Starting phenix.real_space_refine
on Wed Mar 12 07:12:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qot_18541/03_2025/8qot_18541.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qot_18541/03_2025/8qot_18541.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qot_18541/03_2025/8qot_18541.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qot_18541/03_2025/8qot_18541.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qot_18541/03_2025/8qot_18541.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qot_18541/03_2025/8qot_18541.cif"
  }
  resolution = 3.2
  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=   0.000 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    4791      2.51       5
     N    1243      2.21       5
     O    1416      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7493
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2320
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 287, 2309
          Classifications: {'peptide': 287}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276}
      Conformer: "B"
        Number of residues, atoms: 287, 2309
          Classifications: {'peptide': 287}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 276}
          bond proxies already assigned to first conformer: 2355
    Chain: "B"
      Number of atoms: 948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 948
          Classifications: {'peptide': 125}
          Link IDs: {'PTRANS': 3, 'TRANS': 121}
    Chain: "H"
      Number of atoms: 1708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1708
          Classifications: {'peptide': 226}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 214}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 10
    Chain: "L"
      Number of atoms: 1586
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1586
          Classifications: {'peptide': 209}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 198}
    Chain: "K"
      Number of atoms: 931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 931
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  APHE A 320 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 320 " occ=0.50
  Time building chain proxies: 6.05, per 1000 atoms: 0.81
  Number of scatterers: 7493
  At special positions: 0
  Unit cell: (66.3612, 89.7828, 161.999, 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      43     16.00
     O    1416      8.00
     N    1243      7.00
     C    4791      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 140 " - pdb=" SG  CYS A 217 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 140 " - pdb=" SG  CYS H 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " distance=2.04
    Simple disulfide: pdb=" SG  CYS K  22 " - pdb=" SG  CYS K  92 " distance=2.05

  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: 1.68
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1802

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 18 sheets defined
      30.2% alpha, 37.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 66 through 95
    Processing helix  chain 'A' and resid 101 through 131
      Proline residue:  A 122  - end of helix
    Processing helix  chain 'A' and resid 136 through 170
      removed outlier: 3.676A  pdb=" N   CYS A 140 " --> pdb=" O   GLY A 136 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LYS A 141 " --> pdb=" O   ASN A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 177
    Processing helix  chain 'A' and resid 180 through 205
      Proline residue:  A 201  - end of helix
    Processing helix  chain 'A' and resid 224 through 258
      removed outlier: 3.735A  pdb=" N   TRP A 228 " --> pdb=" O   PRO A 224 " (cutoff:3.500A)
      Proline residue:  A 244  - end of helix
    Processing helix  chain 'A' and resid 260 through 266
      removed outlier: 3.863A  pdb=" N   MET A 264 " --> pdb=" O   LYS A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 306
      removed outlier: 3.786A  pdb=" N   LEU A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
      Proline residue:  A 295  - end of helix
    Processing helix  chain 'A' and resid 311 through 339
      removed outlier: 3.793A  pdb=" N   SER A 317 " --> pdb=" O   PHE A 313 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   TRP A 318 " --> pdb=" O   GLN A 314 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   HIS A 319 " --> pdb=" O   THR A 315 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   SER A 329 " --> pdb=" O   GLY A 325 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   CYS A 330 " --> pdb=" O   TYR A 326 " (cutoff:3.500A)
      Proline residue:  A 333  - end of helix
    Processing helix  chain 'A' and resid 341 through 350
