Starting phenix.real_space_refine
on Sat Aug 23 01:07:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w8b_37351/08_2025/8w8b_37351.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w8b_37351/08_2025/8w8b_37351.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w8b_37351/08_2025/8w8b_37351.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w8b_37351/08_2025/8w8b_37351.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w8b_37351/08_2025/8w8b_37351.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w8b_37351/08_2025/8w8b_37351.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.152
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      64      5.16       5
     C    5613      2.51       5
     N    1459      2.21       5
     O    1598      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8734
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1751
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2513
          Classifications: {'peptide': 328}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 322}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "E"
      Number of atoms: 1756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1756
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 10, 'TRANS': 217}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 347
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 347
          Classifications: {'peptide': 45}
          Link IDs: {'PTRANS': 4, 'TRANS': 40}
    Chain: "R"
      Number of atoms: 2197
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2197
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 11, 'TRANS': 266}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 170
          Unusual residues: {'CLR': 5, 'PLM': 1, 'UJL': 1}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
  Time building chain proxies: 1.52, per 1000 atoms: 0.17
  Number of scatterers: 8734
  At special positions: 0
  Unit cell: (86.52, 115.36, 128.544, 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      64     16.00
     O    1598      8.00
     N    1459      7.00
     C    5613      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: 0.60
  Conformation dependent library (CDL) restraints added in 335.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2046

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 12 sheets defined
      40.6% alpha, 23.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.585A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL A  13 " --> pdb=" O   ASP A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 44
      No H-bonds generated for 'chain 'A' and resid 42 through 44'
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.569A  pdb=" N   LYS A 210 " --> pdb=" O   GLU A 207 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 327 through 352
      removed outlier: 4.182A  pdb=" N   ASN A 331 " --> pdb=" O   THR A 327 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   VAL A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 14 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 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 4.177A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'E' and resid 220 through 224
      removed outlier: 3.567A  pdb=" N   VAL E 224 " --> pdb=" O   ALA E 221 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 19 through 23
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'R' and resid 36 through 64
    Processing helix  chain 'R' and resid 65 through 68
      removed outlier: 3.509A  pdb=" N   GLN R  68 " --> pdb=" O   ARG R  65 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 65 through 68'
    Processing helix  chain 'R' and resid 69 through 100
      removed outlier: 4.402A  pdb=" N   LEU R  90 " --> pdb=" O   SER R  86 " (cutoff:3.500A)
      Proline residue:  R  91  - end of helix
    Processing helix  chain 'R' and resid 104 through 140
      removed outlier: 4.092A  pdb=" N   THR R 108 " --> pdb=" O   LEU R 104 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 147
    Processing helix  chain 'R' and resid 149 through 174
      removed outlier: 3.905A  pdb=" N   ALA R 153 " --> pdb=" O   THR R 149 " (cutoff:3.500A)
      Proline residue:  R 170  - end of helix
    Processing helix  chain 'R' and resid 192 through 204
    Processing helix  chain 'R' and resid 204 through 228
    Processing helix  chain 'R' and resid 325 through 371
      Proline residue:  R 360  - end of helix
      Proline residue:  R 369  - end of helix
    Processing helix  chain 'R' and resid 378 through 401
      removed outlier: 3.800A  pdb=" N   ASN R 392 " --> pdb=" O   LEU R 388 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   SER R 393 " --> pdb=" O   GLY R 389 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   LEU R 394 " --> pdb=" O   TYR R 390 " (cutoff:3.500A)
      Proline residue:  R 397  - end of helix
    Processing helix  chain 'R' and resid 404 through 415
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.905A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 4.279A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.053A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.168A  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: 6.782A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.001A  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: 4.011A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.009A  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: 6.604A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.025A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.141A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   MET B 217 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.578A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.769A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 4 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.811A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142
    Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.345A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)

    466 hydrogen bonds defined for protein.
