Starting phenix.real_space_refine
on Fri Jun  6 21:50:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w8a_37350/06_2025/8w8a_37350.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w8a_37350/06_2025/8w8a_37350.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w8a_37350/06_2025/8w8a_37350.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w8a_37350/06_2025/8w8a_37350.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w8a_37350/06_2025/8w8a_37350.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w8a_37350/06_2025/8w8a_37350.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.026
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      63      5.16       5
     C    5250      2.51       5
     N    1422      2.21       5
     O    1525      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8260
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 236, 1934
          Classifications: {'peptide': 236}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 229}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "B"
      Number of atoms: 2597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2597
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 967
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
    Chain: "R"
      Number of atoms: 2309
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2309
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 11, 'TRANS': 275}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "R"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 17
          Unusual residues: {'T5U': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 5.16, per 1000 atoms: 0.62
  Number of scatterers: 8260
  At special positions: 0
  Unit cell: (79.04, 99.84, 133.12, 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      63     16.00
     O    1525      8.00
     N    1422      7.00
     C    5250      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.27
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.35
    Simple disulfide: pdb=" SG  CYS R  96 " - pdb=" SG  CYS R 182 " distance=2.35

  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: 2.32
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1968

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 11 sheets defined
      44.0% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 37
    Processing helix  chain 'A' and resid 52 through 56
    Processing helix  chain 'A' and resid 95 through 101
      removed outlier: 3.752A  pdb=" N   ASN A 101 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 131
    Processing helix  chain 'A' and resid 145 through 156
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 4.129A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 183 through 205
      removed outlier: 3.690A  pdb=" N   ILE A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   SER A 204 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 243
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.575A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 62 through 65
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.724A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 20 through 51
    Processing helix  chain 'R' and resid 56 through 76
    Processing helix  chain 'R' and resid 76 through 86
      removed outlier: 3.685A  pdb=" N   VAL R  82 " --> pdb=" O   PRO R  78 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 92 through 127
    Processing helix  chain 'R' and resid 130 through 135
    Processing helix  chain 'R' and resid 136 through 160
      Proline residue:  R 151  - end of helix
    Processing helix  chain 'R' and resid 168 through 180
    Processing helix  chain 'R' and resid 187 through 199
      removed outlier: 3.562A  pdb=" N   VAL R 192 " --> pdb=" O   LYS R 188 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 199 through 232
    Processing helix  chain 'R' and resid 247 through 274
      Proline residue:  R 266  - end of helix
    Processing helix  chain 'R' and resid 276 through 280
    Processing helix  chain 'R' and resid 282 through 306
      removed outlier: 3.543A  pdb=" N   ASN R 286 " --> pdb=" O   PRO R 282 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ASN R 296 " --> pdb=" O   PHE R 292 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   SER R 297 " --> pdb=" O   GLY R 293 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   THR R 298 " --> pdb=" O   TYR R 294 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
    Processing helix  chain 'R' and resid 308 through 318
      removed outlier: 3.616A  pdb=" N   ARG R 312 " --> pdb=" O   TYR R 308 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 75
      removed outlier: 4.880A  pdb=" N   VAL A  86 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ALA A 105 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.466A  pdb=" N   ILE A 106 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   PHE A 142 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   PHE A 108 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   ASN A 144 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   VAL A 110 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.616A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.753A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.852A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.512A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.719A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.334A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.306A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.457A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.733A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.937A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.427A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 5.588A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 125 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 18 through 20

    435 hydrogen bonds defined for protein.