      removed outlier: 4.250A  pdb=" N   GLU A 349 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.810A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.514A  pdb=" N   THR H  87 " --> pdb=" O   ALA H  84 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 98 through 100C
    Processing helix  chain 'H' and resid 156 through 158
      No H-bonds generated for 'chain 'H' and resid 156 through 158'
    Processing helix  chain 'H' and resid 187 through 189
      No H-bonds generated for 'chain 'H' and resid 187 through 189'
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.688A  pdb=" N   PHE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 121 through 128
    Processing helix  chain 'L' and resid 183 through 189
      removed outlier: 3.676A  pdb=" N   HIS L 189 " --> pdb=" O   ASP L 185 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 83 through 87
      removed outlier: 3.855A  pdb=" N   THR K  87 " --> pdb=" O   PRO K  84 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 210
      removed outlier: 3.532A  pdb=" N   THR A 218 " --> pdb=" O   THR A 207 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 9
      removed outlier: 3.786A  pdb=" N   SER B   9 " --> pdb=" O   SER B  23 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 12 through 14
      removed outlier: 6.167A  pdb=" N   GLY B  12 " --> pdb=" O   THR B 122 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ALA B  51 " --> pdb=" O   TRP B  38 " (cutoff:3.500A)
      removed outlier: 6.056A  pdb=" N   ARG B  40 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 5.729A  pdb=" N   LEU B  49 " --> pdb=" O   ARG B  40 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 14
      removed outlier: 6.167A  pdb=" N   GLY B  12 " --> pdb=" O   THR B 122 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.679A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER H  25 " --> pdb=" O   GLN H   3 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.998A  pdb=" N   ILE H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   TYR H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   TYR H  50 " --> pdb=" O   SER H  58 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   SER H  58 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12
    Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 124
      removed outlier: 3.753A  pdb=" N   GLY H 139 " --> pdb=" O   LEU H 124 " (cutoff:3.500A)
      removed outlier: 5.883A  pdb=" N   TYR H 176 " --> pdb=" O   ASP H 144 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 120 through 124
      removed outlier: 3.753A  pdb=" N   GLY H 139 " --> pdb=" O   LEU H 124 " (cutoff:3.500A)
      removed outlier: 5.883A  pdb=" N   TYR H 176 " --> pdb=" O   ASP H 144 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 151 through 154
      removed outlier: 4.609A  pdb=" N   TYR H 194 " --> pdb=" O   VAL H 211 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 13
      removed outlier: 3.553A  pdb=" N   ILE L  48 " --> pdb=" O   TRP L  35 " (cutoff:3.500A)
      removed outlier: 6.444A  pdb=" N   GLN L  37 " --> pdb=" O   LEU L  46 " (cutoff:3.500A)
      removed outlier: 5.491A  pdb=" N   LEU L  46 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 11 through 13
    Processing sheet with id=AB4, first strand: chain 'L' and resid 19 through 23
    Processing sheet with id=AB5, first strand: chain 'L' and resid 114 through 118
      removed outlier: 3.627A  pdb=" N   VAL L 133 " --> pdb=" O   PHE L 118 " (cutoff:3.500A)
      removed outlier: 5.853A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 153 through 154
      removed outlier: 3.601A  pdb=" N   VAL L 205 " --> pdb=" O   VAL L 196 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'K' and resid 3 through 7
      removed outlier: 3.859A  pdb=" N   GLN K   3 " --> pdb=" O   SER K  25 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   SER K  25 " --> pdb=" O   GLN K   3 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLN K   5 " --> pdb=" O   ALA K  23 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'K' and resid 57 through 59
      removed outlier: 5.636A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ALA K  49 " --> pdb=" O   TRP K  36 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ILE K  94 " --> pdb=" O   TYR K 102 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   TYR K 102 " --> pdb=" O   ILE K  94 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'K' and resid 57 through 59
      removed outlier: 5.636A  pdb=" N   PHE K  47 " --> pdb=" O   ARG K  38 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   ARG K  38 " --> pdb=" O   PHE K  47 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ALA K  49 " --> pdb=" O   TRP K  36 " (cutoff:3.500A)

