Starting phenix.real_space_refine
on Wed Feb  4 03:55:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9q2q_72172/02_2026/9q2q_72172.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9q2q_72172/02_2026/9q2q_72172.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9q2q_72172/02_2026/9q2q_72172.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9q2q_72172/02_2026/9q2q_72172.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9q2q_72172/02_2026/9q2q_72172.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9q2q_72172/02_2026/9q2q_72172.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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      36      5.16       5
     C    5698      2.51       5
     N    1390      2.21       5
     O    1538      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8662
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 2016
          Classifications: {'peptide': 249}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 242}
    Chain: "C"
      Number of atoms: 2315
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2315
          Classifications: {'peptide': 290}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 283}
    Chain: "B"
      Number of atoms: 2016
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 249, 2016
          Classifications: {'peptide': 249}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 242}
    Chain: "D"
      Number of atoms: 2315
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2315
          Classifications: {'peptide': 290}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 283}
  Time building chain proxies: 2.18, per 1000 atoms: 0.25
  Number of scatterers: 8662
  At special positions: 0
  Unit cell: (79.65, 141.75, 91.8, 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      36     16.00
     O    1538      8.00
     N    1390      7.00
     C    5698      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 331.6 milliseconds
  

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2036

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 7 sheets defined
      63.6% alpha, 10.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid -2 through 17
      removed outlier: 3.988A  pdb=" N   SER A  17 " --> pdb=" O   SER A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 17 through 40
      removed outlier: 4.326A  pdb=" N   TYR A  21 " --> pdb=" O   SER A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 81
      removed outlier: 5.072A  pdb=" N   ASP A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
      removed outlier: 5.043A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 87
      removed outlier: 3.846A  pdb=" N   TYR A  86 " --> pdb=" O   THR A  82 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   MET A  87 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 82 through 87'
    Processing helix  chain 'A' and resid 89 through 126
      removed outlier: 3.936A  pdb=" N   ILE A  97 " --> pdb=" O   ARG A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 162
      removed outlier: 3.805A  pdb=" N   TYR A 136 " --> pdb=" O   ALA A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 186
      removed outlier: 5.035A  pdb=" N   VAL A 178 " --> pdb=" O   LEU A 174 " (cutoff:3.500A)
      Proline residue:  A 179  - end of helix
      Proline residue:  A 183  - end of helix
    Processing helix  chain 'A' and resid 191 through 199
    Processing helix  chain 'A' and resid 202 through 210
      removed outlier: 3.738A  pdb=" N   TYR A 206 " --> pdb=" O   ILE A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 242
    Processing helix  chain 'C' and resid 38 through 48
    Processing helix  chain 'C' and resid 79 through 91
    Processing helix  chain 'C' and resid 96 through 108
    Processing helix  chain 'C' and resid 109 through 113
    Processing helix  chain 'C' and resid 116 through 120
    Processing helix  chain 'C' and resid 121 through 135
    Processing helix  chain 'C' and resid 151 through 169
      removed outlier: 3.748A  pdb=" N   ASN C 167 " --> pdb=" O   LYS C 163 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 179 through 186
      removed outlier: 3.825A  pdb=" N   ILE C 183 " --> pdb=" O   LYS C 179 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LEU C 185 " --> pdb=" O   GLU C 181 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   ILE C 186 " --> pdb=" O   ASP C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 218 through 233
      removed outlier: 3.557A  pdb=" N   ASP C 223 " --> pdb=" O   HIS C 219 " (cutoff:3.500A)
      removed outlier: 4.988A  pdb=" N   ARG C 224 " --> pdb=" O   LYS C 220 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 253 through 264
    Processing helix  chain 'C' and resid 276 through 286
    Processing helix  chain 'B' and resid -1 through 16
    Processing helix  chain 'B' and resid 17 through 42
      removed outlier: 4.155A  pdb=" N   TYR B  21 " --> pdb=" O   SER B  17 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   SER B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   MET B  42 " --> pdb=" O   MET B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 81
      removed outlier: 4.570A  pdb=" N   VAL B  54 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   ASP B  77 " --> pdb=" O   THR B  73 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   PHE B  78 " --> pdb=" O   ILE B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 86
    Processing helix  chain 'B' and resid 89 through 126
      removed outlier: 3.927A  pdb=" N   ILE B  97 " --> pdb=" O   ARG B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 162