    1314 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: 0.95

  Time building geometry restraints manager: 0.80 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2760
        1.34 -     1.46: 1943
        1.46 -     1.58: 4132
        1.58 -     1.69: 1
        1.69 -     1.81: 90
  Bond restraints: 8926
  Sorted by residual:
  bond pdb=" C8  UJL R 507 "
       pdb=" S1  UJL R 507 "
    ideal  model  delta    sigma   weight residual
    1.725  1.522  0.203 2.00e-02 2.50e+03 1.03e+02
  bond pdb=" C9  UJL R 507 "
       pdb=" S1  UJL R 507 "
    ideal  model  delta    sigma   weight residual
    1.730  1.536  0.194 2.00e-02 2.50e+03 9.44e+01
  bond pdb=" C6  UJL R 507 "
       pdb=" C7  UJL R 507 "
    ideal  model  delta    sigma   weight residual
    1.428  1.600 -0.172 2.00e-02 2.50e+03 7.36e+01
  bond pdb=" C7  UJL R 507 "
       pdb=" C8  UJL R 507 "
    ideal  model  delta    sigma   weight residual
    1.364  1.419 -0.055 2.00e-02 2.50e+03 7.54e+00
  bond pdb=" N   TYR R  35 "
       pdb=" CA  TYR R  35 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.09e+00
  ... (remaining 8921 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.25: 12064
        3.25 -     6.50: 42
        6.50 -     9.74: 3
        9.74 -    12.99: 0
       12.99 -    16.24: 1
  Bond angle restraints: 12110
  Sorted by residual:
  angle pdb=" C8  UJL R 507 "
        pdb=" S1  UJL R 507 "
        pdb=" C9  UJL R 507 "
      ideal   model   delta    sigma   weight residual
      91.70  107.94  -16.24 3.00e+00 1.11e-01 2.93e+01
  angle pdb=" N   ARG A 242 "
        pdb=" CA  ARG A 242 "
        pdb=" C   ARG A 242 "
      ideal   model   delta    sigma   weight residual
     112.89  108.28    4.61 1.24e+00 6.50e-01 1.38e+01
  angle pdb=" N   THR B 128 "
        pdb=" CA  THR B 128 "
        pdb=" CB  THR B 128 "
      ideal   model   delta    sigma   weight residual
     109.97  115.34   -5.37 1.47e+00 4.63e-01 1.33e+01
  angle pdb=" N   ASP B 291 "
        pdb=" CA  ASP B 291 "
        pdb=" C   ASP B 291 "
      ideal   model   delta    sigma   weight residual
     113.21  109.45    3.76 1.15e+00 7.56e-01 1.07e+01
  angle pdb=" N   SER B 245 "
        pdb=" CA  SER B 245 "
        pdb=" C   SER B 245 "
      ideal   model   delta    sigma   weight residual
     109.69  114.17   -4.48 1.44e+00 4.82e-01 9.69e+00
  ... (remaining 12105 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 4992
       17.94 -    35.87: 409
       35.87 -    53.80: 105
       53.80 -    71.74: 22
       71.74 -    89.67: 7
  Dihedral angle restraints: 5535
    sinusoidal: 2362
      harmonic: 3173
  Sorted by residual:
  dihedral pdb=" CA  ARG E 191 "
           pdb=" C   ARG E 191 "
           pdb=" N   MET E 192 "
           pdb=" CA  MET E 192 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.72   18.28     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  LEU B 117 "
           pdb=" C   LEU B 117 "
           pdb=" N   ASP B 118 "
           pdb=" CA  ASP B 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.30   17.70     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CG  ARG G  62 "
           pdb=" CD  ARG G  62 "
           pdb=" NE  ARG G  62 "
           pdb=" CZ  ARG G  62 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   41.43   48.57     2      1.50e+01 4.44e-03 1.20e+01
  ... (remaining 5532 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1070
       0.040 -    0.080: 221
       0.080 -    0.120: 80
       0.120 -    0.159: 14
       0.159 -    0.199: 1
  Chirality restraints: 1386
  Sorted by residual:
  chirality pdb=" CA  THR B 128 "
            pdb=" N   THR B 128 "
            pdb=" C   THR B 128 "
            pdb=" CB  THR B 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.33    0.20 2.00e-01 2.50e+01 9.92e-01
  chirality pdb=" CB  VAL R  98 "
            pdb=" CA  VAL R  98 "
            pdb=" CG1 VAL R  98 "
            pdb=" CG2 VAL R  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.93e-01
  chirality pdb=" C3  UJL R 507 "
            pdb=" C2  UJL R 507 "
            pdb=" C9  UJL R 507 "
            pdb=" O1  UJL R 507 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.32   -0.14 2.00e-01 2.50e+01 4.84e-01
  ... (remaining 1383 not shown)

  Planarity restraints: 1492
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  62 "    0.172 9.50e-02 1.11e+02   7.74e-02 4.24e+00
        pdb=" NE  ARG G  62 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  62 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  62 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  62 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR E 235 "    0.027 5.00e-02 4.00e+02   4.13e-02 2.73e+00
        pdb=" N   PRO E 236 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO E 236 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO E 236 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 219 "    0.112 9.50e-02 1.11e+02   5.02e-02 1.84e+00
        pdb=" NE  ARG B 219 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 219 "    0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 219 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 219 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1489 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 109
        2.63 -     3.20: 7774
