-30) cc_final: 0.7545 (m-30)
REVERT: C  168 PHE cc_start: 0.8768 (t80) cc_final: 0.8516 (t80)
REVERT: C  200 THR cc_start: 0.8800 (m) cc_final: 0.8492 (p)
REVERT: C  213 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7921 (mt-10)
REVERT: D  170 LYS cc_start: 0.8843 (tttm) cc_final: 0.8535 (tppt)
REVERT: E  166 ASP cc_start: 0.8181 (m-30) cc_final: 0.7889 (m-30)
REVERT: E  171 THR cc_start: 0.8755 (m) cc_final: 0.8401 (p)
REVERT: E  200 THR cc_start: 0.8726 (m) cc_final: 0.8491 (p)
REVERT: E  213 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7976 (mt-10)
REVERT: F    3 VAL cc_start: 0.9077 (t) cc_final: 0.8870 (m)
REVERT: F   70 LYS cc_start: 0.8871 (mmmm) cc_final: 0.8506 (mmtm)
REVERT: F  199 LYS cc_start: 0.8929 (tttt) cc_final: 0.8697 (ttmt)
REVERT: H  200 THR cc_start: 0.8783 (m) cc_final: 0.8554 (p)
REVERT: H  213 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7962 (mt-10)
REVERT: J  167 ARG cc_start: 0.8649 (mtm-85) cc_final: 0.8403 (ttp80)
REVERT: J  170 LYS cc_start: 0.8878 (tttm) cc_final: 0.8655 (tppt)
REVERT: K  166 ASP cc_start: 0.7960 (m-30) cc_final: 0.7685 (m-30)
REVERT: K  167 ARG cc_start: 0.8305 (mtp85) cc_final: 0.8035 (mtp85)
REVERT: K  171 THR cc_start: 0.8749 (m) cc_final: 0.8412 (p)
REVERT: K  182 LYS cc_start: 0.8564 (mttt) cc_final: 0.8217 (mttp)
REVERT: K  192 GLN cc_start: 0.8322 (mt0) cc_final: 0.8049 (tt0)
REVERT: K  200 THR cc_start: 0.8847 (m) cc_final: 0.8615 (p)
REVERT: K  213 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8127 (mt-10)
REVERT: L  179 GLN cc_start: 0.9138 (tp40) cc_final: 0.8842 (tp40)
REVERT: L  192 GLN cc_start: 0.8723 (tp40) cc_final: 0.8274 (tm-30)
REVERT: L  195 ASN cc_start: 0.8630 (p0) cc_final: 0.8361 (p0)
REVERT: L  213 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8348 (mp0)
REVERT: M  170 LYS cc_start: 0.8855 (tttm) cc_final: 0.8594 (tppt)
REVERT: M  198 CYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8240 (m)
REVERT: N  168 PHE cc_start: 0.8931 (t80) cc_final: 0.8728 (t80)
REVERT: N  170 LYS cc_start: 0.8685 (ttpp) cc_final: 0.8409 (ttmm)
REVERT: N  200 THR cc_start: 0.8804 (m) cc_final: 0.8573 (p)
REVERT: N  213 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7979 (mt-10)
REVERT: O    3 VAL cc_start: 0.9056 (t) cc_final: 0.8853 (m)
REVERT: O  195 ASN cc_start: 0.8630 (p0) cc_final: 0.8256 (p0)
  outliers start: 29
  outliers final: 13
  residues processed: 585
  average time/residue: 0.3654
  time to fit residues: 299.9781
Evaluate side-chains
  486 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 472
  time to evaluate  : 1.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain I residue   58 THR
Chi-restraints excluded: chain J residue  221 VAL
Chi-restraints excluded: chain K residue  191 VAL
Chi-restraints excluded: chain L residue   58 THR
Chi-restraints excluded: chain L residue  149 SER
Chi-restraints excluded: chain L residue  178 SER
Chi-restraints excluded: chain M residue  198 CYS
Chi-restraints excluded: chain N residue  189 LEU
Chi-restraints excluded: chain O residue   63 GLN
Chi-restraints excluded: chain O residue  110 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 156 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 122 optimal weight:    1.9990
   chunk 139 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 150 optimal weight:    5.9990
   chunk 134 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 192 GLN
D 183 ASN
E 192 GLN
I 120 HIS
** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 219 GLN
O 193 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.129776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.096725 restraints weight = 22764.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 2.43
r_work: 0.3045 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13595  Z= 0.156
  Angle     :  0.598   9.269  18440  Z= 0.311
  Chirality :  0.043   0.176   2085
  Planarity :  0.005   0.041   2390
  Dihedral  :  4.766  20.757   1820
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 15.56 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.20), residues: 1685
  helix:  1.01 (0.15), residues: 1185
  sheet: -1.78 (0.66), residues: 45
  loop :  1.53 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP L 184 
 HIS   0.003   0.000   HIS I 120 
 PHE   0.019   0.002   PHE H 168 
 TYR   0.009   0.001   TYR H 164 
 ARG   0.006   0.000   ARG F  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04178 (  840)
  hydrogen bonds       : angle       4.33447 ( 2490)
  covalent geometry    : bond        0.00375 (13595)
  covalent geometry    : angle       0.59827 (18440)