    426 hydrogen bonds defined for protein.
    1141 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: 2.27

  Time building geometry restraints manager: 2.03 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2338
        1.35 -     1.47: 2075
        1.47 -     1.59: 3200
        1.59 -     1.71: 0
        1.71 -     1.83: 61
  Bond restraints: 7674
  Sorted by residual:
  bond pdb=" N   VAL K  69 "
       pdb=" CA  VAL K  69 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.030 1.14e-02 7.69e+03 6.73e+00
  bond pdb=" CA  SER K  70 "
       pdb=" CB  SER K  70 "
    ideal  model  delta    sigma   weight residual
    1.533  1.492  0.041 1.69e-02 3.50e+03 5.97e+00
  bond pdb=" N   SER K  70 "
       pdb=" CA  SER K  70 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.029 1.20e-02 6.94e+03 5.68e+00
  bond pdb=" N   ARG K  71 "
       pdb=" CA  ARG K  71 "
    ideal  model  delta    sigma   weight residual
    1.455  1.482 -0.026 1.22e-02 6.72e+03 4.66e+00
  bond pdb=" N   ASP K  72 "
       pdb=" CA  ASP K  72 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.27e-02 6.20e+03 4.45e+00
  ... (remaining 7669 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 10124
        1.57 -     3.14: 254
        3.14 -     4.70: 45
        4.70 -     6.27: 10
        6.27 -     7.84: 1
  Bond angle restraints: 10434
  Sorted by residual:
  angle pdb=" CA  ARG A 258 "
        pdb=" CB  ARG A 258 "
        pdb=" CG  ARG A 258 "
      ideal   model   delta    sigma   weight residual
     114.10  121.94   -7.84 2.00e+00 2.50e-01 1.54e+01
  angle pdb=" N   THR H 160 "
        pdb=" CA  THR H 160 "
        pdb=" C   THR H 160 "
      ideal   model   delta    sigma   weight residual
     114.56  110.30    4.26 1.27e+00 6.20e-01 1.12e+01
  angle pdb=" C   LEU A 257 "
        pdb=" N   ARG A 258 "
        pdb=" CA  ARG A 258 "
      ideal   model   delta    sigma   weight residual
     122.73  117.58    5.15 1.61e+00 3.86e-01 1.02e+01
  angle pdb=" CA  ARG K  71 "
        pdb=" C   ARG K  71 "
        pdb=" O   ARG K  71 "
      ideal   model   delta    sigma   weight residual
     120.80  117.88    2.92 1.11e+00 8.12e-01 6.94e+00
  angle pdb=" CA  VAL K  69 "
        pdb=" C   VAL K  69 "
        pdb=" O   VAL K  69 "
      ideal   model   delta    sigma   weight residual
     120.67  117.65    3.02 1.17e+00 7.31e-01 6.64e+00
  ... (remaining 10429 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4182
       17.98 -    35.95: 279
       35.95 -    53.93: 46
       53.93 -    71.90: 7
       71.90 -    89.88: 8
  Dihedral angle restraints: 4522
    sinusoidal: 1698
      harmonic: 2824
  Sorted by residual:
  dihedral pdb=" CA  ARG A  95 "
           pdb=" C   ARG A  95 "
           pdb=" N   TYR A  96 "
           pdb=" CA  TYR A  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.70  -27.30     0      5.00e+00 4.00e-02 2.98e+01
  dihedral pdb=" CB  CYS K  22 "
           pdb=" SG  CYS K  22 "
           pdb=" SG  CYS K  92 "
           pdb=" CB  CYS K  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   54.46   38.54     1      1.00e+01 1.00e-02 2.09e+01
  dihedral pdb=" CA  LYS A 100 "
           pdb=" C   LYS A 100 "
           pdb=" N   THR A 101 "
           pdb=" CA  THR A 101 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.13   20.87     0      5.00e+00 4.00e-02 1.74e+01
  ... (remaining 4519 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 781
       0.037 -    0.074: 292
       0.074 -    0.111: 80
       0.111 -    0.148: 23
       0.148 -    0.186: 3
  Chirality restraints: 1179
  Sorted by residual:
  chirality pdb=" CA  ARG A 258 "
            pdb=" N   ARG A 258 "
            pdb=" C   ARG A 258 "
            pdb=" CB  ARG A 258 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.61e-01
  chirality pdb=" CA  VAL K  69 "
            pdb=" N   VAL K  69 "
            pdb=" C   VAL K  69 "
            pdb=" CB  VAL K  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.23e-01
  chirality pdb=" CB  THR B  35 "
            pdb=" CA  THR B  35 "
            pdb=" OG1 THR B  35 "
            pdb=" CG2 THR B  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.50e-01
  ... (remaining 1176 not shown)

  Planarity restraints: 1304
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 238 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.05e+00
        pdb=" C   ILE A 238 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ILE A 238 "    0.011 2.00e-02 2.50e+03
        pdb=" N   PHE A 239 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 239 "   -0.008 2.00e-02 2.50e+03   1.58e-02 2.51e+00
        pdb=" C   PHE A 239 "    0.027 2.00e-02 2.50e+03
        pdb=" O   PHE A 239 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ALA A 240 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG K  71 "    0.136 9.50e-02 1.11e+02   6.10e-02 2.29e+00
        pdb=" NE  ARG K  71 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG K  71 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG K  71 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG K  71 "    0.005 2.00e-02 2.50e+03
  ... (remaining 1301 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1004
        2.76 -     3.29: 6956
        3.29 -     3.83: 11499
        3.83 -     4.36: 12874
        4.36 -     4.90: 23368
  Nonbonded interactions: 55701
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 290 "
            pdb=" OG1 THR A 294 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" O   PRO A 122 "
            pdb=" OG  SER A 125 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" ND2 ASN H 100H"
            pdb=" O   ALA L  32 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" OG  SER L  63 "
            pdb=" OG1 THR L  74 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   LYS A 100 "
            pdb=" OG1 THR A 101 "
     model   vdw
     2.304 3.040
  ... (remaining 55696 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=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:             2.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.310
  Find NCS groups from input model:        0.090
  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:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
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   0.045   7674  Z= 0.263
  Angle     :  0.624   7.838  10434  Z= 0.344
  Chirality :  0.043   0.186   1179
  Planarity :  0.004   0.061   1304
  Dihedral  : 12.782  89.878   2699
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.08 (0.26), residues: 959
  helix:  1.34 (0.31), residues: 247
  sheet:  0.33 (0.30), residues: 292
  loop : -0.89 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP H  99 
 HIS   0.003   0.001   HIS H 164 
 PHE   0.021   0.002   PHE L 118 
 TYR   0.024   0.002   TYR L  55 
 ARG   0.004   0.000   ARG A 258 

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.802 
Fit side-chains
REVERT: A  158 LEU cc_start: 0.8111 (tp) cc_final: 0.7897 (tt)
REVERT: L   82 ASP cc_start: 0.7321 (m-30) cc_final: 0.7050 (m-30)
REVERT: K  100 TYR cc_start: 0.8840 (m-80) cc_final: 0.8630 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.1981
  time to fit residues: 51.0885
Evaluate side-chains
  154 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0980
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0670
   chunk 28 optimal weight:    0.2980
   chunk 44 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.3918

