Starting phenix.real_space_refine
on Wed Sep 17 09:05:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5h1b_9566/09_2025/5h1b_9566.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5h1b_9566/09_2025/5h1b_9566.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5h1b_9566/09_2025/5h1b_9566.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5h1b_9566/09_2025/5h1b_9566.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5h1b_9566/09_2025/5h1b_9566.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5h1b_9566/09_2025/5h1b_9566.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 6
    Type Number    sf(0)   Gaussians
     P      18      5.49       5
     Mg      3      5.21       5
     S      39      5.16       5
     C    4557      2.51       5
     N    1287      2.21       5
     O    1455      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7359
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2361
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2361
          Classifications: {'peptide': 308}
          Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 296}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 180
          Classifications: {'DNA': 9}
          Link IDs: {'rna3p': 8}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 1.50, per 1000 atoms: 0.20
  Number of scatterers: 7359
  At special positions: 0
  Unit cell: (107.092, 69.218, 116.234, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      39     16.00
     P      18     15.00
     Mg      3     11.99
     O    1455      8.00
     N    1287      7.00
     C    4557      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=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 388.3 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1686

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 6 sheets defined
      54.1% alpha, 12.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 28
    Processing helix  chain 'A' and resid 34 through 45
      removed outlier: 3.792A  pdb=" N   VAL A  38 " --> pdb=" O   ASN A  34 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLU A  43 " --> pdb=" O   LYS A  39 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY A  45 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 54
      removed outlier: 4.068A  pdb=" N   VAL A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 62
    Processing helix  chain 'A' and resid 67 through 82
    Processing helix  chain 'A' and resid 88 through 99
    Processing helix  chain 'A' and resid 106 through 113
    Processing helix  chain 'A' and resid 132 through 144
    Processing helix  chain 'A' and resid 145 through 146
      No H-bonds generated for 'chain 'A' and resid 145 through 146'
    Processing helix  chain 'A' and resid 147 through 151
    Processing helix  chain 'A' and resid 167 through 179
    Processing helix  chain 'A' and resid 181 through 188
      removed outlier: 3.717A  pdb=" N   ASN A 188 " --> pdb=" O   ASP A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 214
      removed outlier: 3.768A  pdb=" N   THR A 201 " --> pdb=" O   THR A 197 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLN A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLU A 213 " --> pdb=" O   ALA A 209 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER A 214 " --> pdb=" O   MET A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 232
      removed outlier: 3.974A  pdb=" N   ARG A 229 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   THR A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 260
      removed outlier: 3.602A  pdb=" N   ARG A 247 " --> pdb=" O   MET A 243 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   MET A 251 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 296
      removed outlier: 3.804A  pdb=" N   ILE A 292 " --> pdb=" O   GLY A 288 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ALA A 295 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 28
    Processing helix  chain 'B' and resid 34 through 45
      removed outlier: 3.792A  pdb=" N   VAL B  38 " --> pdb=" O   ASN B  34 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLU B  43 " --> pdb=" O   LYS B  39 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY B  45 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 54
      removed outlier: 4.068A  pdb=" N   VAL B  52 " --> pdb=" O   THR B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 62
    Processing helix  chain 'B' and resid 67 through 82
    Processing helix  chain 'B' and resid 89 through 99
    Processing helix  chain 'B' and resid 106 through 113
    Processing helix  chain 'B' and resid 132 through 144
    Processing helix  chain 'B' and resid 145 through 146
      No H-bonds generated for 'chain 'B' and resid 145 through 146'
    Processing helix  chain 'B' and resid 147 through 151
    Processing helix  chain 'B' and resid 167 through 179
    Processing helix  chain 'B' and resid 181 through 188
      removed outlier: 3.716A  pdb=" N   ASN B 188 " --> pdb=" O   ASP B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 214
      removed outlier: 3.768A  pdb=" N   THR B 201 " --> pdb=" O   THR B 197 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLN B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLU B 213 " --> pdb=" O   ALA B 209 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER B 214 " --> pdb=" O   MET B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 232
      removed outlier: 3.974A  pdb=" N   ARG B 229 " --> pdb=" O   THR B 225 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   THR B 230 " --> pdb=" O   ALA B 226 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 260
      removed outlier: 3.602A  pdb=" N   ARG B 247 " --> pdb=" O   MET B 243 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   MET B 251 " --> pdb=" O   ARG B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 296
      removed outlier: 3.804A  pdb=" N   ILE B 292 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ALA B 295 " --> pdb=" O   ILE B 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 24 through 28
    Processing helix  chain 'C' and resid 34 through 45
      removed outlier: 3.792A  pdb=" N   VAL C  38 " --> pdb=" O   ASN C  34 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLU C  43 " --> pdb=" O   LYS C  39 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLY C  45 " --> pdb=" O   LEU C  41 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 54
      removed outlier: 4.067A  pdb=" N   VAL C  52 " --> pdb=" O   THR C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 62
    Processing helix  chain 'C' and resid 67 through 82
    Processing helix  chain 'C' and resid 88 through 99
    Processing helix  chain 'C' and resid 106 through 113
    Processing helix  chain 'C' and resid 132 through 144
    Processing helix  chain 'C' and resid 145 through 146
      No H-bonds generated for 'chain 'C' and resid 145 through 146'
    Processing helix  chain 'C' and resid 147 through 151
    Processing helix  chain 'C' and resid 167 through 179
    Processing helix  chain 'C' and resid 181 through 188
      removed outlier: 3.716A  pdb=" N   ASN C 188 " --> pdb=" O   ASP C 184 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 214
      removed outlier: 3.768A  pdb=" N   THR C 201 " --> pdb=" O   THR C 197 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLN C 202 " --> pdb=" O   ASP C 198 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   GLU C 213 " --> pdb=" O   ALA C 209 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   SER C 214 " --> pdb=" O   MET C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 225 through 232
      removed outlier: 3.973A  pdb=" N   ARG C 229 " --> pdb=" O   THR C 225 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   THR C 230 " --> pdb=" O   ALA C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 238 through 260
      removed outlier: 3.602A  pdb=" N   ARG C 247 " --> pdb=" O   MET C 243 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   MET C 251 " --> pdb=" O   ARG C 247 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 288 through 296
      removed outlier: 3.804A  pdb=" N   ILE C 292 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ALA C 295 " --> pdb=" O   ILE C 291 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 324 through 327
      removed outlier: 8.173A  pdb=" N   LEU A 300 " --> pdb=" O   ILE A 122 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   GLU A 124 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU A 302 " --> pdb=" O   GLU A 124 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   PHE A 126 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   LYS A 304 " --> pdb=" O   PHE A 126 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   THR A 123 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   ASN A 267 " --> pdb=" O   THR A 123 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   MET A 125 " --> pdb=" O   ASN A 267 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   LYS A 156 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU A 219 " --> pdb=" O   LYS A 156 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   MET A 158 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   VAL A 221 " --> pdb=" O   MET A 158 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   ILE A 160 " --> pdb=" O   VAL A 221 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA A 192 " --> pdb=" O   TYR A 159 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ASP A 161 " --> pdb=" O   ALA A 192 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 330
    Processing sheet with id=AA3, first strand: chain 'B' and resid 190 through 193
      removed outlier: 3.717A  pdb=" N   ALA B 192 " --> pdb=" O   TYR B 159 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ASP B 161 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   LYS B 156 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU B 219 " --> pdb=" O   LYS B 156 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   MET B 158 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   VAL B 221 " --> pdb=" O   MET B 158 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   ILE B 160 " --> pdb=" O   VAL B 221 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   THR B 123 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   ASN B 267 " --> pdb=" O   THR B 123 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   MET B 125 " --> pdb=" O   ASN B 267 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   LEU B 300 " --> pdb=" O   ILE B 122 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   GLU B 124 " --> pdb=" O   LEU B 300 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU B 302 " --> pdb=" O   GLU B 124 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   PHE B 126 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   LYS B 304 " --> pdb=" O   PHE B 126 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 329 through 330
    Processing sheet with id=AA5, first strand: chain 'C' and resid 190 through 193
      removed outlier: 3.717A  pdb=" N   ALA C 192 " --> pdb=" O   TYR C 159 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ASP C 161 " --> pdb=" O   ALA C 192 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   LYS C 156 " --> pdb=" O   ALA C 217 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   LEU C 219 " --> pdb=" O   LYS C 156 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   MET C 158 " --> pdb=" O   LEU C 219 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   VAL C 221 " --> pdb=" O   MET C 158 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   ILE C 160 " --> pdb=" O   VAL C 221 " (cutoff:3.500A)
      removed outlier: 5.859A  pdb=" N   THR C 123 " --> pdb=" O   ILE C 265 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   ASN C 267 " --> pdb=" O   THR C 123 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   MET C 125 " --> pdb=" O   ASN C 267 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   LEU C 300 " --> pdb=" O   ILE C 122 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   GLU C 124 " --> pdb=" O   LEU C 300 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU C 302 " --> pdb=" O   GLU C 124 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   PHE C 126 " --> pdb=" O   LEU C 302 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   LYS C 304 " --> pdb=" O   PHE C 126 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 329 through 330