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

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

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  536 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 496
  time to evaluate  : 1.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  175 GLU cc_start: 0.8720 (tp30) cc_final: 0.8443 (tp30)
REVERT: C  166 ASP cc_start: 0.7892 (m-30) cc_final: 0.7524 (m-30)
REVERT: C  168 PHE cc_start: 0.8812 (t80) cc_final: 0.8275 (t80)
REVERT: C  200 THR cc_start: 0.8742 (m) cc_final: 0.8476 (p)
REVERT: A  199 LYS cc_start: 0.9121 (ttmt) cc_final: 0.8877 (ttmt)
REVERT: D  170 LYS cc_start: 0.8867 (tttm) cc_final: 0.8590 (tppt)
REVERT: E  166 ASP cc_start: 0.7931 (m-30) cc_final: 0.7700 (m-30)
REVERT: E  200 THR cc_start: 0.8742 (m) cc_final: 0.8519 (p)
REVERT: E  201 ILE cc_start: 0.9027 (mm) cc_final: 0.8820 (mm)
REVERT: E  213 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8083 (mp0)
REVERT: F    3 VAL cc_start: 0.9055 (t) cc_final: 0.8843 (m)
REVERT: F   70 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8544 (mmtm)
REVERT: F   82 ARG cc_start: 0.8219 (ttp80) cc_final: 0.7988 (ttp80)
REVERT: F  199 LYS cc_start: 0.8998 (tttt) cc_final: 0.8788 (ttmt)
REVERT: H  213 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7921 (mt-10)
REVERT: J  170 LYS cc_start: 0.8969 (tttm) cc_final: 0.8759 (tppt)
REVERT: K  167 ARG cc_start: 0.8303 (mtp85) cc_final: 0.8028 (mtp85)
REVERT: K  200 THR cc_start: 0.8838 (m) cc_final: 0.8618 (p)
REVERT: K  203 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8486 (mmtp)
REVERT: K  213 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8061 (mt-10)
REVERT: K  215 MET cc_start: 0.8418 (mtp) cc_final: 0.8157 (mtp)
REVERT: L  192 GLN cc_start: 0.8894 (tp40) cc_final: 0.8455 (tm-30)
REVERT: L  197 ASP cc_start: 0.8322 (p0) cc_final: 0.8104 (p0)
REVERT: M  170 LYS cc_start: 0.8895 (tttm) cc_final: 0.8650 (tppt)
REVERT: M  199 LYS cc_start: 0.9080 (ttmm) cc_final: 0.8559 (ttmt)
REVERT: N  170 LYS cc_start: 0.8751 (ttpp) cc_final: 0.8509 (ttmm)
REVERT: N  200 THR cc_start: 0.8788 (m) cc_final: 0.8583 (p)
REVERT: N  213 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7972 (mt-10)
REVERT: O  135 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8829 (mm)
REVERT: O  192 GLN cc_start: 0.8750 (tp40) cc_final: 0.8390 (tm-30)
  outliers start: 40
  outliers final: 26
  residues processed: 513
  average time/residue: 0.2962
  time to fit residues: 208.4288
Evaluate side-chains
  482 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 455
  time to evaluate  : 1.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain C residue  191 VAL
Chi-restraints excluded: chain A residue    2 ILE
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain E residue  181 VAL
Chi-restraints excluded: chain F residue    2 ILE
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain G residue  197 ASP
Chi-restraints excluded: chain G residue  221 VAL
Chi-restraints excluded: chain I residue    2 ILE
Chi-restraints excluded: chain I residue  124 ILE
Chi-restraints excluded: chain J residue  221 VAL
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   71 GLU
Chi-restraints excluded: chain M residue  197 ASP
Chi-restraints excluded: chain M residue  198 CYS
Chi-restraints excluded: chain M residue  221 VAL
Chi-restraints excluded: chain N residue  181 VAL
Chi-restraints excluded: chain N residue  189 LEU
Chi-restraints excluded: chain O residue   63 GLN
Chi-restraints excluded: chain O residue  110 THR
Chi-restraints excluded: chain O residue  124 ILE
Chi-restraints excluded: chain O residue  135 ILE
Chi-restraints excluded: chain O residue  178 SER
Chi-restraints excluded: chain O residue  189 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 22 optimal weight:    0.0970
   chunk 15 optimal weight:    3.9990
   chunk 106 optimal weight:    0.9990
   chunk 133 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 134 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 103 optimal weight:    4.9990
   chunk 139 optimal weight:    0.9980
   chunk 56 optimal weight:    6.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
B 155 GLN
A 183 ASN
A 195 ASN
G 193 ASN
H 192 GLN
I 195 ASN
L 193 ASN
L 195 ASN
M 219 GLN
O  50 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.134513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.101565 restraints weight = 22337.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.53
r_work: 0.3160 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.4254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13595  Z= 0.126
  Angle     :  0.566   9.058  18440  Z= 0.296
  Chirality :  0.041   0.176   2085
  Planarity :  0.005   0.041   2390
  Dihedral  :  4.528  20.596   1820
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 16.76 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.20), residues: 1685
  helix:  1.17 (0.15), residues: 1180
  sheet: -1.66 (0.68), residues: 45
  loop :  1.47 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP F 184 
 HIS   0.001   0.000   HIS A  12 
 PHE   0.015   0.001   PHE H 168 
 TYR   0.018   0.001   TYR E 164 
 ARG   0.008   0.000   ARG I  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03749 (  840)
  hydrogen bonds       : angle       4.15134 ( 2490)
  covalent geometry    : bond        0.00289 (13595)
  covalent geometry    : angle       0.56620 (18440)