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  97 GLN
L 124 GLN
L 160 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.142737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.111035 restraints weight = 32752.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 5.52
r_work: 0.3257 rms_B_bonded: 5.36 restraints_weight: 2.0000
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3260
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3260 r_free = 0.3260    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3259 r_free = 0.3259    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3259
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7674  Z= 0.197
  Angle     :  0.643  11.943  10434  Z= 0.336
  Chirality :  0.043   0.168   1179
  Planarity :  0.004   0.032   1304
  Dihedral  :  4.542  25.821   1061
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 10.52 %
    Favored  : 88.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.50 (0.27), residues: 959
  helix:  1.51 (0.32), residues: 247
  sheet:  0.84 (0.29), residues: 307
  loop : -0.81 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  99 
 HIS   0.004   0.001   HIS H 164 
 PHE   0.018   0.002   PHE A 108 
 TYR   0.019   0.001   TYR K  79 
 ARG   0.011   0.000   ARG A 258 

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 163
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 THR cc_start: 0.7242 (m) cc_final: 0.7019 (p)
REVERT: A  158 LEU cc_start: 0.8122 (tp) cc_final: 0.7917 (tt)
REVERT: A  255 MET cc_start: 0.5728 (mmt) cc_final: 0.4793 (mmp)
REVERT: A  336 TYR cc_start: 0.8485 (m-80) cc_final: 0.8232 (m-80)
REVERT: B  102 TYR cc_start: 0.8135 (m-80) cc_final: 0.7884 (m-80)
REVERT: L   82 ASP cc_start: 0.8135 (m-30) cc_final: 0.7658 (m-30)
REVERT: L  161 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8337 (mt-10)
REVERT: K   34 MET cc_start: 0.8661 (mmm) cc_final: 0.8181 (mmm)
REVERT: K   82 ASN cc_start: 0.8448 (m110) cc_final: 0.8221 (m-40)
REVERT: K  100 TYR cc_start: 0.8901 (m-80) cc_final: 0.8660 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 164
  average time/residue: 0.2024
  time to fit residues: 43.6175
Evaluate side-chains
  155 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 150
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain H residue  184 VAL
Chi-restraints excluded: chain K residue   87 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 57 optimal weight:    0.3980
   chunk 40 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.139116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.107865 restraints weight = 30022.975|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 5.22
r_work: 0.3226 rms_B_bonded: 5.13 restraints_weight: 2.0000
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3230
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3230
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7674  Z= 0.242
  Angle     :  0.620   9.455  10434  Z= 0.326
  Chirality :  0.043   0.222   1179
  Planarity :  0.004   0.045   1304
  Dihedral  :  4.494  27.021   1061
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 13.18 %
    Favored  : 84.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.68 (0.27), residues: 959
  helix:  1.51 (0.33), residues: 247
  sheet:  1.18 (0.29), residues: 302
  loop : -0.77 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  99 
 HIS   0.005   0.001   HIS H 164 
 PHE   0.020   0.002   PHE A 108 
 TYR   0.016   0.001   TYR K  79 
 ARG   0.005   0.000   ARG H  83 

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 154
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 TRP cc_start: 0.8443 (t-100) cc_final: 0.8107 (t-100)
REVERT: A  153 THR cc_start: 0.7285 (m) cc_final: 0.7044 (p)
REVERT: A  336 TYR cc_start: 0.8544 (m-80) cc_final: 0.8307 (m-80)
REVERT: B  102 TYR cc_start: 0.8204 (m-80) cc_final: 0.7951 (m-80)
REVERT: H  116 THR cc_start: 0.8308 (m) cc_final: 0.7858 (t)
REVERT: H  171 GLN cc_start: 0.8633 (mt0) cc_final: 0.8051 (mt0)
REVERT: H  177 SER cc_start: 0.8902 (p) cc_final: 0.8447 (m)
REVERT: L   81 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7559 (tm-30)
REVERT: L   82 ASP cc_start: 0.8128 (m-30) cc_final: 0.7532 (m-30)
REVERT: K   34 MET cc_start: 0.8634 (mmm) cc_final: 0.8168 (mmm)
REVERT: K  100 TYR cc_start: 0.9005 (m-80) cc_final: 0.8753 (m-80)
  outliers start: 16
  outliers final: 13
  residues processed: 163
  average time/residue: 0.1901
  time to fit residues: 41.6962
Evaluate side-chains
  157 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain H residue  142 VAL
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  208 SER
Chi-restraints excluded: chain K residue   87 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 71 optimal weight:    0.5980
   chunk 79 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 61 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 124 GLN
K  82AASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.138513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.106464 restraints weight = 36110.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 5.78
r_work: 0.3192 rms_B_bonded: 5.57 restraints_weight: 2.0000
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3191
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3191 r_free = 0.3191    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3191
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7674  Z= 0.238
  Angle     :  0.603   9.602  10434  Z= 0.317
  Chirality :  0.042   0.174   1179
  Planarity :  0.004   0.044   1304
  Dihedral  :  4.485  27.424   1061
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.87 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.74 (0.27), residues: 959
  helix:  1.58 (0.33), residues: 247
  sheet:  1.18 (0.28), residues: 320
  loop : -0.81 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  99 
 HIS   0.005   0.001   HIS H 164 
 PHE   0.021   0.002   PHE A 338 
 TYR   0.017   0.001   TYR K  79 
 ARG   0.003   0.000   ARG H  83 