    1236 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.36

  Time building geometry restraints manager: 2.64 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1394
        1.32 -     1.44: 2329
        1.44 -     1.56: 4624
        1.56 -     1.69: 2
        1.69 -     1.81: 92
  Bond restraints: 8441
  Sorted by residual:
  bond pdb=" CA  CYS N  96 "
       pdb=" C   CYS N  96 "
    ideal  model  delta    sigma   weight residual
    1.524  1.447  0.077 1.25e-02 6.40e+03 3.78e+01
  bond pdb=" CA  ASP N 109 "
       pdb=" C   ASP N 109 "
    ideal  model  delta    sigma   weight residual
    1.528  1.477  0.051 1.04e-02 9.25e+03 2.40e+01
  bond pdb=" C13 T5U R 401 "
       pdb=" N03 T5U R 401 "
    ideal  model  delta    sigma   weight residual
    1.275  1.354 -0.079 2.00e-02 2.50e+03 1.57e+01
  bond pdb=" CA  SER R 183 "
       pdb=" C   SER R 183 "
    ideal  model  delta    sigma   weight residual
    1.530  1.488  0.042 1.08e-02 8.57e+03 1.54e+01
  bond pdb=" CA  LYS B  57 "
       pdb=" C   LYS B  57 "
    ideal  model  delta    sigma   weight residual
    1.524  1.476  0.048 1.26e-02 6.30e+03 1.46e+01
  ... (remaining 8436 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 11228
        2.32 -     4.64: 173
        4.64 -     6.97: 20
        6.97 -     9.29: 7
        9.29 -    11.61: 4
  Bond angle restraints: 11432
  Sorted by residual:
  angle pdb=" N   ASP N 109 "
        pdb=" CA  ASP N 109 "
        pdb=" C   ASP N 109 "
      ideal   model   delta    sigma   weight residual
     109.71  119.49   -9.78 1.41e+00 5.03e-01 4.81e+01
  angle pdb=" N   ASN A  66 "
        pdb=" CA  ASN A  66 "
        pdb=" C   ASN A  66 "
      ideal   model   delta    sigma   weight residual
     111.30  101.74    9.56 1.43e+00 4.89e-01 4.47e+01
  angle pdb=" N   CYS N  96 "
        pdb=" CA  CYS N  96 "
        pdb=" C   CYS N  96 "
      ideal   model   delta    sigma   weight residual
     110.17  100.08   10.09 1.61e+00 3.86e-01 3.93e+01
  angle pdb=" N   GLY A  68 "
        pdb=" CA  GLY A  68 "
        pdb=" C   GLY A  68 "
      ideal   model   delta    sigma   weight residual
     112.49  119.46   -6.97 1.21e+00 6.83e-01 3.32e+01
  angle pdb=" N   HIS A  64 "
        pdb=" CA  HIS A  64 "
        pdb=" C   HIS A  64 "
      ideal   model   delta    sigma   weight residual
     110.06  102.44    7.62 1.43e+00 4.89e-01 2.84e+01
  ... (remaining 11427 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 4581
       17.53 -    35.07: 362
       35.07 -    52.60: 66
       52.60 -    70.14: 14
       70.14 -    87.67: 3
  Dihedral angle restraints: 5026
    sinusoidal: 1979
      harmonic: 3047
  Sorted by residual:
  dihedral pdb=" CB  CYS R  96 "
           pdb=" SG  CYS R  96 "
           pdb=" SG  CYS R 182 "
           pdb=" CB  CYS R 182 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  179.74  -86.74     1      1.00e+01 1.00e-02 9.05e+01
  dihedral pdb=" CB  CYS N  22 "
           pdb=" SG  CYS N  22 "
           pdb=" SG  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  160.94  -67.94     1      1.00e+01 1.00e-02 5.99e+01
  dihedral pdb=" C   CYS N  96 "
           pdb=" N   CYS N  96 "
           pdb=" CA  CYS N  96 "
           pdb=" CB  CYS N  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.09  -13.51     0      2.50e+00 1.60e-01 2.92e+01
  ... (remaining 5023 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1025
       0.059 -    0.117: 200
       0.117 -    0.176: 36
       0.176 -    0.234: 8
       0.234 -    0.293: 6
  Chirality restraints: 1275
  Sorted by residual:
  chirality pdb=" CA  LYS A 126 "
            pdb=" N   LYS A 126 "
            pdb=" C   LYS A 126 "
            pdb=" CB  LYS A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.14e+00
  chirality pdb=" CA  MET A  60 "
            pdb=" N   MET A  60 "
            pdb=" C   MET A  60 "
            pdb=" CB  MET A  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.07e+00
  chirality pdb=" CA  GLU R 162 "
            pdb=" N   GLU R 162 "
            pdb=" C   GLU R 162 "
            pdb=" CB  GLU R 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.96e+00
  ... (remaining 1272 not shown)

  Planarity restraints: 1456
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR N  94 "    0.014 2.00e-02 2.50e+03   2.81e-02 7.91e+00
        pdb=" C   TYR N  94 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   TYR N  94 "    0.018 2.00e-02 2.50e+03
        pdb=" N   TYR N  95 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B  57 "   -0.011 2.00e-02 2.50e+03   2.28e-02 5.19e+00
        pdb=" C   LYS B  57 "    0.039 2.00e-02 2.50e+03
        pdb=" O   LYS B  57 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ILE B  58 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 125 "   -0.010 2.00e-02 2.50e+03   2.02e-02 4.09e+00