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

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

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  520 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 480
  time to evaluate  : 1.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  175 GLU cc_start: 0.8668 (tp30) cc_final: 0.8422 (tp30)
REVERT: C  164 TYR cc_start: 0.7607 (t80) cc_final: 0.7329 (t80)
REVERT: C  166 ASP cc_start: 0.7593 (m-30) cc_final: 0.7234 (m-30)
REVERT: C  168 PHE cc_start: 0.8414 (t80) cc_final: 0.8165 (t80)
REVERT: C  200 THR cc_start: 0.8758 (m) cc_final: 0.8513 (p)
REVERT: A   68 MET cc_start: 0.8561 (mtp) cc_final: 0.8348 (mtm)
REVERT: A  199 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8821 (ttmt)
REVERT: D  170 LYS cc_start: 0.8800 (tttm) cc_final: 0.8586 (tppt)
REVERT: D  203 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8116 (mtmt)
REVERT: E  166 ASP cc_start: 0.7900 (m-30) cc_final: 0.7647 (m-30)
REVERT: E  168 PHE cc_start: 0.8875 (t80) cc_final: 0.8382 (t80)
REVERT: E  200 THR cc_start: 0.8713 (m) cc_final: 0.8499 (p)
REVERT: E  201 ILE cc_start: 0.9034 (mm) cc_final: 0.8830 (mm)
REVERT: E  213 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8058 (mp0)
REVERT: F    3 VAL cc_start: 0.9016 (t) cc_final: 0.8771 (m)
REVERT: F   70 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8549 (mmtm)
REVERT: F  199 LYS cc_start: 0.8979 (tttt) cc_final: 0.8751 (ttmt)
REVERT: H  168 PHE cc_start: 0.8264 (t80) cc_final: 0.7825 (t80)
REVERT: H  213 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8003 (mt-10)
REVERT: I  195 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8489 (p0)
REVERT: K  200 THR cc_start: 0.8783 (m) cc_final: 0.8562 (p)
REVERT: K  203 LYS cc_start: 0.8678 (mmtt) cc_final: 0.8398 (mmtp)
REVERT: K  213 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8085 (mt-10)
REVERT: L  192 GLN cc_start: 0.8875 (tp40) cc_final: 0.8305 (tm-30)
REVERT: L  197 ASP cc_start: 0.8074 (p0) cc_final: 0.7839 (p0)
REVERT: M  199 LYS cc_start: 0.8898 (ttmm) cc_final: 0.8415 (ttmt)
REVERT: N  170 LYS cc_start: 0.8687 (ttpp) cc_final: 0.8463 (ttmm)
REVERT: N  200 THR cc_start: 0.8814 (m) cc_final: 0.8612 (p)
REVERT: N  213 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8096 (mm-30)
REVERT: O  192 GLN cc_start: 0.8690 (tp40) cc_final: 0.8440 (tm-30)
  outliers start: 40
  outliers final: 22
  residues processed: 500
  average time/residue: 0.2838
  time to fit residues: 196.3071
Evaluate side-chains
  461 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 438
  time to evaluate  : 1.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain C residue  189 LEU
Chi-restraints excluded: chain A residue    2 ILE
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain E residue  181 VAL
Chi-restraints excluded: chain F residue    2 ILE
Chi-restraints excluded: chain F residue  124 ILE
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain G residue  221 VAL
Chi-restraints excluded: chain I residue    2 ILE
Chi-restraints excluded: chain I residue  124 ILE
Chi-restraints excluded: chain I residue  195 ASN
Chi-restraints excluded: chain I residue  210 THR
Chi-restraints excluded: chain J residue  218 CYS
Chi-restraints excluded: chain J residue  221 VAL
Chi-restraints excluded: chain L residue   58 THR
Chi-restraints excluded: chain L residue   71 GLU
Chi-restraints excluded: chain M residue  198 CYS
Chi-restraints excluded: chain O residue    2 ILE
Chi-restraints excluded: chain O residue   63 GLN
Chi-restraints excluded: chain O residue  124 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0060
   chunk 76 optimal weight:    0.4980
   chunk 20 optimal weight:    0.0570
   chunk 47 optimal weight:    0.5980
   chunk 23 optimal weight:    4.9990
   chunk 163 optimal weight:    7.9990
   chunk 2 optimal weight:    0.0670
   chunk 141 optimal weight:    3.9990
   chunk 103 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.2452

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

Flipped N/Q/H residues before XYZ refinement:
H 192 GLN
M 219 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.137351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.105010 restraints weight = 22559.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.55
r_work: 0.3211 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.4597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  13595  Z= 0.114
  Angle     :  0.547   9.843  18440  Z= 0.285
  Chirality :  0.040   0.158   2085
  Planarity :  0.005   0.041   2390
  Dihedral  :  4.329  19.618   1820
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 17.25 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.80 (0.20), residues: 1685
  helix:  1.32 (0.15), residues: 1180
  sheet: -1.52 (0.70), residues: 45
  loop :  1.52 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP O 184 
 HIS   0.001   0.000   HIS F 120 
 PHE   0.013   0.001   PHE N 168 
 TYR   0.008   0.001   TYR H 164 
 ARG   0.008   0.000   ARG I  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03572 (  840)
  hydrogen bonds       : angle       4.04520 ( 2490)
  covalent geometry    : bond        0.00245 (13595)
  covalent geometry    : angle       0.54665 (18440)