        3.20 -     3.77: 13188
        3.77 -     4.33: 19297
        4.33 -     4.90: 32905
  Nonbonded interactions: 73273
  Sorted by model distance:
  nonbonded pdb=" OG  SER G  57 "
            pdb=" OE1 GLU G  58 "
     model   vdw
     2.063 3.040
  nonbonded pdb=" O   ASP B 333 "
            pdb=" OG  SER B 334 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" O   ARG B 314 "
            pdb=" OG  SER B 331 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   SER E  85 "
            pdb=" OG  SER E  85 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" OG1 THR B  29 "
            pdb=" OE1 GLN B  32 "
     model   vdw
     2.232 3.040
  ... (remaining 73268 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:             0.880
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.340
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:5.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
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      :  0.005   0.203   8926  Z= 0.229
  Angle     :  0.576  16.239  12110  Z= 0.314
  Chirality :  0.040   0.199   1386
  Planarity :  0.004   0.077   1492
  Dihedral  : 14.501  89.673   3489
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 14.72 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.26), residues: 1076
  helix:  2.56 (0.27), residues: 375
  sheet:  0.50 (0.31), residues: 275
  loop : -0.32 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG G  62 
 TYR   0.010   0.001   TYR E 190 
 PHE   0.020   0.001   PHE B 292 
 TRP   0.011   0.001   TRP E  47 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 ( 8926)
  covalent geometry    : angle       0.57572 (12110)
  hydrogen bonds       : bond        0.17407 (  466)
  hydrogen bonds       : angle       6.46289 ( 1314)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A    8 GLU cc_start: 0.8761 (pt0) cc_final: 0.8298 (pt0)
REVERT: A  275 GLU cc_start: 0.7322 (tp30) cc_final: 0.7075 (tp30)
REVERT: E   18 ARG cc_start: 0.8008 (ttt180) cc_final: 0.7769 (tpt170)
REVERT: E  218 ARG cc_start: 0.7539 (mtm110) cc_final: 0.7250 (ptt90)
  outliers start: 5
  outliers final: 3
  residues processed: 112
  average time/residue: 0.5584
  time to fit residues: 66.4244
Evaluate side-chains
  101 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  245 SER
Chi-restraints excluded: chain R residue   61 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
E  82 GLN
R 408 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.141969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.105042 restraints weight = 9904.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 1.88
r_work: 0.2896 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2756 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8926  Z= 0.177
  Angle     :  0.576  10.504  12110  Z= 0.308
  Chirality :  0.044   0.143   1386
  Planarity :  0.004   0.052   1492
  Dihedral  :  5.807  56.342   1542
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 12.67 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.26), residues: 1076
  helix:  2.54 (0.27), residues: 378
  sheet:  0.56 (0.30), residues: 278
  loop : -0.38 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  62 
 TYR   0.016   0.001   TYR E 190 
 PHE   0.013   0.002   PHE A 196 
 TRP   0.020   0.002   TRP B  82 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 8926)
  covalent geometry    : angle       0.57607 (12110)
  hydrogen bonds       : bond        0.04858 (  466)
  hydrogen bonds       : angle       4.96685 ( 1314)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8041 (mttt)
REVERT: B   59 TYR cc_start: 0.9100 (m-80) cc_final: 0.8892 (m-80)
REVERT: B  134 ARG cc_start: 0.8136 (mtm110) cc_final: 0.7777 (ptp90)
REVERT: B  217 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7137 (pp-130)
REVERT: B  270 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7810 (pp)
REVERT: B  333 ASP cc_start: 0.7950 (t0) cc_final: 0.7643 (t0)
REVERT: G   38 MET cc_start: 0.7648 (mtp) cc_final: 0.7294 (mtp)
REVERT: R  227 ARG cc_start: 0.7285 (mmt90) cc_final: 0.7082 (mmt90)
  outliers start: 24
  outliers final: 5
  residues processed: 112
  average time/residue: 0.5645
  time to fit residues: 67.2402
Evaluate side-chains
  101 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 LYS
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  217 MET
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 13 optimal weight:    5.9990
   chunk 50 optimal weight:    7.9990
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 94 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:
A 304 GLN
B  75 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.146678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.111879 restraints weight = 9763.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 1.66
r_work: 0.3020 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.1314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8926  Z= 0.128
  Angle     :  0.514   8.953  12110  Z= 0.276
  Chirality :  0.041   0.135   1386
  Planarity :  0.004   0.049   1492
  Dihedral  :  5.460  54.669   1537
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.72 %
    Favored  : 83.03 %
  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 aren not related in a simple way.