        pdb=" C   PHE A 125 "    0.035 2.00e-02 2.50e+03
        pdb=" O   PHE A 125 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   LYS A 126 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1453 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2228
        2.80 -     3.33: 7744
        3.33 -     3.85: 14024
        3.85 -     4.38: 16667
        4.38 -     4.90: 29104
  Nonbonded interactions: 69767
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A  90 "
            pdb=" OD1 ASP B 186 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" OH  TYR B  59 "
            pdb=" OE1 GLN B  75 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OG1 THR B 128 "
            pdb=" O   ASN B 132 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.320 3.040
  ... (remaining 69762 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.100
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
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   0.321   8444  Z= 0.445
  Angle     :  0.766  23.600  11438  Z= 0.448
  Chirality :  0.053   0.293   1275
  Planarity :  0.004   0.039   1456
  Dihedral  : 12.995  87.674   3049
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  1.12 %
    Favored  : 97.99 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.27), residues: 1033
  helix:  2.09 (0.26), residues: 409
  sheet: -0.20 (0.35), residues: 213
  loop : -0.61 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP R  89 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.027   0.002   PHE R 185 
 TYR   0.016   0.001   TYR N  60 
 ARG   0.003   0.000   ARG N 118 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15468 (  435)
  hydrogen bonds       : angle       6.33955 ( 1236)
  SS BOND              : bond        0.29441 (    3)
  SS BOND              : angle      12.36876 (    6)
  covalent geometry    : bond        0.00517 ( 8441)
  covalent geometry    : angle       0.71182 (11432)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 167
  time to evaluate  : 0.887 
Fit side-chains
REVERT: N    3 GLN cc_start: 0.8194 (pt0) cc_final: 0.7623 (pt0)
REVERT: R   60 TRP cc_start: 0.8292 (m100) cc_final: 0.8079 (m100)
  outliers start: 8
  outliers final: 2
  residues processed: 174
  average time/residue: 1.2301
  time to fit residues: 227.9911
Evaluate side-chains
  132 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 130
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain R residue  225 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 48 optimal weight:    0.1980
   chunk 58 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  59 GLN
A 130 ASN
A 146 GLN
G  24 ASN
R 300 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.150798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.111128 restraints weight = 9618.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 2.41
r_work: 0.3193 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3047 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.1166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8444  Z= 0.143
  Angle     :  0.528   6.381  11438  Z= 0.282
  Chirality :  0.042   0.134   1275
  Planarity :  0.004   0.038   1456
  Dihedral  :  4.898  43.499   1160
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 11.74 %
    Favored  : 86.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.27), residues: 1033
  helix:  2.35 (0.26), residues: 409
  sheet: -0.18 (0.37), residues: 193
  loop : -0.58 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 169 
 HIS   0.005   0.001   HIS A 209 
 PHE   0.014   0.001   PHE B 292 
 TYR   0.012   0.001   TYR R 279 
 ARG   0.005   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04134 (  435)
  hydrogen bonds       : angle       4.94460 ( 1236)
  SS BOND              : bond        0.00398 (    3)
  SS BOND              : angle       1.80701 (    6)
  covalent geometry    : bond        0.00321 ( 8441)
  covalent geometry    : angle       0.52641 (11432)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 1.019 
Fit side-chains
REVERT: B   19 ARG cc_start: 0.8131 (ttm110) cc_final: 0.7619 (ttp-110)
REVERT: N    3 GLN cc_start: 0.8185 (pt0) cc_final: 0.7489 (pt0)
REVERT: R  188 LYS cc_start: 0.8446 (mmtp) cc_final: 0.8164 (mmtp)
  outliers start: 20
  outliers final: 8
  residues processed: 147
  average time/residue: 1.4215
  time to fit residues: 221.8287
Evaluate side-chains
  131 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 123
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  318 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 73 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 22 optimal weight:    0.6980
   chunk 100 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 82 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 26 optimal weight:    0.4980