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 0.844 
Fit side-chains
REVERT: A  133 TRP cc_start: 0.8457 (t-100) cc_final: 0.8122 (t-100)
REVERT: A  251 CYS cc_start: 0.7523 (m) cc_final: 0.7031 (m)
REVERT: A  255 MET cc_start: 0.5656 (mmt) cc_final: 0.4832 (mmp)
REVERT: A  336 TYR cc_start: 0.8555 (m-80) cc_final: 0.8253 (m-80)
REVERT: B  102 TYR cc_start: 0.8271 (m-80) cc_final: 0.7979 (m-80)
REVERT: H   83 ARG cc_start: 0.8192 (mtm-85) cc_final: 0.7587 (mtm-85)
REVERT: H  116 THR cc_start: 0.8399 (m) cc_final: 0.7980 (t)
REVERT: H  171 GLN cc_start: 0.8697 (mt0) cc_final: 0.8058 (mt0)
REVERT: H  177 SER cc_start: 0.8944 (p) cc_final: 0.8447 (m)
REVERT: L   81 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7652 (tm-30)
REVERT: L   82 ASP cc_start: 0.8220 (m-30) cc_final: 0.7654 (m-30)
REVERT: K   34 MET cc_start: 0.8664 (mmm) cc_final: 0.8276 (mmm)
REVERT: K  100 TYR cc_start: 0.9027 (m-80) cc_final: 0.8638 (m-80)
  outliers start: 18
  outliers final: 13
  residues processed: 161
  average time/residue: 0.1852
  time to fit residues: 40.8640
Evaluate side-chains
  164 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 151
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  208 SER
Chi-restraints excluded: chain K residue   87 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 86 optimal weight:    0.0570
   chunk 70 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0980
   chunk 88 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 83 optimal weight:    0.6980
   chunk 60 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  82AASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.139125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.108083 restraints weight = 28464.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 5.12
r_work: 0.3231 rms_B_bonded: 5.09 restraints_weight: 2.0000
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3233
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3233 r_free = 0.3233    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3233
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.2872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7674  Z= 0.183
  Angle     :  0.586  10.479  10434  Z= 0.306
  Chirality :  0.042   0.163   1179
  Planarity :  0.004   0.042   1304
  Dihedral  :  4.346  27.966   1061
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.99 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.82 (0.27), residues: 959
  helix:  1.70 (0.34), residues: 248
  sheet:  1.25 (0.29), residues: 318
  loop : -0.84 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  99 
 HIS   0.003   0.001   HIS H 164 
 PHE   0.018   0.001   PHE H 146 
 TYR   0.015   0.001   TYR K  79 
 ARG   0.008   0.000   ARG A 258 

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 153
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 TRP cc_start: 0.8464 (t-100) cc_final: 0.8052 (t-100)
REVERT: A  336 TYR cc_start: 0.8525 (m-80) cc_final: 0.8208 (m-80)
REVERT: B  102 TYR cc_start: 0.8176 (m-80) cc_final: 0.7962 (m-80)
REVERT: H   83 ARG cc_start: 0.8148 (mtm-85) cc_final: 0.7543 (mtm-85)
REVERT: H  116 THR cc_start: 0.8368 (m) cc_final: 0.7964 (t)
REVERT: H  171 GLN cc_start: 0.8658 (mt0) cc_final: 0.8014 (mt0)
REVERT: H  177 SER cc_start: 0.8898 (p) cc_final: 0.8417 (m)
REVERT: L   42 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8514 (mmmm)
REVERT: L   81 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7674 (tm-30)
REVERT: L   82 ASP cc_start: 0.8186 (m-30) cc_final: 0.7609 (m-30)
REVERT: K   34 MET cc_start: 0.8590 (mmm) cc_final: 0.8239 (mpp)
REVERT: K  100 TYR cc_start: 0.9026 (m-80) cc_final: 0.8808 (m-80)
  outliers start: 18
  outliers final: 13
  residues processed: 160
  average time/residue: 0.1758
  time to fit residues: 38.6172
Evaluate side-chains
  159 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 146
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  208 SER
Chi-restraints excluded: chain K residue   87 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 28 optimal weight:    0.4980
   chunk 47 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 81 optimal weight:    0.3980
   chunk 17 optimal weight:    0.6980
   chunk 0 optimal weight:    9.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
H 197 ASN
L 124 GLN
K  82AASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.137674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.107068 restraints weight = 27367.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 5.02
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3398
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3398 r_free = 0.3398    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3398 r_free = 0.3398    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3398
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   7674  Z= 0.231
  Angle     :  0.608  10.123  10434  Z= 0.315
  Chirality :  0.042   0.218   1179
  Planarity :  0.004   0.040   1304
  Dihedral  :  4.410  28.314   1061
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.48 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.75 (0.27), residues: 959
  helix:  1.55 (0.33), residues: 248
  sheet:  1.29 (0.29), residues: 324
  loop : -0.93 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  99 
 HIS   0.003   0.001   HIS H 164 
 PHE   0.019   0.001   PHE A 108 
 TYR   0.015   0.001   TYR K  79 
 ARG   0.004   0.000   ARG A 258 