      removed outlier: 3.764A  pdb=" N   TYR B 136 " --> pdb=" O   ALA B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 186
      removed outlier: 4.685A  pdb=" N   VAL B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
      Proline residue:  B 179  - end of helix
      Proline residue:  B 183  - end of helix
    Processing helix  chain 'B' and resid 191 through 199
    Processing helix  chain 'B' and resid 202 through 210
      removed outlier: 4.044A  pdb=" N   TYR B 206 " --> pdb=" O   ILE B 202 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 242
    Processing helix  chain 'D' and resid 38 through 48
    Processing helix  chain 'D' and resid 79 through 91
    Processing helix  chain 'D' and resid 96 through 108
    Processing helix  chain 'D' and resid 109 through 113
    Processing helix  chain 'D' and resid 116 through 120
    Processing helix  chain 'D' and resid 121 through 135
    Processing helix  chain 'D' and resid 151 through 169
    Processing helix  chain 'D' and resid 179 through 186
      removed outlier: 3.839A  pdb=" N   ILE D 183 " --> pdb=" O   LYS D 179 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU D 185 " --> pdb=" O   GLU D 181 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   ILE D 186 " --> pdb=" O   ASP D 182 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 221 through 233
    Processing helix  chain 'D' and resid 253 through 263
    Processing helix  chain 'D' and resid 276 through 290
      removed outlier: 4.287A  pdb=" N   ARG D 287 " --> pdb=" O   ASN D 283 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   GLY D 288 " --> pdb=" O   ILE D 284 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ASP D 289 " --> pdb=" O   ASN D 285 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 19 through 22
      removed outlier: 5.481A  pdb=" N   ILE C  19 " --> pdb=" O   HIS C   5 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   LYS C   2 " --> pdb=" O   ASP C  58 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ASP C  58 " --> pdb=" O   LYS C   2 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   GLU C   4 " --> pdb=" O   LYS C  56 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LYS C  56 " --> pdb=" O   GLU C   4 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 9 through 10
    Processing sheet with id=AA3, first strand: chain 'C' and resid 65 through 68
      removed outlier: 6.462A  pdb=" N   LEU C 141 " --> pdb=" O   LEU C 174 " (cutoff:3.500A)
      removed outlier: 7.894A  pdb=" N   SER C 176 " --> pdb=" O   LEU C 141 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   LEU C 143 " --> pdb=" O   SER C 176 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   VAL C  29 " --> pdb=" O   ILE C 175 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   ILE C  28 " --> pdb=" O   ARG C 189 " (cutoff:3.500A)
      removed outlier: 7.987A  pdb=" N   VAL C 191 " --> pdb=" O   ILE C  28 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   GLY C  30 " --> pdb=" O   VAL C 191 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   LEU C 193 " --> pdb=" O   GLY C  30 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ILE C  32 " --> pdb=" O   LEU C 193 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   ALA C 190 " --> pdb=" O   ASP C 201 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   ASP C 201 " --> pdb=" O   ALA C 190 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   PHE C 192 " --> pdb=" O   VAL C 199 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 235 through 239
      removed outlier: 8.564A  pdb=" N   LEU C 235 " --> pdb=" O   ASN C 248 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   ASN C 248 " --> pdb=" O   LEU C 235 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE C 214 " --> pdb=" O   GLU C 271 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   GLU C 271 " --> pdb=" O   ILE C 214 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 3 through 10
      removed outlier: 4.176A  pdb=" N   GLU D   4 " --> pdb=" O   ILE D  19 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ILE D  19 " --> pdb=" O   GLU D   4 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   ILE D   6 " --> pdb=" O   ASN D  17 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ASN D  17 " --> pdb=" O   ILE D   6 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   LYS D   8 " --> pdb=" O   VAL D  15 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 65 through 68
      removed outlier: 6.394A  pdb=" N   VAL D  29 " --> pdb=" O   ILE D 175 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   ILE D  28 " --> pdb=" O   ARG D 189 " (cutoff:3.500A)
      removed outlier: 7.966A  pdb=" N   VAL D 191 " --> pdb=" O   ILE D  28 " (cutoff:3.500A)
      removed outlier: 6.180A  pdb=" N   GLY D  30 " --> pdb=" O   VAL D 191 " (cutoff:3.500A)
      removed outlier: 7.503A  pdb=" N   LEU D 193 " --> pdb=" O   GLY D  30 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ILE D  32 " --> pdb=" O   LEU D 193 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   ALA D 190 " --> pdb=" O   ASP D 201 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   ASP D 201 " --> pdb=" O   ALA D 190 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   PHE D 192 " --> pdb=" O   VAL D 199 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 235 through 239
      removed outlier: 3.771A  pdb=" N   ASN D 237 " --> pdb=" O   MET D 246 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   TYR D 269 " --> pdb=" O   THR D 216 " (cutoff:3.500A)