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

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

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  501 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 468
  time to evaluate  : 1.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  159 GLU cc_start: 0.8832 (tt0) cc_final: 0.8355 (tt0)
REVERT: B  175 GLU cc_start: 0.8566 (tp30) cc_final: 0.8362 (tp30)
REVERT: C  166 ASP cc_start: 0.7321 (m-30) cc_final: 0.6986 (m-30)
REVERT: C  168 PHE cc_start: 0.8344 (t80) cc_final: 0.8114 (t80)
REVERT: E  166 ASP cc_start: 0.7708 (m-30) cc_final: 0.7420 (m-30)
REVERT: E  213 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8068 (mp0)
REVERT: F    3 VAL cc_start: 0.9044 (t) cc_final: 0.8842 (m)
REVERT: F   70 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8592 (mmtm)
REVERT: F  152 ASP cc_start: 0.8745 (m-30) cc_final: 0.8522 (m-30)
REVERT: F  182 LYS cc_start: 0.8894 (mttt) cc_final: 0.8692 (mmmt)
REVERT: H  213 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7851 (mt-10)
REVERT: J  158 LYS cc_start: 0.8395 (mmtm) cc_final: 0.8135 (tppt)
REVERT: J  167 ARG cc_start: 0.8694 (ttp80) cc_final: 0.8493 (ttp-110)
REVERT: K  213 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8025 (mt-10)
REVERT: L  197 ASP cc_start: 0.7843 (p0) cc_final: 0.7368 (p0)
REVERT: N  166 ASP cc_start: 0.7599 (m-30) cc_final: 0.7322 (m-30)
REVERT: N  168 PHE cc_start: 0.7964 (t80) cc_final: 0.7669 (t80)
REVERT: N  213 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8141 (mm-30)
REVERT: O   39 MET cc_start: 0.8664 (mtt) cc_final: 0.8416 (mtp)
REVERT: O  192 GLN cc_start: 0.8584 (tp40) cc_final: 0.8296 (tm-30)
  outliers start: 33
  outliers final: 16
  residues processed: 480
  average time/residue: 0.2701
  time to fit residues: 181.6856
Evaluate side-chains
  456 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 440
  time to evaluate  : 1.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain C residue  190 LEU
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain F residue    2 ILE
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain F residue  178 SER
Chi-restraints excluded: chain I residue   71 GLU
Chi-restraints excluded: chain I residue  210 THR
Chi-restraints excluded: chain J residue  218 CYS
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   71 GLU
Chi-restraints excluded: chain M residue  198 CYS
Chi-restraints excluded: chain M residue  221 VAL
Chi-restraints excluded: chain N residue  191 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 101 optimal weight:    0.7980
   chunk 32 optimal weight:    5.9990
   chunk 120 optimal weight:    0.0980
   chunk 87 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 115 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9980
   chunk 123 optimal weight:    0.8980
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
D 183 ASN
G 183 ASN
I 195 ASN
M 219 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.136064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.102337 restraints weight = 22831.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 2.64
r_work: 0.3164 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.4714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13595  Z= 0.126
  Angle     :  0.576  11.380  18440  Z= 0.298
  Chirality :  0.041   0.163   2085
  Planarity :  0.005   0.042   2390
  Dihedral  :  4.295  19.189   1820
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.59 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.20), residues: 1685
  helix:  1.27 (0.15), residues: 1180
  sheet: -1.34 (0.70), residues: 45
  loop :  1.45 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F 184 
 HIS   0.001   0.000   HIS I  62 
 PHE   0.014   0.001   PHE E 168 
 TYR   0.008   0.001   TYR H 164 
 ARG   0.008   0.000   ARG I  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03630 (  840)
  hydrogen bonds       : angle       4.15837 ( 2490)
  covalent geometry    : bond        0.00292 (13595)
  covalent geometry    : angle       0.57586 (18440)