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
REVERT: A  336 TYR cc_start: 0.8424 (m-80) cc_final: 0.8110 (m-80)
REVERT: H   83 ARG cc_start: 0.7700 (mtm-85) cc_final: 0.7149 (mtm-85)
REVERT: H  116 THR cc_start: 0.8134 (m) cc_final: 0.7740 (t)
REVERT: L   82 ASP cc_start: 0.7704 (m-30) cc_final: 0.7013 (m-30)
REVERT: K   97 ASP cc_start: 0.8967 (t0) cc_final: 0.8743 (t70)
REVERT: K  100 TYR cc_start: 0.8946 (m-80) cc_final: 0.8508 (m-80)
  outliers start: 22
  outliers final: 17
  residues processed: 150
  average time/residue: 0.1852
  time to fit residues: 37.9114
Evaluate side-chains
  158 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain B residue   77 LYS
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  208 SER
Chi-restraints excluded: chain K residue   87 THR
Chi-restraints excluded: chain K residue   89 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0270
   chunk 77 optimal weight:    1.9990
   chunk 46 optimal weight:    0.4980
   chunk 74 optimal weight:    1.9990
   chunk 28 optimal weight:    0.2980
   chunk 12 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.3238

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

Flipped N/Q/H residues before XYZ refinement:
H  35 HIS
H 171 GLN
K  82AASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.139139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.107954 restraints weight = 31158.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 5.39
r_work: 0.3221 rms_B_bonded: 5.30 restraints_weight: 2.0000
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3221
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3221
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.3201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7674  Z= 0.161
  Angle     :  0.585  10.876  10434  Z= 0.302
  Chirality :  0.042   0.202   1179
  Planarity :  0.004   0.041   1304
  Dihedral  :  4.266  28.264   1061
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.96 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.88 (0.27), residues: 959
  helix:  1.68 (0.33), residues: 249
  sheet:  1.35 (0.29), residues: 326
  loop : -0.86 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 192 
 HIS   0.002   0.000   HIS H 164 
 PHE   0.023   0.001   PHE A 338 
 TYR   0.013   0.001   TYR K  79 
 ARG   0.013   0.000   ARG A 258 

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 0.854 
Fit side-chains
REVERT: A  336 TYR cc_start: 0.8507 (m-80) cc_final: 0.8211 (m-80)
REVERT: B  102 TYR cc_start: 0.8271 (m-80) cc_final: 0.8041 (m-80)
REVERT: H   83 ARG cc_start: 0.8174 (mtm-85) cc_final: 0.7593 (mtm-85)
REVERT: H  116 THR cc_start: 0.8396 (m) cc_final: 0.7999 (t)
REVERT: H  171 GLN cc_start: 0.8715 (mt0) cc_final: 0.8349 (mt0)
REVERT: H  177 SER cc_start: 0.8959 (p) cc_final: 0.8704 (m)
REVERT: L   42 LYS cc_start: 0.8752 (mmtm) cc_final: 0.8476 (mmmm)
REVERT: L   79 GLN cc_start: 0.8623 (mm110) cc_final: 0.8239 (mm-40)
REVERT: L   82 ASP cc_start: 0.8137 (m-30) cc_final: 0.7769 (m-30)
REVERT: L  187 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7746 (mt-10)
REVERT: K   82 MET cc_start: 0.7511 (mtp) cc_final: 0.7110 (ttm)
REVERT: K   97 ASP cc_start: 0.9035 (t0) cc_final: 0.8770 (t70)
REVERT: K  100 TYR cc_start: 0.9016 (m-80) cc_final: 0.8610 (m-80)
  outliers start: 21
  outliers final: 15
  residues processed: 157
  average time/residue: 0.1901
  time to fit residues: 40.3154
Evaluate side-chains
  159 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 143
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  208 SER
Chi-restraints excluded: chain K residue   87 THR
Chi-restraints excluded: chain K residue  100 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 67 optimal weight:    0.2980
   chunk 40 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9980
   chunk 76 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 63 optimal weight:    0.0000
   chunk 56 optimal weight:    0.0980
   overall best weight:    0.3384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.139490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.108618 restraints weight = 31081.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 5.28
r_work: 0.3229 rms_B_bonded: 5.17 restraints_weight: 2.0000
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3231
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3231 r_free = 0.3231    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3231
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.3308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7674  Z= 0.165
  Angle     :  0.588  10.974  10434  Z= 0.302
  Chirality :  0.041   0.177   1179
  Planarity :  0.004   0.039   1304
  Dihedral  :  4.180  27.413   1061
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.41 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.91 (0.27), residues: 959
  helix:  1.73 (0.33), residues: 249
  sheet:  1.38 (0.29), residues: 326
  loop : -0.86 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  99 
 HIS   0.002   0.001   HIS H 164 
 PHE   0.022   0.001   PHE A 338 
 TYR   0.013   0.001   TYR K  79 
 ARG   0.011   0.000   ARG A 258 