   chunk 15 optimal weight:    0.0370
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R 300 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.152778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.112931 restraints weight = 9829.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 2.45
r_work: 0.3221 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8444  Z= 0.104
  Angle     :  0.477   6.800  11438  Z= 0.252
  Chirality :  0.041   0.147   1275
  Planarity :  0.003   0.039   1456
  Dihedral  :  4.264  24.695   1158
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.42 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.27), residues: 1033
  helix:  2.46 (0.26), residues: 411
  sheet: -0.18 (0.37), residues: 195
  loop : -0.47 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 169 
 HIS   0.004   0.001   HIS A 209 
 PHE   0.010   0.001   PHE R 267 
 TYR   0.012   0.001   TYR R 308 
 ARG   0.004   0.000   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03617 (  435)
  hydrogen bonds       : angle       4.65837 ( 1236)
  SS BOND              : bond        0.00243 (    3)
  SS BOND              : angle       1.29344 (    6)
  covalent geometry    : bond        0.00225 ( 8441)
  covalent geometry    : angle       0.47613 (11432)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 1.014 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.8483 (m-80) cc_final: 0.8247 (m-80)
REVERT: N    3 GLN cc_start: 0.8168 (pt0) cc_final: 0.7497 (pt0)
REVERT: R   83 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6033 (ttm170)
REVERT: R  188 LYS cc_start: 0.8394 (mmtp) cc_final: 0.8187 (mmtp)
  outliers start: 20
  outliers final: 12
  residues processed: 145
  average time/residue: 1.2014
  time to fit residues: 185.6693
Evaluate side-chains
  134 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ASP
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   83 ARG
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  318 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 25 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9980
   chunk 92 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0470
   overall best weight:    0.6880

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R 300 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.152155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.112446 restraints weight = 9687.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 2.42
r_work: 0.3189 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8444  Z= 0.114
  Angle     :  0.487   8.333  11438  Z= 0.256
  Chirality :  0.041   0.138   1275
  Planarity :  0.003   0.039   1456
  Dihedral  :  4.200  24.571   1158
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 15.55 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.27), residues: 1033
  helix:  2.53 (0.26), residues: 408
  sheet: -0.17 (0.36), residues: 190
  loop : -0.52 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 169 
 HIS   0.004   0.001   HIS A 209 
 PHE   0.010   0.001   PHE R 267 
 TYR   0.011   0.001   TYR R 308 
 ARG   0.005   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03551 (  435)
  hydrogen bonds       : angle       4.57247 ( 1236)
  SS BOND              : bond        0.00291 (    3)
  SS BOND              : angle       1.27127 (    6)
  covalent geometry    : bond        0.00255 ( 8441)
  covalent geometry    : angle       0.48652 (11432)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 1.018 
Fit side-chains
REVERT: B   19 ARG cc_start: 0.8158 (ttm110) cc_final: 0.7670 (ttp-110)
REVERT: B  217 MET cc_start: 0.7587 (ptt) cc_final: 0.7338 (pmt)
REVERT: N    3 GLN cc_start: 0.8168 (pt0) cc_final: 0.7532 (pt0)
REVERT: R   83 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6030 (ttm170)
  outliers start: 24
  outliers final: 12
  residues processed: 139
  average time/residue: 1.1668
  time to fit residues: 172.7971
Evaluate side-chains
  131 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   83 ARG
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  318 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 96 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 79 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
R 300 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.148965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.111668 restraints weight = 9709.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 2.29
r_work: 0.3203 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8444  Z= 0.131
  Angle     :  0.501   9.331  11438  Z= 0.261
  Chirality :  0.042   0.139   1275
  Planarity :  0.003   0.038   1456
  Dihedral  :  4.236  24.500   1158