    527 hydrogen bonds defined for protein.
    1530 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.28

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2500
        1.34 -     1.47: 2219
        1.47 -     1.59: 4049
        1.59 -     1.72: 0
        1.72 -     1.84: 70
  Bond restraints: 8838
  Sorted by residual:
  bond pdb=" C   ILE A 181 "
       pdb=" N   LYS A 182 "
    ideal  model  delta    sigma   weight residual
    1.332  1.380 -0.048 1.50e-02 4.44e+03 1.03e+01
  bond pdb=" CB  MET D  43 "
       pdb=" CG  MET D  43 "
    ideal  model  delta    sigma   weight residual
    1.520  1.442  0.078 3.00e-02 1.11e+03 6.75e+00
  bond pdb=" CG  LEU C 257 "
       pdb=" CD1 LEU C 257 "
    ideal  model  delta    sigma   weight residual
    1.521  1.437  0.084 3.30e-02 9.18e+02 6.52e+00
  bond pdb=" C   VAL B 178 "
       pdb=" N   PRO B 179 "
    ideal  model  delta    sigma   weight residual
    1.335  1.366 -0.031 1.28e-02 6.10e+03 5.93e+00
  bond pdb=" C   ARG C 110 "
       pdb=" N   PRO C 111 "
    ideal  model  delta    sigma   weight residual
    1.335  1.366 -0.031 1.28e-02 6.10e+03 5.93e+00
  ... (remaining 8833 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.54: 11334
        3.54 -     7.08: 510
        7.08 -    10.63: 69
       10.63 -    14.17: 17
       14.17 -    17.71: 2
  Bond angle restraints: 11932
  Sorted by residual:
  angle pdb=" CA  LYS D 258 "
        pdb=" CB  LYS D 258 "
        pdb=" CG  LYS D 258 "
      ideal   model   delta    sigma   weight residual
     114.10  126.38  -12.28 2.00e+00 2.50e-01 3.77e+01
  angle pdb=" C   ASP D 170 "
        pdb=" N   MET D 171 "
        pdb=" CA  MET D 171 "
      ideal   model   delta    sigma   weight residual
     122.37  132.66  -10.29 1.72e+00 3.38e-01 3.58e+01
  angle pdb=" N   ARG C 287 "
        pdb=" CA  ARG C 287 "
        pdb=" C   ARG C 287 "
      ideal   model   delta    sigma   weight residual
     111.36  117.79   -6.43 1.09e+00 8.42e-01 3.48e+01
  angle pdb=" CA  ARG C 273 "
        pdb=" CB  ARG C 273 "
        pdb=" CG  ARG C 273 "
      ideal   model   delta    sigma   weight residual
     114.10  125.54  -11.44 2.00e+00 2.50e-01 3.27e+01
  angle pdb=" CA  GLN A 162 "
        pdb=" CB  GLN A 162 "
        pdb=" CG  GLN A 162 "
      ideal   model   delta    sigma   weight residual
     114.10  125.40  -11.30 2.00e+00 2.50e-01 3.19e+01
  ... (remaining 11927 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.51: 4644
       16.51 -    33.02: 514
       33.02 -    49.53: 103
       49.53 -    66.04: 17
       66.04 -    82.55: 4
  Dihedral angle restraints: 5282
    sinusoidal: 2126
      harmonic: 3156
  Sorted by residual:
  dihedral pdb=" CA  ILE D  69 "
           pdb=" C   ILE D  69 "
           pdb=" N   GLU D  70 "
           pdb=" CA  GLU D  70 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.34  -38.66     0      5.00e+00 4.00e-02 5.98e+01
  dihedral pdb=" C   PHE D  53 "
           pdb=" N   PHE D  53 "
           pdb=" CA  PHE D  53 "
           pdb=" CB  PHE D  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.45   11.85     0      2.50e+00 1.60e-01 2.25e+01
  dihedral pdb=" C   VAL A 178 "
           pdb=" N   VAL A 178 "
           pdb=" CA  VAL A 178 "
           pdb=" CB  VAL A 178 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -133.73   11.73     0      2.50e+00 1.60e-01 2.20e+01
  ... (remaining 5279 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.125: 1178
       0.125 -    0.249: 193
       0.249 -    0.374: 17
       0.374 -    0.498: 1
       0.498 -    0.623: 3
  Chirality restraints: 1392
  Sorted by residual:
  chirality pdb=" CB  ILE C 247 "
            pdb=" CA  ILE C 247 "
            pdb=" CG1 ILE C 247 "
            pdb=" CG2 ILE C 247 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.02    0.62 2.00e-01 2.50e+01 9.70e+00
  chirality pdb=" CB  ILE C 142 "
            pdb=" CA  ILE C 142 "
            pdb=" CG1 ILE C 142 "
            pdb=" CG2 ILE C 142 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.06    0.58 2.00e-01 2.50e+01 8.50e+00
  chirality pdb=" CB  ILE C 265 "
            pdb=" CA  ILE C 265 "
            pdb=" CG1 ILE C 265 "
            pdb=" CG2 ILE C 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.13    0.52 2.00e-01 2.50e+01 6.67e+00
  ... (remaining 1389 not shown)