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 146
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
REVERT: A  336 TYR cc_start: 0.8490 (m-80) cc_final: 0.8193 (m-80)
REVERT: B  102 TYR cc_start: 0.8187 (m-80) cc_final: 0.7964 (m-80)
REVERT: H   43 LYS cc_start: 0.9219 (mtmt) cc_final: 0.8997 (mttm)
REVERT: H   83 ARG cc_start: 0.8127 (mtm-85) cc_final: 0.7533 (mtm-85)
REVERT: H  116 THR cc_start: 0.8406 (m) cc_final: 0.8002 (t)
REVERT: L   42 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8432 (mmmm)
REVERT: L   79 GLN cc_start: 0.8661 (mm110) cc_final: 0.8284 (mm-40)
REVERT: L   82 ASP cc_start: 0.8079 (m-30) cc_final: 0.7704 (m-30)
REVERT: L  187 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7779 (mt-10)
REVERT: K   82 MET cc_start: 0.7554 (mtp) cc_final: 0.7157 (ttm)
REVERT: K   97 ASP cc_start: 0.9006 (t0) cc_final: 0.8773 (t70)
REVERT: K  100 TYR cc_start: 0.8992 (m-80) cc_final: 0.8586 (m-80)
  outliers start: 21
  outliers final: 17
  residues processed: 157
  average time/residue: 0.1862
  time to fit residues: 39.6198
Evaluate side-chains
  161 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  208 SER
Chi-restraints excluded: chain K residue   87 THR
Chi-restraints excluded: chain K residue   89 VAL
Chi-restraints excluded: chain K residue  100 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 66 optimal weight:    0.3980
   chunk 93 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   chunk 64 optimal weight:    6.9990
   chunk 89 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0050
   chunk 32 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.4594

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

Flipped N/Q/H residues before XYZ refinement:
H 171 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.138117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.109988 restraints weight = 17837.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 3.80
r_work: 0.3298 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3302
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3302 r_free = 0.3302    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3302 r_free = 0.3302    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3302
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7674  Z= 0.190
  Angle     :  0.611  10.882  10434  Z= 0.311
  Chirality :  0.042   0.183   1179
  Planarity :  0.004   0.039   1304
  Dihedral  :  4.258  28.432   1061
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.02 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.93 (0.27), residues: 959
  helix:  1.70 (0.33), residues: 249
  sheet:  1.49 (0.29), residues: 319
  loop : -0.89 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  99 
 HIS   0.003   0.001   HIS H 164 
 PHE   0.020   0.001   PHE A 338 
 TYR   0.013   0.001   TYR K  79 
 ARG   0.010   0.000   ARG A 258 