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 16.33 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.27), residues: 1033
  helix:  2.54 (0.26), residues: 408
  sheet: -0.14 (0.36), residues: 198
  loop : -0.53 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 169 
 HIS   0.004   0.001   HIS A 209 
 PHE   0.011   0.001   PHE R 267 
 TYR   0.012   0.001   TYR R 308 
 ARG   0.003   0.000   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03633 (  435)
  hydrogen bonds       : angle       4.57098 ( 1236)
  SS BOND              : bond        0.00254 (    3)
  SS BOND              : angle       1.35401 (    6)
  covalent geometry    : bond        0.00301 ( 8441)
  covalent geometry    : angle       0.50031 (11432)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 128
  time to evaluate  : 1.034 
Fit side-chains
REVERT: B   19 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7692 (ttp-110)
REVERT: B  217 MET cc_start: 0.7529 (ptt) cc_final: 0.7291 (pmt)
REVERT: N    3 GLN cc_start: 0.8143 (pt0) cc_final: 0.7505 (pt0)
REVERT: R   83 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6042 (ttm170)
  outliers start: 29
  outliers final: 16
  residues processed: 146
  average time/residue: 1.1370
  time to fit residues: 177.1890
Evaluate side-chains
  133 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue   37 VAL
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   83 ARG
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  318 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 14 optimal weight:    0.0980
   chunk 57 optimal weight:    0.9980
   chunk 66 optimal weight:    0.3980
   chunk 79 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 23 optimal weight:    8.9990
   chunk 58 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 20 optimal weight:    0.4980
   chunk 50 optimal weight:    2.9990
   chunk 2 optimal weight:   10.0000
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
N   5 GLN
R 300 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.150558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.113349 restraints weight = 9709.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.29
r_work: 0.3227 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8444  Z= 0.105
  Angle     :  0.490   9.979  11438  Z= 0.254
  Chirality :  0.041   0.183   1275
  Planarity :  0.003   0.039   1456
  Dihedral  :  4.094  24.167   1158
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.67 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.27), residues: 1033
  helix:  2.58 (0.26), residues: 408
  sheet: -0.05 (0.36), residues: 196
  loop : -0.52 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 169 
 HIS   0.003   0.001   HIS A 209 
 PHE   0.010   0.001   PHE R 267 
 TYR   0.014   0.001   TYR N  80 
 ARG   0.003   0.000   ARG N  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03409 (  435)
  hydrogen bonds       : angle       4.49054 ( 1236)
  SS BOND              : bond        0.00202 (    3)
  SS BOND              : angle       1.15195 (    6)
  covalent geometry    : bond        0.00233 ( 8441)
  covalent geometry    : angle       0.48965 (11432)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 128
  time to evaluate  : 1.002 
Fit side-chains
REVERT: A   34 GLU cc_start: 0.7415 (tt0) cc_final: 0.6938 (mt-10)
REVERT: A  196 GLU cc_start: 0.8295 (tp30) cc_final: 0.8067 (tp30)
REVERT: B  217 MET cc_start: 0.7529 (ptt) cc_final: 0.7303 (pmt)
REVERT: N    3 GLN cc_start: 0.8135 (pt0) cc_final: 0.7476 (pt0)
REVERT: N   85 SER cc_start: 0.8690 (m) cc_final: 0.8309 (p)
REVERT: R   83 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.5968 (ttm170)
  outliers start: 27
  outliers final: 14
  residues processed: 144
  average time/residue: 1.2365
  time to fit residues: 189.8991
Evaluate side-chains
  133 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   83 ARG
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0770
   chunk 32 optimal weight:    0.0370
   chunk 8 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 23 optimal weight:    7.9990
   overall best weight:    0.4616

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

Flipped N/Q/H residues before XYZ refinement:
R 300 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.152145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.114789 restraints weight = 9738.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.31
r_work: 0.3215 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8444  Z= 0.101
  Angle     :  0.494  11.143  11438  Z= 0.254
  Chirality :  0.041   0.170   1275
  Planarity :  0.003   0.044   1456
  Dihedral  :  4.012  24.343   1158
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.90 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.27), residues: 1033
  helix:  2.62 (0.26), residues: 408
  sheet:  0.01 (0.35), residues: 203