  Planarity restraints: 1464
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B  64 "   -0.024 2.00e-02 2.50e+03   4.79e-02 2.30e+01
        pdb=" C   ILE B  64 "    0.083 2.00e-02 2.50e+03
        pdb=" O   ILE B  64 "   -0.031 2.00e-02 2.50e+03
        pdb=" N   ILE B  65 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  81 "   -0.024 2.00e-02 2.50e+03   4.74e-02 2.25e+01
        pdb=" C   GLY A  81 "    0.082 2.00e-02 2.50e+03
        pdb=" O   GLY A  81 "   -0.030 2.00e-02 2.50e+03
        pdb=" N   THR A  82 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 187 "    0.027 2.00e-02 2.50e+03   3.54e-02 2.19e+01
        pdb=" CG  PHE A 187 "   -0.081 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 187 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 187 "    0.026 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 187 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 187 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 187 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1461 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1299
        2.77 -     3.30: 8423
        3.30 -     3.83: 13633
        3.83 -     4.37: 14837
        4.37 -     4.90: 26386
  Nonbonded interactions: 64578
  Sorted by model distance:
  nonbonded pdb=" O   TYR D 112 "
            pdb=" OH  TYR D 120 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   ASN C 283 "
            pdb=" NH1 ARG C 287 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" O   PHE A 204 "
            pdb=" OG1 THR A 208 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   ILE D 130 "
            pdb=" OG  SER D 133 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OH  TYR D 253 "
            pdb=" OG1 THR D 272 "
     model   vdw
     2.322 3.040
  ... (remaining 64573 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.610
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6606
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      :  0.008   0.085   8838  Z= 0.390
  Angle     :  1.670  17.711  11932  Z= 0.925
  Chirality :  0.091   0.623   1392
  Planarity :  0.008   0.050   1464
  Dihedral  : 13.937  82.552   3246
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.46 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Cbeta Deviations :  0.29 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.25), residues: 1070
  helix:  1.63 (0.21), residues: 599
  sheet:  2.26 (0.55), residues: 89
  loop : -1.78 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A   2 
 TYR   0.047   0.004   TYR D 281 
 PHE   0.081   0.005   PHE A 187 
 TRP   0.048   0.003   TRP B  60 
 HIS   0.023   0.003   HIS D 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00786 ( 8838)
  covalent geometry    : angle       1.67020 (11932)
  hydrogen bonds       : bond        0.10805 (  527)
  hydrogen bonds       : angle       5.58350 ( 1530)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 ILE cc_start: 0.5215 (mm) cc_final: 0.4531 (tp)
REVERT: B   14 ILE cc_start: 0.7663 (mm) cc_final: 0.7142 (mm)
REVERT: B   15 PHE cc_start: 0.6575 (m-80) cc_final: 0.6364 (m-80)
REVERT: B  206 TYR cc_start: 0.7314 (p90) cc_final: 0.7029 (p90)
REVERT: D  204 MET cc_start: 0.7448 (ptp) cc_final: 0.7233 (ptp)
REVERT: D  268 LYS cc_start: 0.6921 (ttmm) cc_final: 0.6342 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 0.0763
  time to fit residues: 26.0683
Evaluate side-chains
  184 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:   10.0000
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B   5 ASN
B  84 GLN
B 115 HIS
D 197 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.150853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.135016 restraints weight = 17976.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.136679 restraints weight = 12859.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.137508 restraints weight = 10032.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.138640 restraints weight = 8605.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.139142 restraints weight = 7440.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6665
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8838  Z= 0.148
  Angle     :  0.694  10.123  11932  Z= 0.367
  Chirality :  0.045   0.212   1392
  Planarity :  0.004   0.035   1464
  Dihedral  :  4.788  31.640   1152
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.76 %
    Favored  : 95.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.25), residues: 1070
  helix:  1.59 (0.20), residues: 621
  sheet:  1.95 (0.53), residues: 95
  loop : -1.97 (0.29), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 287 
 TYR   0.018   0.002   TYR B 206 
 PHE   0.030   0.002   PHE B 199 
 TRP   0.023   0.002   TRP B  60 
 HIS   0.004   0.001   HIS B 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8838)
  covalent geometry    : angle       0.69380 (11932)
  hydrogen bonds       : bond        0.04978 (  527)
  hydrogen bonds       : angle       4.71346 ( 1530)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 223
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A  129 LYS cc_start: 0.6527 (pptt) cc_final: 0.6222 (pptt)
REVERT: A  166 MET cc_start: 0.6771 (mmm) cc_final: 0.6352 (tmm)
REVERT: C  266 TYR cc_start: 0.4144 (m-80) cc_final: 0.3653 (m-80)
REVERT: B   14 ILE cc_start: 0.7494 (mm) cc_final: 0.7096 (mm)
REVERT: D   53 PHE cc_start: 0.6530 (p90) cc_final: 0.6126 (p90)
REVERT: D  141 LEU cc_start: 0.9161 (tp) cc_final: 0.8712 (tp)
REVERT: D  268 LYS cc_start: 0.6764 (ttmm) cc_final: 0.6011 (tptt)
  outliers start: 2
  outliers final: 0
  residues processed: 225
  average time/residue: 0.0658
  time to fit residues: 22.1301
Evaluate side-chains
  170 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0370
   chunk 11 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 83 optimal weight:    7.9990
   overall best weight:    0.8260

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

Flipped N/Q/H residues before XYZ refinement:
D 244 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.149546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.133353 restraints weight = 17644.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.134943 restraints weight = 12444.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.136298 restraints weight = 9753.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.137011 restraints weight = 8088.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.137674 restraints weight = 7156.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6702
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8838  Z= 0.140
  Angle     :  0.645   7.433  11932  Z= 0.345
  Chirality :  0.044   0.195   1392
  Planarity :  0.003   0.034   1464
  Dihedral  :  4.691  31.819   1152
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.14 %
    Favored  : 95.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.25), residues: 1070
  helix:  1.56 (0.20), residues: 622
  sheet:  1.90 (0.52), residues: 100
  loop : -1.97 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 287 
 TYR   0.023   0.002   TYR D 266 
 PHE   0.025   0.002   PHE A 150 
 TRP   0.016   0.001   TRP B  60 
 HIS   0.003   0.001   HIS D 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8838)
  covalent geometry    : angle       0.64458 (11932)
  hydrogen bonds       : bond        0.04612 (  527)
  hydrogen bonds       : angle       4.55398 ( 1530)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 225
  time to evaluate  : 0.397 
Fit side-chains
REVERT: C  266 TYR cc_start: 0.3882 (m-80) cc_final: 0.3608 (m-80)
REVERT: C  269 TYR cc_start: 0.6938 (t80) cc_final: 0.6608 (t80)
REVERT: B   14 ILE cc_start: 0.7568 (mm) cc_final: 0.7042 (mm)
REVERT: D    1 MET cc_start: 0.6742 (mmm) cc_final: 0.6204 (mmp)
REVERT: D   46 MET cc_start: 0.8397 (tpp) cc_final: 0.8038 (tpp)
REVERT: D   53 PHE cc_start: 0.6619 (p90) cc_final: 0.6263 (p90)
REVERT: D  141 LEU cc_start: 0.9159 (tp) cc_final: 0.8795 (tp)
REVERT: D  144 ASP cc_start: 0.6553 (t0) cc_final: 0.6073 (t70)
REVERT: D  168 GLU cc_start: 0.6691 (mp0) cc_final: 0.6369 (tp30)
REVERT: D  246 MET cc_start: 0.6060 (mpp) cc_final: 0.5705 (mtt)
REVERT: D  266 TYR cc_start: 0.6178 (m-10) cc_final: 0.4213 (p90)
REVERT: D  268 LYS cc_start: 0.7384 (ttmm) cc_final: 0.6616 (tptt)
  outliers start: 2
  outliers final: 0
  residues processed: 226
  average time/residue: 0.0747
  time to fit residues: 25.1461
Evaluate side-chains
  176 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 72 optimal weight:    0.0980
   chunk 69 optimal weight:    1.9990
   chunk 37 optimal weight:    8.9990
   chunk 47 optimal weight:    0.0980
   chunk 44 optimal weight:    7.9990
   chunk 102 optimal weight:    9.9990
   chunk 71 optimal weight:    0.9980
   chunk 31 optimal weight:    0.1980
   chunk 6 optimal weight:    0.3980
   chunk 97 optimal weight:    0.5980
   overall best weight:    0.2780