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

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

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  479 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 448
  time to evaluate  : 1.454 
Fit side-chains
   revert: symmetry clash
REVERT: B  175 GLU cc_start: 0.8586 (tp30) cc_final: 0.8351 (tp30)
REVERT: C  166 ASP cc_start: 0.7350 (m-30) cc_final: 0.7048 (m-30)
REVERT: C  168 PHE cc_start: 0.8428 (t80) cc_final: 0.8201 (t80)
REVERT: C  213 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8266 (mp0)
REVERT: D  202 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8932 (mt)
REVERT: E  166 ASP cc_start: 0.7731 (m-30) cc_final: 0.7467 (m-30)
REVERT: F   70 LYS cc_start: 0.8962 (mmmm) cc_final: 0.8599 (mmtm)
REVERT: F  215 MET cc_start: 0.8614 (mtp) cc_final: 0.8272 (mtp)
REVERT: H  213 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7895 (mt-10)
REVERT: J  158 LYS cc_start: 0.8432 (mmtm) cc_final: 0.8147 (tppt)
REVERT: K  213 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8083 (mt-10)
REVERT: L  152 ASP cc_start: 0.8845 (m-30) cc_final: 0.8602 (m-30)
REVERT: L  197 ASP cc_start: 0.8028 (p0) cc_final: 0.7722 (p0)
REVERT: N  166 ASP cc_start: 0.7612 (m-30) cc_final: 0.7220 (m-30)
REVERT: N  213 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8191 (mp0)
REVERT: O   39 MET cc_start: 0.8763 (mtt) cc_final: 0.8501 (mtp)
REVERT: O  192 GLN cc_start: 0.8669 (tp40) cc_final: 0.8401 (tm-30)
  outliers start: 31
  outliers final: 17
  residues processed: 463
  average time/residue: 0.2667
  time to fit residues: 173.1296
Evaluate side-chains
  445 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 427
  time to evaluate  : 1.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain D residue  202 LEU
Chi-restraints excluded: chain D residue  214 MET
Chi-restraints excluded: chain F residue    2 ILE
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain H residue  215 MET
Chi-restraints excluded: chain I residue    2 ILE
Chi-restraints excluded: chain I residue  124 ILE
Chi-restraints excluded: chain I residue  210 THR
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   71 GLU
Chi-restraints excluded: chain L residue  178 SER
Chi-restraints excluded: chain M residue  198 CYS
Chi-restraints excluded: chain M residue  218 CYS
Chi-restraints excluded: chain M residue  221 VAL
Chi-restraints excluded: chain O residue  151 LEU
Chi-restraints excluded: chain O residue  185 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 86 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   chunk 159 optimal weight:    4.9990
   chunk 104 optimal weight:    0.0870
   chunk 124 optimal weight:    0.6980
   chunk 133 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 153 optimal weight:    0.5980
   overall best weight:    0.7960

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

Flipped N/Q/H residues before XYZ refinement:
I 179 GLN
I 183 ASN
J 155 GLN
L  63 GLN
M 219 GLN
** O 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.135912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.102194 restraints weight = 22555.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 2.62
r_work: 0.3163 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.4824

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13595  Z= 0.129
  Angle     :  0.578  10.874  18440  Z= 0.301
  Chirality :  0.041   0.162   2085
  Planarity :  0.005   0.042   2390
  Dihedral  :  4.284  19.634   1820
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 19.37 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.20), residues: 1685
  helix:  1.16 (0.15), residues: 1190
  sheet: -1.25 (0.69), residues: 45
  loop :  1.61 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 184 
 HIS   0.007   0.001   HIS I 120 
 PHE   0.022   0.001   PHE H 168 
 TYR   0.010   0.001   TYR E 164 
 ARG   0.009   0.000   ARG I  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03632 (  840)
  hydrogen bonds       : angle       4.25521 ( 2490)
  covalent geometry    : bond        0.00302 (13595)
  covalent geometry    : angle       0.57840 (18440)

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

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

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  478 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 445
  time to evaluate  : 1.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  166 ASP cc_start: 0.7443 (m-30) cc_final: 0.7137 (m-30)
REVERT: C  213 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8295 (mp0)
REVERT: D  203 LYS cc_start: 0.8439 (mtpp) cc_final: 0.8171 (mtmt)
REVERT: E  166 ASP cc_start: 0.7713 (m-30) cc_final: 0.7497 (m-30)
REVERT: E  213 GLU cc_start: 0.8398 (mp0) cc_final: 0.8026 (mp0)
REVERT: F   70 LYS cc_start: 0.8958 (mmmm) cc_final: 0.8604 (mmtm)
REVERT: F  111 LEU cc_start: 0.8264 (mp) cc_final: 0.8002 (mt)
REVERT: F  112 GLN cc_start: 0.8703 (tp40) cc_final: 0.8211 (mp10)
REVERT: F  192 GLN cc_start: 0.8925 (tp40) cc_final: 0.8279 (tm-30)
REVERT: F  197 ASP cc_start: 0.8044 (p0) cc_final: 0.7844 (p0)
REVERT: F  215 MET cc_start: 0.8623 (mtp) cc_final: 0.8248 (mtp)
REVERT: H  213 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7887 (mt-10)
REVERT: I  152 ASP cc_start: 0.8958 (m-30) cc_final: 0.8680 (m-30)
REVERT: K  213 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8063 (mt-10)
REVERT: L   70 LYS cc_start: 0.8565 (mptt) cc_final: 0.8295 (mmtm)
REVERT: L  152 ASP cc_start: 0.8834 (m-30) cc_final: 0.8612 (m-30)
REVERT: L  197 ASP cc_start: 0.7952 (p0) cc_final: 0.7623 (p0)
REVERT: M  199 LYS cc_start: 0.8715 (ttmm) cc_final: 0.8429 (ttmt)
REVERT: N  166 ASP cc_start: 0.7629 (m-30) cc_final: 0.7187 (m-30)
REVERT: N  213 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8170 (mp0)
REVERT: O   39 MET cc_start: 0.8753 (mtt) cc_final: 0.8485 (mtp)
REVERT: O   68 MET cc_start: 0.8517 (mtp) cc_final: 0.8303 (mtt)
REVERT: O  192 GLN cc_start: 0.8761 (tp40) cc_final: 0.8478 (tm-30)
  outliers start: 33
  outliers final: 24
  residues processed: 459
  average time/residue: 0.2648
  time to fit residues: 170.5407
Evaluate side-chains
  446 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 422
  time to evaluate  : 1.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain A residue   18 ARG
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain D residue  214 MET
Chi-restraints excluded: chain F residue    2 ILE
Chi-restraints excluded: chain F residue   18 ARG
Chi-restraints excluded: chain F residue  124 ILE
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain H residue  215 MET
Chi-restraints excluded: chain I residue    2 ILE
Chi-restraints excluded: chain I residue   71 GLU
Chi-restraints excluded: chain I residue  124 ILE
Chi-restraints excluded: chain I residue  210 THR
Chi-restraints excluded: chain J residue  221 VAL
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   71 GLU
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain M residue  198 CYS
Chi-restraints excluded: chain M residue  221 VAL
Chi-restraints excluded: chain O residue  151 LEU
Chi-restraints excluded: chain O residue  178 SER
Chi-restraints excluded: chain O residue  191 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 122 optimal weight:    0.0970
   chunk 8 optimal weight:    3.9990
   chunk 112 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0970
   chunk 33 optimal weight:   10.0000
   chunk 11 optimal weight:    0.1980
   chunk 154 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 67 optimal weight:    0.1980
   chunk 152 optimal weight:    4.9990
   overall best weight:    0.2576