  loop : -0.43 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 209 
 PHE   0.009   0.001   PHE R 267 
 TYR   0.010   0.001   TYR R 308 
 ARG   0.011   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03311 (  435)
  hydrogen bonds       : angle       4.42813 ( 1236)
  SS BOND              : bond        0.00191 (    3)
  SS BOND              : angle       1.05754 (    6)
  covalent geometry    : bond        0.00225 ( 8441)
  covalent geometry    : angle       0.49390 (11432)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 1.003 
Fit side-chains
REVERT: A   34 GLU cc_start: 0.7409 (tt0) cc_final: 0.6928 (mt-10)
REVERT: A  196 GLU cc_start: 0.8254 (tp30) cc_final: 0.8018 (tp30)
REVERT: B   19 ARG cc_start: 0.8248 (ttm110) cc_final: 0.7748 (ttp-110)
REVERT: B  217 MET cc_start: 0.7525 (ptt) cc_final: 0.7306 (pmt)
REVERT: N    3 GLN cc_start: 0.8108 (pt0) cc_final: 0.7425 (pt0)
REVERT: N   85 SER cc_start: 0.8751 (m) cc_final: 0.8373 (p)
REVERT: R   83 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.5878 (ttm170)
  outliers start: 22
  outliers final: 16
  residues processed: 146
  average time/residue: 1.1524
  time to fit residues: 179.6658
Evaluate side-chains
  141 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   83 ARG
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain R residue  318 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 17 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 92 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 60 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
N 120 GLN
R 300 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.147669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.106974 restraints weight = 9866.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.44
r_work: 0.3134 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8444  Z= 0.226
  Angle     :  0.588   7.387  11438  Z= 0.310
  Chirality :  0.045   0.164   1275
  Planarity :  0.004   0.045   1456
  Dihedral  :  4.589  27.535   1158
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.23 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.27), residues: 1033
  helix:  2.33 (0.26), residues: 408
  sheet: -0.26 (0.36), residues: 198
  loop : -0.58 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 148 
 HIS   0.006   0.001   HIS R  63 
 PHE   0.015   0.002   PHE B 292 
 TYR   0.016   0.002   TYR R 304 
 ARG   0.009   0.001   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04254 (  435)
  hydrogen bonds       : angle       4.73644 ( 1236)
  SS BOND              : bond        0.00363 (    3)
  SS BOND              : angle       1.81270 (    6)
  covalent geometry    : bond        0.00534 ( 8441)
  covalent geometry    : angle       0.58658 (11432)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 0.906 
Fit side-chains
REVERT: B   19 ARG cc_start: 0.8114 (ttm110) cc_final: 0.7648 (ttp-110)
REVERT: G   21 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8230 (mpp)
REVERT: G   58 GLU cc_start: 0.7839 (tp30) cc_final: 0.7610 (tp30)
REVERT: N    3 GLN cc_start: 0.8162 (pt0) cc_final: 0.7505 (pt0)
REVERT: R   83 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6090 (ttm170)
  outliers start: 25
  outliers final: 15
  residues processed: 137
  average time/residue: 1.3712
  time to fit residues: 202.4442
Evaluate side-chains
  130 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 1.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  307 VAL
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   83 ARG
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  318 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 94 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 44 optimal weight:    0.4980
   chunk 28 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 37 optimal weight:    0.1980
   chunk 6 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
R 300 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.149590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.112093 restraints weight = 9894.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 2.30
r_work: 0.3206 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.1808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8444  Z= 0.114
  Angle     :  0.522  13.110  11438  Z= 0.267
  Chirality :  0.042   0.151   1275
  Planarity :  0.003   0.039   1456
  Dihedral  :  4.243  24.586   1158
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 19.35 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.27), residues: 1033
  helix:  2.42 (0.26), residues: 410
  sheet: -0.25 (0.35), residues: 205
  loop : -0.42 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 169 
 HIS   0.003   0.001   HIS A 209 
 PHE   0.010   0.001   PHE B 292 
 TYR   0.015   0.001   TYR N  80 