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

Flipped N/Q/H residues before XYZ refinement:
C 232 HIS
B   5 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.150632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.134567 restraints weight = 18077.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.136247 restraints weight = 13933.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.137101 restraints weight = 10532.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.137455 restraints weight = 9114.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.137574 restraints weight = 8337.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6697
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8838  Z= 0.129
  Angle     :  0.611   7.619  11932  Z= 0.324
  Chirality :  0.043   0.202   1392
  Planarity :  0.003   0.054   1464
  Dihedral  :  4.602  34.364   1152
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.42 %
    Favored  : 96.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.26), residues: 1070
  helix:  1.64 (0.20), residues: 623
  sheet:  1.84 (0.52), residues: 100
  loop : -1.94 (0.31), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  93 
 TYR   0.023   0.001   TYR D 266 
 PHE   0.038   0.001   PHE B  55 
 TRP   0.015   0.001   TRP B  60 
 HIS   0.003   0.001   HIS D 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8838)
  covalent geometry    : angle       0.61143 (11932)
  hydrogen bonds       : bond        0.04113 (  527)
  hydrogen bonds       : angle       4.38306 ( 1530)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 235
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  166 MET cc_start: 0.6254 (tmm) cc_final: 0.5169 (mmm)
REVERT: C  266 TYR cc_start: 0.4013 (m-80) cc_final: 0.3599 (m-80)
REVERT: B    9 TYR cc_start: 0.7355 (m-80) cc_final: 0.7138 (m-80)
REVERT: B   14 ILE cc_start: 0.7509 (mm) cc_final: 0.7027 (mm)
REVERT: D    1 MET cc_start: 0.6698 (mmm) cc_final: 0.6111 (mmp)
REVERT: D  141 LEU cc_start: 0.9116 (tp) cc_final: 0.8525 (tp)
REVERT: D  144 ASP cc_start: 0.6205 (t0) cc_final: 0.5882 (t70)
REVERT: D  266 TYR cc_start: 0.6149 (m-10) cc_final: 0.4435 (p90)
REVERT: D  268 LYS cc_start: 0.6608 (ttmm) cc_final: 0.5951 (tptt)
  outliers start: 1
  outliers final: 0
  residues processed: 235
  average time/residue: 0.0827
  time to fit residues: 28.0682
Evaluate side-chains
  173 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 47 optimal weight:    7.9990
   chunk 62 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 78 optimal weight:    6.9990
   chunk 35 optimal weight:    0.8980
   chunk 74 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.8986

-------------------------------------------------------------------------------
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 = 0.3910 r_free = 0.3910 target = 0.148496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.132611 restraints weight = 17869.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.133853 restraints weight = 13462.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.135561 restraints weight = 9978.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.135761 restraints weight = 8699.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.135831 restraints weight = 7471.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6755
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8838  Z= 0.137
  Angle     :  0.626   7.277  11932  Z= 0.335
  Chirality :  0.044   0.198   1392
  Planarity :  0.003   0.031   1464
  Dihedral  :  4.604  35.407   1152
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.26), residues: 1070
  helix:  1.61 (0.20), residues: 621
  sheet:  1.57 (0.53), residues: 101
  loop : -1.88 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  93 
 TYR   0.029   0.002   TYR D 266 
 PHE   0.029   0.002   PHE A 233 
 TRP   0.011   0.001   TRP B  60 
 HIS   0.005   0.001   HIS D 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8838)
  covalent geometry    : angle       0.62632 (11932)
  hydrogen bonds       : bond        0.04215 (  527)
  hydrogen bonds       : angle       4.36359 ( 1530)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  166 MET cc_start: 0.6669 (tmm) cc_final: 0.5068 (mmm)
REVERT: C  266 TYR cc_start: 0.3671 (m-80) cc_final: 0.3449 (m-80)
REVERT: C  274 LYS cc_start: 0.6537 (mmmt) cc_final: 0.6303 (pptt)
REVERT: D    1 MET cc_start: 0.6543 (mmm) cc_final: 0.6112 (mmp)
REVERT: D   46 MET cc_start: 0.8421 (tpp) cc_final: 0.8039 (tpp)
REVERT: D  110 ARG cc_start: 0.8167 (mmt90) cc_final: 0.7909 (mmt180)
REVERT: D  141 LEU cc_start: 0.9080 (tp) cc_final: 0.8708 (tp)
REVERT: D  144 ASP cc_start: 0.6380 (t0) cc_final: 0.6001 (t70)
REVERT: D  168 GLU cc_start: 0.8029 (pt0) cc_final: 0.7363 (pt0)
REVERT: D  174 LEU cc_start: 0.7572 (tt) cc_final: 0.7248 (tt)
REVERT: D  246 MET cc_start: 0.6221 (mpp) cc_final: 0.5917 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.0791
  time to fit residues: 24.4533
Evaluate side-chains
  171 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 43 optimal weight:    0.0770
   chunk 19 optimal weight:    0.4980
   overall best weight:    0.7142