  whole:  1.40 (0.26), residues: 1076
  helix:  2.63 (0.27), residues: 381
  sheet:  0.45 (0.31), residues: 270
  loop : -0.29 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 219 
 TYR   0.015   0.001   TYR E 190 
 PHE   0.011   0.001   PHE E  29 
 TRP   0.020   0.002   TRP B  82 
 HIS   0.003   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8926)
  covalent geometry    : angle       0.51398 (12110)
  hydrogen bonds       : bond        0.04164 (  466)
  hydrogen bonds       : angle       4.65686 ( 1314)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  205 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7511 (mpp80)
REVERT: B  134 ARG cc_start: 0.8117 (mtm110) cc_final: 0.7826 (ptp90)
REVERT: B  146 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8587 (tp)
REVERT: B  270 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7989 (pp)
REVERT: B  333 ASP cc_start: 0.7710 (t0) cc_final: 0.7504 (t0)
REVERT: G   38 MET cc_start: 0.7716 (mtp) cc_final: 0.7368 (mtp)
REVERT: G   58 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8220 (pm20)
  outliers start: 21
  outliers final: 7
  residues processed: 119
  average time/residue: 0.5561
  time to fit residues: 70.2416
Evaluate side-chains
  101 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ARG
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue  109 CYS
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0770
   chunk 91 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.7542

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 266 HIS
E  82 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.147157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.111611 restraints weight = 9943.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3174 rms_B_bonded: 1.73
r_work: 0.3035 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2895 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8926  Z= 0.114
  Angle     :  0.490   8.663  12110  Z= 0.262
  Chirality :  0.041   0.129   1386
  Planarity :  0.003   0.039   1492
  Dihedral  :  5.273  51.453   1537
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 16.43 %
    Favored  : 81.74 %
  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 aren not related in a simple way.
  whole:  1.44 (0.26), residues: 1076
  helix:  2.65 (0.27), residues: 383
  sheet:  0.43 (0.31), residues: 266
  loop : -0.24 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 219 
 TYR   0.014   0.001   TYR E 190 
 PHE   0.010   0.001   PHE E  29 
 TRP   0.019   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8926)
  covalent geometry    : angle       0.49022 (12110)
  hydrogen bonds       : bond        0.03820 (  466)
  hydrogen bonds       : angle       4.50088 ( 1314)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.371 
Fit side-chains
REVERT: A  205 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7429 (mpp80)
REVERT: B   79 LEU cc_start: 0.8756 (pt) cc_final: 0.8532 (pt)
REVERT: B  134 ARG cc_start: 0.8126 (mtm110) cc_final: 0.7626 (ptt-90)
REVERT: B  146 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8592 (tp)
REVERT: B  270 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8061 (pp)
REVERT: E   38 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8519 (ptt180)
REVERT: E   87 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6449 (mtt180)
REVERT: G   38 MET cc_start: 0.7677 (mtp) cc_final: 0.7288 (mtp)
REVERT: G   58 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8144 (pm20)
  outliers start: 17
  outliers final: 5
  residues processed: 114
  average time/residue: 0.5732
  time to fit residues: 69.5980
Evaluate side-chains
  111 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 ARG
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue  109 CYS
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 71 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 101 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0370
   chunk 23 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.7260

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 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 = 0.3610 r_free = 0.3610 target = 0.147569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.110678 restraints weight = 9791.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 1.82
r_work: 0.3027 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.1727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8926  Z= 0.112
  Angle     :  0.487   8.466  12110  Z= 0.261
  Chirality :  0.041   0.128   1386
  Planarity :  0.003   0.039   1492
  Dihedral  :  5.174  46.736   1537
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 16.76 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.26), residues: 1076