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

Flipped N/Q/H residues before XYZ refinement:
M 219 GLN
O  63 GLN
** O 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.139712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.106284 restraints weight = 22595.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.64
r_work: 0.3233 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.5172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13595  Z= 0.117
  Angle     :  0.576  10.046  18440  Z= 0.301
  Chirality :  0.040   0.167   2085
  Planarity :  0.005   0.042   2390
  Dihedral  :  4.202  18.753   1820
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 20.49 %
    Favored  : 77.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.20), residues: 1685
  helix:  1.23 (0.15), residues: 1190
  sheet: -1.03 (0.70), residues: 45
  loop :  1.61 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F 184 
 HIS   0.007   0.000   HIS I 120 
 PHE   0.023   0.001   PHE H 168 
 TYR   0.008   0.001   TYR N 169 
 ARG   0.008   0.000   ARG I  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03394 (  840)
  hydrogen bonds       : angle       4.25365 ( 2490)
  covalent geometry    : bond        0.00260 (13595)
  covalent geometry    : angle       0.57609 (18440)

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

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

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  484 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 450
  time to evaluate  : 1.462 
Fit side-chains
REVERT: C  213 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8226 (mp0)
REVERT: A  192 GLN cc_start: 0.8874 (tp40) cc_final: 0.8445 (tm-30)
REVERT: E  164 TYR cc_start: 0.5288 (t80) cc_final: 0.5051 (t80)
REVERT: E  213 GLU cc_start: 0.8389 (mp0) cc_final: 0.7966 (mp0)
REVERT: F   70 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8658 (mmtm)
REVERT: F  112 GLN cc_start: 0.8695 (tp40) cc_final: 0.8236 (mp10)
REVERT: F  192 GLN cc_start: 0.8903 (tp40) cc_final: 0.8272 (tm-30)
REVERT: F  197 ASP cc_start: 0.7938 (p0) cc_final: 0.7708 (p0)
REVERT: H  213 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7831 (mt-10)
REVERT: J  167 ARG cc_start: 0.8694 (ttp80) cc_final: 0.8355 (ttp-170)
REVERT: K  167 ARG cc_start: 0.8291 (mtp85) cc_final: 0.7743 (mtp-110)
REVERT: K  192 GLN cc_start: 0.7848 (mt0) cc_final: 0.7586 (tt0)
REVERT: K  213 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8041 (mt-10)
REVERT: L   70 LYS cc_start: 0.8570 (mptt) cc_final: 0.8328 (mmtm)
REVERT: L  111 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8249 (mp)
REVERT: L  112 GLN cc_start: 0.8790 (tp40) cc_final: 0.8414 (mp10)
REVERT: L  197 ASP cc_start: 0.7942 (p0) cc_final: 0.7619 (p0)
REVERT: M  199 LYS cc_start: 0.8731 (ttmm) cc_final: 0.8514 (ttmt)
REVERT: N  167 ARG cc_start: 0.8427 (mtp180) cc_final: 0.8201 (mtp180)
REVERT: N  203 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7862 (mmtp)
REVERT: N  213 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8124 (mp0)
REVERT: O   39 MET cc_start: 0.8671 (mtt) cc_final: 0.8407 (mtp)
REVERT: O   68 MET cc_start: 0.8454 (mtp) cc_final: 0.8234 (mtt)
REVERT: O  192 GLN cc_start: 0.8831 (tp40) cc_final: 0.8601 (tm-30)
  outliers start: 34
  outliers final: 25
  residues processed: 467
  average time/residue: 0.2633
  time to fit residues: 172.6715
Evaluate side-chains
  446 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 420
  time to evaluate  : 1.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain A residue   18 ARG
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain F residue    2 ILE
Chi-restraints excluded: chain F residue   18 ARG
Chi-restraints excluded: chain F residue  124 ILE
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain F residue  178 SER
Chi-restraints excluded: chain I residue    2 ILE
Chi-restraints excluded: chain I residue   18 ARG
Chi-restraints excluded: chain I residue   71 GLU
Chi-restraints excluded: chain I residue  124 ILE
Chi-restraints excluded: chain I residue  210 THR
Chi-restraints excluded: chain J residue  221 VAL
Chi-restraints excluded: chain L residue    2 ILE
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain L residue  178 SER
Chi-restraints excluded: chain M residue  198 CYS
Chi-restraints excluded: chain M residue  218 CYS
Chi-restraints excluded: chain M residue  221 VAL
Chi-restraints excluded: chain O residue   18 ARG
Chi-restraints excluded: chain O residue  124 ILE
Chi-restraints excluded: chain O residue  151 LEU
Chi-restraints excluded: chain O residue  178 SER
Chi-restraints excluded: chain O residue  191 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 99 optimal weight:   10.0000
   chunk 154 optimal weight:    3.9990
   chunk 126 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
M 219 GLN
O  63 GLN
** O 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.134009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.099481 restraints weight = 22603.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.64
r_work: 0.3120 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.4864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13595  Z= 0.177
  Angle     :  0.643  10.298  18440  Z= 0.334
  Chirality :  0.044   0.173   2085
  Planarity :  0.005   0.044   2390
  Dihedral  :  4.367  21.287   1820
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 21.48 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.20), residues: 1685
  helix:  1.06 (0.15), residues: 1185
  sheet: -0.87 (0.69), residues: 45
  loop :  1.74 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 184 
 HIS   0.008   0.001   HIS I 120 
 PHE   0.023   0.001   PHE H 168 
 TYR   0.013   0.001   TYR N 164 
 ARG   0.009   0.001   ARG I  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03800 (  840)
  hydrogen bonds       : angle       4.51770 ( 2490)
  covalent geometry    : bond        0.00432 (13595)
  covalent geometry    : angle       0.64346 (18440)