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

Flipped N/Q/H residues before XYZ refinement:
B  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.147488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.132270 restraints weight = 18061.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.133890 restraints weight = 12979.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.135033 restraints weight = 10172.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.135599 restraints weight = 8535.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.136224 restraints weight = 7657.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6736
moved from start:          0.2996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8838  Z= 0.130
  Angle     :  0.617   7.968  11932  Z= 0.328
  Chirality :  0.044   0.207   1392
  Planarity :  0.003   0.031   1464
  Dihedral  :  4.629  39.113   1152
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.26), residues: 1070
  helix:  1.62 (0.21), residues: 620
  sheet:  1.47 (0.53), residues: 100
  loop : -1.82 (0.30), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 278 
 TYR   0.022   0.001   TYR D 266 
 PHE   0.029   0.001   PHE A 233 
 TRP   0.008   0.001   TRP A 223 
 HIS   0.002   0.000   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8838)
  covalent geometry    : angle       0.61663 (11932)
  hydrogen bonds       : bond        0.04089 (  527)
  hydrogen bonds       : angle       4.34796 ( 1530)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A  166 MET cc_start: 0.6561 (tmm) cc_final: 0.5211 (mmm)
REVERT: C  211 ASP cc_start: 0.6604 (t0) cc_final: 0.6113 (p0)
REVERT: C  266 TYR cc_start: 0.3526 (m-80) cc_final: 0.3246 (m-80)
REVERT: C  274 LYS cc_start: 0.6586 (mmmt) cc_final: 0.6171 (pptt)
REVERT: B    9 TYR cc_start: 0.7794 (m-80) cc_final: 0.7523 (m-80)
REVERT: B  120 ILE cc_start: 0.8103 (tt) cc_final: 0.7778 (tt)
REVERT: D    1 MET cc_start: 0.6589 (mmm) cc_final: 0.6122 (mmp)
REVERT: D   43 MET cc_start: 0.6836 (mtt) cc_final: 0.5779 (mtt)
REVERT: D   46 MET cc_start: 0.8422 (tpp) cc_final: 0.8000 (tpp)
REVERT: D  112 TYR cc_start: 0.7901 (p90) cc_final: 0.6954 (p90)
REVERT: D  141 LEU cc_start: 0.9108 (tp) cc_final: 0.8482 (tp)
REVERT: D  142 ILE cc_start: 0.8587 (tt) cc_final: 0.8123 (mt)
REVERT: D  144 ASP cc_start: 0.6163 (t0) cc_final: 0.5843 (t70)
REVERT: D  174 LEU cc_start: 0.7660 (tt) cc_final: 0.7068 (tt)
REVERT: D  201 ASP cc_start: 0.6956 (t70) cc_final: 0.6680 (t0)
REVERT: D  246 MET cc_start: 0.5984 (mpp) cc_final: 0.5711 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.0765
  time to fit residues: 24.4961
Evaluate side-chains
  165 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 33 optimal weight:    0.0980
   chunk 43 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 80 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   5 ASN
B  84 GLN
B 130 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.147262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.131902 restraints weight = 18333.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.133526 restraints weight = 13445.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.134441 restraints weight = 10591.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.135278 restraints weight = 9010.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.135713 restraints weight = 7964.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6752
moved from start:          0.3231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8838  Z= 0.130
  Angle     :  0.636   8.279  11932  Z= 0.335
  Chirality :  0.044   0.227   1392
  Planarity :  0.003   0.031   1464
  Dihedral  :  4.614  43.431   1152
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.26), residues: 1070
  helix:  1.59 (0.20), residues: 622
  sheet:  1.37 (0.54), residues: 100
  loop : -1.82 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 278 
 TYR   0.029   0.001   TYR D 266 
 PHE   0.029   0.002   PHE A 233 
 TRP   0.008   0.001   TRP A 223 
 HIS   0.001   0.000   HIS C 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8838)
  covalent geometry    : angle       0.63576 (11932)
  hydrogen bonds       : bond        0.04102 (  527)
  hydrogen bonds       : angle       4.31094 ( 1530)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A  166 MET cc_start: 0.6540 (tmm) cc_final: 0.5336 (mmm)
REVERT: C  211 ASP cc_start: 0.6644 (t0) cc_final: 0.6074 (p0)
REVERT: C  274 LYS cc_start: 0.6611 (mmmt) cc_final: 0.6118 (pptt)
REVERT: B    9 TYR cc_start: 0.7735 (m-80) cc_final: 0.7492 (m-80)
REVERT: B  120 ILE cc_start: 0.8213 (tt) cc_final: 0.7914 (tt)
REVERT: D    1 MET cc_start: 0.6613 (mmm) cc_final: 0.5841 (mmp)
REVERT: D   43 MET cc_start: 0.6539 (mtt) cc_final: 0.5553 (mtt)
REVERT: D   46 MET cc_start: 0.8410 (tpp) cc_final: 0.8078 (tpp)
REVERT: D   89 GLN cc_start: 0.7146 (mm-40) cc_final: 0.6899 (mt0)
REVERT: D  112 TYR cc_start: 0.8053 (p90) cc_final: 0.7073 (p90)
REVERT: D  141 LEU cc_start: 0.9073 (tp) cc_final: 0.8521 (tp)
REVERT: D  142 ILE cc_start: 0.8554 (tt) cc_final: 0.8273 (mt)
REVERT: D  144 ASP cc_start: 0.6118 (t0) cc_final: 0.5848 (t70)
REVERT: D  186 ILE cc_start: 0.6699 (tp) cc_final: 0.6459 (tp)
REVERT: D  201 ASP cc_start: 0.7018 (t70) cc_final: 0.6730 (t0)
REVERT: D  266 TYR cc_start: 0.6349 (m-10) cc_final: 0.5695 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.0719
  time to fit residues: 23.1304
Evaluate side-chains
  163 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 94 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 85 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 103 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 130 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.145872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.130058 restraints weight = 18013.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.131320 restraints weight = 13432.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.132893 restraints weight = 10103.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.133125 restraints weight = 8994.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.133213 restraints weight = 7651.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6815