  helix:  2.69 (0.27), residues: 383
  sheet:  0.45 (0.31), residues: 266
  loop : -0.28 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 219 
 TYR   0.013   0.001   TYR E 190 
 PHE   0.010   0.001   PHE A 196 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B 311 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8926)
  covalent geometry    : angle       0.48740 (12110)
  hydrogen bonds       : bond        0.03714 (  466)
  hydrogen bonds       : angle       4.39268 ( 1314)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.245 
Fit side-chains
REVERT: B   79 LEU cc_start: 0.8763 (pt) cc_final: 0.8543 (pt)
REVERT: B  134 ARG cc_start: 0.8151 (mtm110) cc_final: 0.7608 (ptt-90)
REVERT: B  146 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8598 (tp)
REVERT: B  270 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8057 (pp)
REVERT: E   38 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8479 (ptt180)
REVERT: E   87 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6342 (mtt180)
REVERT: G   38 MET cc_start: 0.7615 (mtp) cc_final: 0.7207 (mtp)
  outliers start: 18
  outliers final: 6
  residues processed: 110
  average time/residue: 0.5352
  time to fit residues: 62.4262
Evaluate side-chains
  102 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain R residue  109 CYS
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 36 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0570
   chunk 81 optimal weight:    7.9990
   chunk 85 optimal weight:    6.9990
   chunk 60 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   overall best weight:    1.5302

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  82 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.150311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.114654 restraints weight = 9586.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 1.69
r_work: 0.3090 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8926  Z= 0.171
  Angle     :  0.542  10.110  12110  Z= 0.287
  Chirality :  0.042   0.140   1386
  Planarity :  0.004   0.040   1492
  Dihedral  :  5.537  50.306   1537
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 16.65 %
    Favored  : 80.56 %
  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 aren not related in a simple way.
  whole:  1.30 (0.26), residues: 1076
  helix:  2.59 (0.27), residues: 381
  sheet:  0.34 (0.30), residues: 279
  loop : -0.38 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 219 
 TYR   0.014   0.002   TYR E 190 
 PHE   0.013   0.002   PHE A 196 
 TRP   0.016   0.002   TRP E  47 
 HIS   0.003   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 8926)
  covalent geometry    : angle       0.54195 (12110)
  hydrogen bonds       : bond        0.04234 (  466)
  hydrogen bonds       : angle       4.56297 ( 1314)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A  263 SER cc_start: 0.8793 (p) cc_final: 0.8483 (m)
REVERT: B  134 ARG cc_start: 0.8077 (mtm110) cc_final: 0.7760 (ptp90)
REVERT: B  146 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8583 (tp)
REVERT: B  197 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8126 (ttp-110)
REVERT: B  270 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8056 (pp)
REVERT: E   87 ARG cc_start: 0.6831 (OUTLIER) cc_final: 0.6321 (mtt180)
REVERT: E  194 ASN cc_start: 0.8972 (m110) cc_final: 0.8629 (m110)
REVERT: G   38 MET cc_start: 0.7612 (mtp) cc_final: 0.7227 (mtp)
REVERT: G   58 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8170 (pm20)
  outliers start: 26
  outliers final: 11
  residues processed: 114
  average time/residue: 0.5015
  time to fit residues: 61.0151
Evaluate side-chains
  108 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue  109 CYS
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 87 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 71 optimal weight:    9.9990
   chunk 105 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 96 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  82 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.151643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.115984 restraints weight = 9619.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 1.70
r_work: 0.3108 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8926  Z= 0.137
  Angle     :  0.518   9.424  12110  Z= 0.275
  Chirality :  0.041   0.138   1386
  Planarity :  0.004   0.039   1492
  Dihedral  :  5.455  50.763   1537
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.72 %
    Favored  : 79.91 %
  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 aren not related in a simple way.