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

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

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  453 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 421
  time to evaluate  : 1.566 
Fit side-chains
   revert: symmetry clash
REVERT: B  203 LYS cc_start: 0.8496 (mtpp) cc_final: 0.8230 (mtmt)
REVERT: C  166 ASP cc_start: 0.7469 (m-30) cc_final: 0.7164 (m-30)
REVERT: C  211 LEU cc_start: 0.8438 (tt) cc_final: 0.8166 (tt)
REVERT: C  213 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8222 (mp0)
REVERT: A   70 LYS cc_start: 0.8663 (mptt) cc_final: 0.8456 (mptt)
REVERT: D  203 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8207 (mtmt)
REVERT: E  166 ASP cc_start: 0.7910 (m-30) cc_final: 0.7695 (m-30)
REVERT: E  213 GLU cc_start: 0.8339 (mp0) cc_final: 0.7925 (mp0)
REVERT: F   70 LYS cc_start: 0.8983 (mmmm) cc_final: 0.8632 (mmtm)
REVERT: F  197 ASP cc_start: 0.8044 (p0) cc_final: 0.7829 (p0)
REVERT: H  213 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7873 (mt-10)
REVERT: I  178 SER cc_start: 0.8539 (p) cc_final: 0.8312 (t)
REVERT: K  213 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8100 (mt-10)
REVERT: L  185 MET cc_start: 0.8896 (ttm) cc_final: 0.8616 (mtm)
REVERT: L  197 ASP cc_start: 0.7993 (p0) cc_final: 0.7679 (p0)
REVERT: M  199 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8547 (ttmt)
REVERT: O   68 MET cc_start: 0.8640 (mtp) cc_final: 0.8426 (mtt)
REVERT: O  192 GLN cc_start: 0.8928 (tp40) cc_final: 0.8616 (tm-30)
  outliers start: 32
  outliers final: 24
  residues processed: 439
  average time/residue: 0.2815
  time to fit residues: 175.5922
Evaluate side-chains
  429 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 405
  time to evaluate  : 1.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain A residue    2 ILE
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain F residue    2 ILE
Chi-restraints excluded: chain F residue   18 ARG
Chi-restraints excluded: chain F residue  124 ILE
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain F residue  178 SER
Chi-restraints excluded: chain H residue  215 MET
Chi-restraints excluded: chain I residue    2 ILE
Chi-restraints excluded: chain I residue   18 ARG
Chi-restraints excluded: chain I residue   71 GLU
Chi-restraints excluded: chain I residue  210 THR
Chi-restraints excluded: chain J residue  221 VAL
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   71 GLU
Chi-restraints excluded: chain L residue  178 SER
Chi-restraints excluded: chain M residue  198 CYS
Chi-restraints excluded: chain M residue  218 CYS
Chi-restraints excluded: chain M residue  221 VAL
Chi-restraints excluded: chain O residue   18 ARG
Chi-restraints excluded: chain O residue  124 ILE
Chi-restraints excluded: chain O residue  178 SER
Chi-restraints excluded: chain O residue  191 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 144 optimal weight:    4.9990
   chunk 119 optimal weight:    2.9990
   chunk 15 optimal weight:    0.4980
   chunk 112 optimal weight:    0.0980
   chunk 70 optimal weight:    3.9990
   chunk 159 optimal weight:    0.4980
   chunk 104 optimal weight:    0.0050
   chunk 54 optimal weight:    0.0870
   chunk 76 optimal weight:    0.8980
   chunk 84 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.2372

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

Flipped N/Q/H residues before XYZ refinement:
A 183 ASN
K 192 GLN
L 179 GLN
L 183 ASN
L 193 ASN
M 219 GLN
O 179 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.138052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.105634 restraints weight = 22477.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.53
r_work: 0.3250 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.5272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13595  Z= 0.122
  Angle     :  0.605  10.082  18440  Z= 0.316
  Chirality :  0.041   0.171   2085
  Planarity :  0.005   0.043   2390
  Dihedral  :  4.234  20.301   1820
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 22.32 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.20), residues: 1685
  helix:  1.11 (0.15), residues: 1185
  sheet: -0.65 (0.70), residues: 45
  loop :  1.65 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L 133 
 HIS   0.008   0.001   HIS I 120 
 PHE   0.024   0.001   PHE H 168 
 TYR   0.006   0.001   TYR O 169 
 ARG   0.008   0.001   ARG I  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03512 (  840)
  hydrogen bonds       : angle       4.41409 ( 2490)
  covalent geometry    : bond        0.00275 (13595)
  covalent geometry    : angle       0.60461 (18440)