moved from start:          0.3484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8838  Z= 0.149
  Angle     :  0.692  17.043  11932  Z= 0.364
  Chirality :  0.046   0.288   1392
  Planarity :  0.003   0.032   1464
  Dihedral  :  4.738  44.913   1152
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.26), residues: 1070
  helix:  1.43 (0.20), residues: 623
  sheet:  1.28 (0.54), residues: 100
  loop : -1.84 (0.31), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 278 
 TYR   0.020   0.001   TYR D 266 
 PHE   0.030   0.002   PHE A 233 
 TRP   0.010   0.001   TRP A 223 
 HIS   0.003   0.001   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8838)
  covalent geometry    : angle       0.69175 (11932)
  hydrogen bonds       : bond        0.04202 (  527)
  hydrogen bonds       : angle       4.47748 ( 1530)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.350 
Fit side-chains
REVERT: C   46 MET cc_start: 0.7086 (tpp) cc_final: 0.6760 (tpp)
REVERT: C  211 ASP cc_start: 0.6767 (t0) cc_final: 0.6063 (p0)
REVERT: B  120 ILE cc_start: 0.8258 (tt) cc_final: 0.7947 (tt)
REVERT: D   43 MET cc_start: 0.6706 (mtt) cc_final: 0.6089 (mtt)
REVERT: D   46 MET cc_start: 0.8357 (tpp) cc_final: 0.8020 (tpp)
REVERT: D  112 TYR cc_start: 0.7917 (p90) cc_final: 0.7392 (p90)
REVERT: D  124 MET cc_start: 0.7984 (mtm) cc_final: 0.7712 (mtm)
REVERT: D  140 PHE cc_start: 0.8030 (m-80) cc_final: 0.7743 (m-10)
REVERT: D  141 LEU cc_start: 0.9029 (tp) cc_final: 0.8518 (tp)
REVERT: D  144 ASP cc_start: 0.6349 (t0) cc_final: 0.6044 (t70)
REVERT: D  174 LEU cc_start: 0.7638 (tt) cc_final: 0.7202 (tt)
REVERT: D  201 ASP cc_start: 0.7023 (t70) cc_final: 0.6814 (t0)
REVERT: D  246 MET cc_start: 0.5972 (mpp) cc_final: 0.5529 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.0749
  time to fit residues: 22.9389
Evaluate side-chains
  158 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 102 optimal weight:    0.0980
   chunk 34 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 46 optimal weight:    8.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.145944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.129652 restraints weight = 18214.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.131483 restraints weight = 12867.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.132737 restraints weight = 9904.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.133385 restraints weight = 8236.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.134010 restraints weight = 7334.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6790
moved from start:          0.3635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8838  Z= 0.137
  Angle     :  0.678  15.751  11932  Z= 0.354
  Chirality :  0.046   0.256   1392
  Planarity :  0.003   0.029   1464
  Dihedral  :  4.764  47.941   1152
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.26), residues: 1070
  helix:  1.39 (0.20), residues: 623
  sheet:  1.15 (0.54), residues: 101
  loop : -1.79 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 278 
 TYR   0.020   0.001   TYR C 266 
 PHE   0.036   0.002   PHE A 150 
 TRP   0.013   0.001   TRP B  60 
 HIS   0.003   0.001   HIS C 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8838)
  covalent geometry    : angle       0.67753 (11932)
  hydrogen bonds       : bond        0.04137 (  527)
  hydrogen bonds       : angle       4.47331 ( 1530)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A  156 LEU cc_start: 0.8243 (tp) cc_final: 0.8026 (tp)
REVERT: A  157 ILE cc_start: 0.8217 (tp) cc_final: 0.7873 (tp)
REVERT: A  166 MET cc_start: 0.6374 (tmm) cc_final: 0.5373 (mmm)
REVERT: C  211 ASP cc_start: 0.5789 (t0) cc_final: 0.5453 (p0)
REVERT: C  266 TYR cc_start: 0.3214 (m-80) cc_final: 0.2996 (m-80)
REVERT: B    9 TYR cc_start: 0.7765 (m-80) cc_final: 0.7527 (m-80)
REVERT: B   14 ILE cc_start: 0.7798 (mm) cc_final: 0.7268 (mm)
REVERT: B  120 ILE cc_start: 0.8153 (tt) cc_final: 0.7883 (tt)
REVERT: B  159 LEU cc_start: 0.7192 (mt) cc_final: 0.6964 (mt)
REVERT: D   43 MET cc_start: 0.6462 (mtt) cc_final: 0.5963 (mtt)
REVERT: D   46 MET cc_start: 0.8344 (tpp) cc_final: 0.8130 (tpp)
REVERT: D  112 TYR cc_start: 0.7841 (p90) cc_final: 0.7349 (p90)
REVERT: D  124 MET cc_start: 0.7990 (mtm) cc_final: 0.7780 (mtm)
REVERT: D  141 LEU cc_start: 0.8987 (tp) cc_final: 0.8503 (tp)
REVERT: D  144 ASP cc_start: 0.6237 (t0) cc_final: 0.5974 (t70)
REVERT: D  174 LEU cc_start: 0.7580 (tt) cc_final: 0.7163 (tt)
REVERT: D  246 MET cc_start: 0.5994 (mpp) cc_final: 0.5550 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 208
  average time/residue: 0.0751
  time to fit residues: 23.2177
Evaluate side-chains
  157 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 6 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0870
   chunk 103 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 18 optimal weight:    0.4980
   chunk 25 optimal weight:    0.1980
   chunk 7 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.146532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.130584 restraints weight = 18341.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.132366 restraints weight = 12899.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.133630 restraints weight = 9944.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.134422 restraints weight = 8246.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.134889 restraints weight = 7218.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6767
moved from start:          0.3724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8838  Z= 0.131
  Angle     :  0.675  17.714  11932  Z= 0.350
  Chirality :  0.045   0.266   1392
  Planarity :  0.003   0.028   1464
  Dihedral  :  4.787  50.119   1152
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.26), residues: 1070
  helix:  1.43 (0.20), residues: 620
  sheet:  1.12 (0.53), residues: 101
  loop : -1.73 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 278 
 TYR   0.016   0.001   TYR C 266 
 PHE   0.015   0.001   PHE B 143 
 TRP   0.018   0.002   TRP A 223 
 HIS   0.002   0.000   HIS A 115 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8838)
  covalent geometry    : angle       0.67533 (11932)
  hydrogen bonds       : bond        0.03971 (  527)
  hydrogen bonds       : angle       4.45280 ( 1530)