  whole:  1.26 (0.26), residues: 1076
  helix:  2.62 (0.27), residues: 379
  sheet:  0.37 (0.30), residues: 274
  loop : -0.48 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 219 
 TYR   0.014   0.001   TYR E 190 
 PHE   0.011   0.001   PHE A 196 
 TRP   0.016   0.002   TRP B  82 
 HIS   0.002   0.001   HIS A 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 8926)
  covalent geometry    : angle       0.51754 (12110)
  hydrogen bonds       : bond        0.03935 (  466)
  hydrogen bonds       : angle       4.49134 ( 1314)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  263 SER cc_start: 0.8767 (p) cc_final: 0.8476 (m)
REVERT: B  134 ARG cc_start: 0.8084 (mtm110) cc_final: 0.7769 (ptp90)
REVERT: B  146 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8566 (tp)
REVERT: B  197 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8101 (ttp-110)
REVERT: B  270 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8091 (pp)
REVERT: E   87 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6254 (mtt180)
REVERT: G   38 MET cc_start: 0.7605 (mtp) cc_final: 0.7224 (mtp)
REVERT: G   58 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8131 (pm20)
  outliers start: 22
  outliers final: 11
  residues processed: 108
  average time/residue: 0.6284
  time to fit residues: 72.2932
Evaluate side-chains
  106 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   69 THR
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue  109 CYS
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 5 optimal weight:    0.0980
   chunk 28 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 23 optimal weight:    0.3980
   chunk 46 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    9.9990
   chunk 61 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 322 HIS
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
E  82 GLN
R 193 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.154872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.119827 restraints weight = 9511.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.68
r_work: 0.3180 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8926  Z= 0.101
  Angle     :  0.483   8.247  12110  Z= 0.257
  Chirality :  0.040   0.128   1386
  Planarity :  0.003   0.038   1492
  Dihedral  :  5.079  50.681   1537
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 18.15 %
    Favored  : 80.13 %
  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 aren not related in a simple way.
  whole:  1.41 (0.26), residues: 1076
  helix:  2.72 (0.27), residues: 384
  sheet:  0.41 (0.30), residues: 275
  loop : -0.38 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 219 
 TYR   0.013   0.001   TYR E 190 
 PHE   0.010   0.001   PHE E  29 
 TRP   0.020   0.001   TRP B  82 
 HIS   0.002   0.000   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 8926)
  covalent geometry    : angle       0.48292 (12110)
  hydrogen bonds       : bond        0.03456 (  466)
  hydrogen bonds       : angle       4.30959 ( 1314)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.318 
Fit side-chains
REVERT: B   79 LEU cc_start: 0.8763 (pt) cc_final: 0.8546 (pt)
REVERT: B  134 ARG cc_start: 0.8062 (mtm110) cc_final: 0.7485 (ptt-90)
REVERT: B  146 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8514 (tp)
REVERT: B  153 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7760 (m-30)
REVERT: B  270 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8109 (pp)
REVERT: E   87 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6388 (mtt180)
REVERT: G   38 MET cc_start: 0.7565 (mtp) cc_final: 0.7207 (mtp)
REVERT: G   58 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8011 (pm20)
  outliers start: 16
  outliers final: 6
  residues processed: 119
  average time/residue: 0.6243
  time to fit residues: 79.1334
Evaluate side-chains
  108 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue  109 CYS
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0470
   chunk 72 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 37 optimal weight:    5.9990
   overall best weight:    0.7280

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
E  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.154005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.118652 restraints weight = 9543.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.70
r_work: 0.3163 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.2020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8926  Z= 0.113
  Angle     :  0.503   8.530  12110  Z= 0.267
  Chirality :  0.041   0.140   1386
  Planarity :  0.003   0.039   1492
  Dihedral  :  5.119  52.596   1537
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 18.90 %
    Favored  : 79.16 %
  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 aren not related in a simple way.