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 0.794 
Fit side-chains
REVERT: A  336 TYR cc_start: 0.8394 (m-80) cc_final: 0.8071 (m-80)
REVERT: B  102 TYR cc_start: 0.8111 (m-80) cc_final: 0.7874 (m-80)
REVERT: H   83 ARG cc_start: 0.8027 (mtm-85) cc_final: 0.7459 (mtm-85)
REVERT: H  116 THR cc_start: 0.8338 (m) cc_final: 0.7958 (t)
REVERT: H  171 GLN cc_start: 0.8632 (mt0) cc_final: 0.8136 (mt0)
REVERT: H  177 SER cc_start: 0.8960 (p) cc_final: 0.8579 (m)
REVERT: L   42 LYS cc_start: 0.8707 (mmtm) cc_final: 0.8468 (mmmm)
REVERT: L   79 GLN cc_start: 0.8579 (mm110) cc_final: 0.8198 (mm-40)
REVERT: L   82 ASP cc_start: 0.7976 (m-30) cc_final: 0.7628 (m-30)
REVERT: L  187 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7652 (mt-10)
REVERT: K   82 MET cc_start: 0.7366 (mtp) cc_final: 0.7008 (ttm)
REVERT: K   97 ASP cc_start: 0.8988 (t0) cc_final: 0.8759 (t70)
REVERT: K  100 TYR cc_start: 0.9030 (m-80) cc_final: 0.8584 (m-80)
  outliers start: 18
  outliers final: 17
  residues processed: 151
  average time/residue: 0.1918
  time to fit residues: 38.9441
Evaluate side-chains
  160 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  208 SER
Chi-restraints excluded: chain K residue   87 THR
Chi-restraints excluded: chain K residue   89 VAL
Chi-restraints excluded: chain K residue  100 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 67 optimal weight:    0.4980
   chunk 42 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 29 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:
L 124 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.135661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.104846 restraints weight = 29699.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 5.20
r_work: 0.3193 rms_B_bonded: 5.12 restraints_weight: 2.0000
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3195
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7674  Z= 0.266
  Angle     :  0.643  10.552  10434  Z= 0.331
  Chirality :  0.042   0.186   1179
  Planarity :  0.004   0.038   1304
  Dihedral  :  4.446  29.129   1061
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 18.14 %
    Favored  : 79.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.78 (0.27), residues: 959
  helix:  1.56 (0.33), residues: 249
  sheet:  1.38 (0.29), residues: 323
  loop : -0.95 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  99 
 HIS   0.005   0.001   HIS H 164 
 PHE   0.020   0.002   PHE A 350 
 TYR   0.015   0.001   TYR K  79 
 ARG   0.006   0.000   ARG A 258 

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

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

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1918 Ramachandran restraints generated.
    959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 140
  time to evaluate  : 0.866 
Fit side-chains
REVERT: A  161 MET cc_start: 0.6895 (ttm) cc_final: 0.6688 (ttm)
REVERT: A  336 TYR cc_start: 0.8524 (m-80) cc_final: 0.8243 (m-80)
REVERT: B    4 VAL cc_start: 0.7830 (OUTLIER) cc_final: 0.7618 (t)
REVERT: B  102 TYR cc_start: 0.8233 (m-80) cc_final: 0.8009 (m-80)
REVERT: H   83 ARG cc_start: 0.8133 (mtm-85) cc_final: 0.7501 (mtm-85)
REVERT: H  116 THR cc_start: 0.8436 (m) cc_final: 0.8072 (t)
REVERT: H  171 GLN cc_start: 0.8709 (mt0) cc_final: 0.8087 (mt0)
REVERT: H  177 SER cc_start: 0.8920 (p) cc_final: 0.8445 (m)
REVERT: L   42 LYS cc_start: 0.8794 (mmtm) cc_final: 0.8505 (mmmm)
REVERT: L   79 GLN cc_start: 0.8649 (mm110) cc_final: 0.8271 (mm-40)
REVERT: L   82 ASP cc_start: 0.8099 (m-30) cc_final: 0.7739 (m-30)
REVERT: L  187 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7809 (mt-10)
REVERT: K   97 ASP cc_start: 0.9008 (t0) cc_final: 0.8804 (t70)
  outliers start: 19
  outliers final: 17
  residues processed: 150
  average time/residue: 0.1923
  time to fit residues: 39.1005
Evaluate side-chains
  161 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 142
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 SER
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain B residue    4 VAL
Chi-restraints excluded: chain B residue   35 THR
Chi-restraints excluded: chain H residue   73 THR
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue  107 THR
Chi-restraints excluded: chain H residue  151 THR
Chi-restraints excluded: chain H residue  169 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   29 VAL
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue  107 LYS
Chi-restraints excluded: chain L residue  154 LEU
Chi-restraints excluded: chain L residue  187 GLU
Chi-restraints excluded: chain L residue  208 SER
Chi-restraints excluded: chain K residue   87 THR
Chi-restraints excluded: chain K residue   89 VAL
Chi-restraints excluded: chain K residue  100 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0170
   chunk 47 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0370
   chunk 49 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.5096

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.136529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.105238 restraints weight = 32225.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 5.47
r_work: 0.3196 rms_B_bonded: 5.32 restraints_weight: 2.0000
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3198
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3198 r_free = 0.3198    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3198 r_free = 0.3198    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3198
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.3560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7674  Z= 0.205
  Angle     :  0.629  10.740  10434  Z= 0.323
  Chirality :  0.042   0.182   1179
  Planarity :  0.004   0.038   1304
  Dihedral  :  4.377  29.419   1061
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 18.50 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.11 %
    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:  0.87 (0.27), residues: 959
  helix:  1.63 (0.33), residues: 249
  sheet:  1.44 (0.29), residues: 321
  loop : -0.91 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  99 
 HIS   0.003   0.001   HIS H 164 
 PHE   0.026   0.001   PHE A 338 
 TYR   0.013   0.001   TYR K  79 
 ARG   0.004   0.000   ARG A 258 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4253.84 seconds
wall clock time: 73 minutes 49.66 seconds (4429.66 seconds total)