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

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

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2140 Ramachandran restraints generated.
    1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A  157 ILE cc_start: 0.7943 (tp) cc_final: 0.7564 (tp)
REVERT: A  166 MET cc_start: 0.6389 (tmm) cc_final: 0.5138 (mmm)
REVERT: C   73 LYS cc_start: 0.8441 (mtmt) cc_final: 0.8190 (mttm)
REVERT: C  200 GLN cc_start: 0.7576 (tt0) cc_final: 0.7357 (tt0)
REVERT: C  211 ASP cc_start: 0.5950 (t0) cc_final: 0.5506 (p0)
REVERT: C  266 TYR cc_start: 0.3162 (m-80) cc_final: 0.2955 (m-80)
REVERT: B    9 TYR cc_start: 0.7635 (m-80) cc_final: 0.7399 (m-80)
REVERT: B   14 ILE cc_start: 0.7685 (mm) cc_final: 0.7118 (mm)
REVERT: B  120 ILE cc_start: 0.8019 (tt) cc_final: 0.7721 (tt)
REVERT: D    1 MET cc_start: 0.6823 (mmm) cc_final: 0.6416 (mmp)
REVERT: D   43 MET cc_start: 0.6538 (mtt) cc_final: 0.5939 (mtt)
REVERT: D   46 MET cc_start: 0.8388 (tpp) cc_final: 0.8184 (tpp)
REVERT: D  112 TYR cc_start: 0.7876 (p90) cc_final: 0.7348 (p90)
REVERT: D  141 LEU cc_start: 0.9049 (tp) cc_final: 0.8604 (tp)
REVERT: D  142 ILE cc_start: 0.8382 (tt) cc_final: 0.7826 (mt)
REVERT: D  144 ASP cc_start: 0.6225 (t0) cc_final: 0.5776 (t70)
REVERT: D  246 MET cc_start: 0.5919 (mpp) cc_final: 0.5649 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.0747
  time to fit residues: 22.5802
Evaluate side-chains
  161 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 63 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 85 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
C 200 GLN
** C 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.145030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.129480 restraints weight = 18472.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.131002 restraints weight = 14938.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.131724 restraints weight = 11640.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.132697 restraints weight = 9789.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.132711 restraints weight = 8811.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6823
moved from start:          0.3847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8838  Z= 0.140
  Angle     :  0.674   8.190  11932  Z= 0.353
  Chirality :  0.044   0.259   1392
  Planarity :  0.003   0.028   1464
  Dihedral  :  4.804  50.964   1152
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.26), residues: 1070
  helix:  1.39 (0.20), residues: 622
  sheet:  1.14 (0.54), residues: 101
  loop : -1.72 (0.31), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 278 
 TYR   0.022   0.002   TYR D  99 
 PHE   0.038   0.002   PHE A 233 
 TRP   0.017   0.002   TRP B  60 
 HIS   0.003   0.001   HIS C 219 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8838)
  covalent geometry    : angle       0.67362 (11932)
  hydrogen bonds       : bond        0.04037 (  527)
  hydrogen bonds       : angle       4.46334 ( 1530)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1295.42 seconds
wall clock time: 23 minutes 17.11 seconds (1397.11 seconds total)