  whole:  1.39 (0.26), residues: 1076
  helix:  2.71 (0.27), residues: 383
  sheet:  0.40 (0.30), residues: 275
  loop : -0.40 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 219 
 TYR   0.014   0.001   TYR E 190 
 PHE   0.009   0.001   PHE A 196 
 TRP   0.018   0.001   TRP B  82 
 HIS   0.002   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8926)
  covalent geometry    : angle       0.50302 (12110)
  hydrogen bonds       : bond        0.03587 (  466)
  hydrogen bonds       : angle       4.33565 ( 1314)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.289 
Fit side-chains
REVERT: B   79 LEU cc_start: 0.8787 (pt) cc_final: 0.8547 (pt)
REVERT: B  134 ARG cc_start: 0.8071 (mtm110) cc_final: 0.7765 (ptp90)
REVERT: B  146 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8544 (tp)
REVERT: B  197 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8071 (ttp-110)
REVERT: B  270 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8124 (pp)
REVERT: E   87 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6441 (mtt180)
REVERT: G   38 MET cc_start: 0.7579 (mtp) cc_final: 0.7213 (mtp)
REVERT: G   58 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8045 (pm20)
  outliers start: 18
  outliers final: 7
  residues processed: 109
  average time/residue: 0.5843
  time to fit residues: 67.9998
Evaluate side-chains
  107 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue  109 CYS
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 99 optimal weight:    0.9990
   chunk 100 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
E  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.153045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.117435 restraints weight = 9564.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 1.70
r_work: 0.3146 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8926  Z= 0.125
  Angle     :  0.516   9.073  12110  Z= 0.273
  Chirality :  0.041   0.138   1386
  Planarity :  0.003   0.038   1492
  Dihedral  :  5.234  54.084   1537
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 19.12 %
    Favored  : 79.27 %
  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 aren not related in a simple way.
  whole:  1.34 (0.26), residues: 1076
  helix:  2.68 (0.27), residues: 382
  sheet:  0.41 (0.30), residues: 273
  loop : -0.46 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 219 
 TYR   0.014   0.001   TYR E 190 
 PHE   0.010   0.001   PHE A 196 
 TRP   0.017   0.001   TRP B  82 
 HIS   0.002   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 8926)
  covalent geometry    : angle       0.51640 (12110)
  hydrogen bonds       : bond        0.03751 (  466)
  hydrogen bonds       : angle       4.40243 ( 1314)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.253 
Fit side-chains
REVERT: B  134 ARG cc_start: 0.8074 (mtm110) cc_final: 0.7448 (ptt-90)
REVERT: B  197 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8042 (ttp-110)
REVERT: B  270 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8131 (pp)
REVERT: E   43 LYS cc_start: 0.8085 (mmmm) cc_final: 0.7814 (mmmt)
REVERT: E   87 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6425 (mtt180)
REVERT: E  194 ASN cc_start: 0.8817 (m110) cc_final: 0.8523 (m110)
REVERT: G   38 MET cc_start: 0.7586 (mtp) cc_final: 0.7213 (mtp)
REVERT: G   58 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8114 (pm20)
  outliers start: 15
  outliers final: 8
  residues processed: 107
  average time/residue: 0.6225
  time to fit residues: 70.8119
Evaluate side-chains
  108 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain E residue   87 ARG
Chi-restraints excluded: chain E residue  141 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain G residue   58 GLU
Chi-restraints excluded: chain R residue  109 CYS
Chi-restraints excluded: chain R residue  159 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 102 optimal weight:    0.0980
   chunk 22 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
E  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.153997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.118649 restraints weight = 9502.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 1.69
r_work: 0.3182 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3047 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8926  Z= 0.112
  Angle     :  0.508   8.570  12110  Z= 0.268
  Chirality :  0.041   0.137   1386
  Planarity :  0.003   0.039   1492
  Dihedral  :  5.158  54.753   1537
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 19.44 %
    Favored  : 79.27 %
  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 aren not related in a simple way.
  whole:  1.39 (0.26), residues: 1076
  helix:  2.70 (0.27), residues: 383
  sheet:  0.40 (0.30), residues: 275
  loop : -0.39 (0.31), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 219 
 TYR   0.013   0.001   TYR E 190 
 PHE   0.009   0.001   PHE E  29 
 TRP   0.018   0.001   TRP B  82 
 HIS   0.002   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 8926)
  covalent geometry    : angle       0.50762 (12110)
  hydrogen bonds       : bond        0.03603 (  466)
  hydrogen bonds       : angle       4.34392 ( 1314)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2893.55 seconds
wall clock time: 50 minutes 10.47 seconds (3010.47 seconds total)