 ARG   0.009   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03548 (  435)
  hydrogen bonds       : angle       4.52427 ( 1236)
  SS BOND              : bond        0.00201 (    3)
  SS BOND              : angle       1.14949 (    6)
  covalent geometry    : bond        0.00258 ( 8441)
  covalent geometry    : angle       0.52173 (11432)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.858 
Fit side-chains
REVERT: B   19 ARG cc_start: 0.8111 (ttm110) cc_final: 0.7795 (ttp-110)
REVERT: B  217 MET cc_start: 0.7498 (ptt) cc_final: 0.7284 (pmt)
REVERT: G   21 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8191 (mpp)
REVERT: N    3 GLN cc_start: 0.8105 (pt0) cc_final: 0.7429 (pt0)
REVERT: R   83 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.5890 (ttm170)
  outliers start: 17
  outliers final: 11
  residues processed: 135
  average time/residue: 1.2528
  time to fit residues: 179.9080
Evaluate side-chains
  134 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   83 ARG
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  277 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 96 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
R 300 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.148948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.111638 restraints weight = 9781.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 2.25
r_work: 0.3175 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8444  Z= 0.135
  Angle     :  0.535   9.347  11438  Z= 0.276
  Chirality :  0.042   0.151   1275
  Planarity :  0.003   0.038   1456
  Dihedral  :  4.244  24.844   1158
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 20.25 %
    Favored  : 77.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.27), residues: 1033
  helix:  2.43 (0.26), residues: 410
  sheet: -0.17 (0.36), residues: 205
  loop : -0.43 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 169 
 HIS   0.004   0.001   HIS A 209 
 PHE   0.011   0.001   PHE B 292 
 TYR   0.012   0.001   TYR R 308 
 ARG   0.009   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03631 (  435)
  hydrogen bonds       : angle       4.51887 ( 1236)
  SS BOND              : bond        0.00243 (    3)
  SS BOND              : angle       1.27300 (    6)
  covalent geometry    : bond        0.00314 ( 8441)
  covalent geometry    : angle       0.53426 (11432)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.896 
Fit side-chains
REVERT: B   19 ARG cc_start: 0.8111 (ttm110) cc_final: 0.7644 (ttp-110)
REVERT: B  217 MET cc_start: 0.7565 (ptt) cc_final: 0.7352 (pmt)
REVERT: G   21 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8225 (mpp)
REVERT: N    3 GLN cc_start: 0.8142 (pt0) cc_final: 0.7469 (pt0)
REVERT: R   83 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.5889 (ttm170)
  outliers start: 16
  outliers final: 12
  residues processed: 133
  average time/residue: 1.1767
  time to fit residues: 166.4808
Evaluate side-chains
  134 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain G residue   21 MET
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   21 SER
Chi-restraints excluded: chain R residue   35 LEU
Chi-restraints excluded: chain R residue   83 ARG
Chi-restraints excluded: chain R residue   90 TYR
Chi-restraints excluded: chain R residue  277 LEU
Chi-restraints excluded: chain R residue  290 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 77 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 120 GLN
R 300 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.148943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.111514 restraints weight = 9836.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 2.26
r_work: 0.3174 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8444  Z= 0.137
  Angle     :  0.540  13.081  11438  Z= 0.276
  Chirality :  0.042   0.150   1275
  Planarity :  0.003   0.038   1456
  Dihedral  :  4.261  24.932   1158
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 19.91 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.27), residues: 1033
  helix:  2.40 (0.26), residues: 410
  sheet: -0.14 (0.36), residues: 205
  loop : -0.43 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP N  47 
 HIS   0.004   0.001   HIS R  63 
 PHE   0.011   0.001   PHE B 292 
 TYR   0.013   0.001   TYR N  80 
 ARG   0.008   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03643 (  435)
  hydrogen bonds       : angle       4.50887 ( 1236)
  SS BOND              : bond        0.00255 (    3)
  SS BOND              : angle       1.27559 (    6)
  covalent geometry    : bond        0.00320 ( 8441)
  covalent geometry    : angle       0.53941 (11432)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7273.15 seconds
wall clock time: 126 minutes 35.11 seconds (7595.11 seconds total)