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

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

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3370 Ramachandran restraints generated.
    1685 Oldfield, 0 Emsley, 1685 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  440 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 418
  time to evaluate  : 1.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  166 ASP cc_start: 0.7399 (m-30) cc_final: 0.7066 (m-30)
REVERT: C  203 LYS cc_start: 0.8216 (tppt) cc_final: 0.7956 (mmtm)
REVERT: E  164 TYR cc_start: 0.5226 (t80) cc_final: 0.4956 (t80)
REVERT: E  166 ASP cc_start: 0.7726 (m-30) cc_final: 0.7493 (m-30)
REVERT: E  175 GLU cc_start: 0.4048 (mt-10) cc_final: 0.3839 (mt-10)
REVERT: E  213 GLU cc_start: 0.8227 (mp0) cc_final: 0.7909 (mp0)
REVERT: F   70 LYS cc_start: 0.8979 (mmmm) cc_final: 0.8676 (mmtm)
REVERT: F  112 GLN cc_start: 0.8572 (tp40) cc_final: 0.8188 (mp10)
REVERT: F  197 ASP cc_start: 0.7764 (p0) cc_final: 0.7536 (p0)
REVERT: G  210 THR cc_start: 0.9327 (p) cc_final: 0.7749 (p)
REVERT: H  164 TYR cc_start: 0.5672 (t80) cc_final: 0.5400 (t80)
REVERT: H  213 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7809 (mt-10)
REVERT: I   70 LYS cc_start: 0.8559 (mptt) cc_final: 0.8276 (mmtt)
REVERT: K  213 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7995 (mt-10)
REVERT: L  185 MET cc_start: 0.8803 (ttm) cc_final: 0.8556 (mtm)
REVERT: L  197 ASP cc_start: 0.7798 (p0) cc_final: 0.7443 (p0)
REVERT: M  199 LYS cc_start: 0.8749 (ttmm) cc_final: 0.8545 (ttmt)
REVERT: N  199 LYS cc_start: 0.8760 (ttpt) cc_final: 0.8397 (ttmt)
REVERT: N  203 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7832 (mmtp)
REVERT: N  213 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8102 (mp0)
REVERT: O   66 MET cc_start: 0.8751 (tpp) cc_final: 0.8379 (tpp)
REVERT: O   68 MET cc_start: 0.8460 (mtp) cc_final: 0.8250 (mtt)
REVERT: O  192 GLN cc_start: 0.8904 (tp40) cc_final: 0.8630 (tm-30)
  outliers start: 22
  outliers final: 19
  residues processed: 432
  average time/residue: 0.2593
  time to fit residues: 158.9933
Evaluate side-chains
  431 residues out of total 1485 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 412
  time to evaluate  : 1.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  218 CYS
Chi-restraints excluded: chain A residue   18 ARG
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain F residue    2 ILE
Chi-restraints excluded: chain F residue   18 ARG
Chi-restraints excluded: chain F residue  124 ILE
Chi-restraints excluded: chain F residue  135 ILE
Chi-restraints excluded: chain I residue    2 ILE
Chi-restraints excluded: chain I residue   18 ARG
Chi-restraints excluded: chain I residue   71 GLU
Chi-restraints excluded: chain J residue  221 VAL
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue  178 SER
Chi-restraints excluded: chain M residue  198 CYS
Chi-restraints excluded: chain M residue  221 VAL
Chi-restraints excluded: chain O residue   18 ARG
Chi-restraints excluded: chain O residue  124 ILE
Chi-restraints excluded: chain O residue  178 SER
Chi-restraints excluded: chain O residue  191 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 45 optimal weight:    0.0020
   chunk 160 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 145 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 152 optimal weight:    6.9990
   chunk 56 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.8992

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

Flipped N/Q/H residues before XYZ refinement:
B 183 ASN
O 179 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.136295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.102953 restraints weight = 22654.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.57
r_work: 0.3197 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.5223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13595  Z= 0.141
  Angle     :  0.634   9.848  18440  Z= 0.330
  Chirality :  0.043   0.176   2085
  Planarity :  0.005   0.043   2390
  Dihedral  :  4.289  21.092   1820
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 22.75 %
    Favored  : 75.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.20), residues: 1685
  helix:  1.02 (0.15), residues: 1185
  sheet: -0.64 (0.70), residues: 45
  loop :  1.61 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP F 184 
 HIS   0.001   0.000   HIS I  62 
 PHE   0.026   0.001   PHE H 168 
 TYR   0.010   0.001   TYR F 130 
 ARG   0.008   0.001   ARG I  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03613 (  840)
  hydrogen bonds       : angle       4.50739 ( 2490)
  covalent geometry    : bond        0.00336 (13595)
  covalent geometry    : angle       0.63393 (18440)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7942.41 seconds
wall clock time: 137 minutes 41.43 seconds (8261.43 seconds total)