    334 hydrogen bonds defined for protein.
    918 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.18

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2372
        1.33 -     1.45: 1159
        1.45 -     1.57: 3854
        1.57 -     1.69: 33
        1.69 -     1.81: 63
  Bond restraints: 7481
  Sorted by residual:
  bond pdb=" O3A ANP A 600 "
       pdb=" PB  ANP A 600 "
    ideal  model  delta    sigma   weight residual
    1.700  1.550  0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" O3A ANP B 600 "
       pdb=" PB  ANP B 600 "
    ideal  model  delta    sigma   weight residual
    1.700  1.550  0.150 2.00e-02 2.50e+03 5.63e+01
  bond pdb=" O3A ANP C 600 "
       pdb=" PB  ANP C 600 "
    ideal  model  delta    sigma   weight residual
    1.700  1.550  0.150 2.00e-02 2.50e+03 5.60e+01
  bond pdb=" N3B ANP C 600 "
       pdb=" PG  ANP C 600 "
    ideal  model  delta    sigma   weight residual
    1.795  1.689  0.106 2.00e-02 2.50e+03 2.82e+01
  bond pdb=" N3B ANP A 600 "
       pdb=" PG  ANP A 600 "
    ideal  model  delta    sigma   weight residual
    1.795  1.689  0.106 2.00e-02 2.50e+03 2.80e+01
  ... (remaining 7476 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.75: 9923
        3.75 -     7.51: 204
        7.51 -    11.26: 15
       11.26 -    15.01: 0
       15.01 -    18.77: 3
  Bond angle restraints: 10145
  Sorted by residual:
  angle pdb=" PB  ANP C 600 "
        pdb=" N3B ANP C 600 "
        pdb=" PG  ANP C 600 "
      ideal   model   delta    sigma   weight residual
     126.95  108.18   18.77 3.00e+00 1.11e-01 3.91e+01
  angle pdb=" PB  ANP B 600 "
        pdb=" N3B ANP B 600 "
        pdb=" PG  ANP B 600 "
      ideal   model   delta    sigma   weight residual
     126.95  108.18   18.77 3.00e+00 1.11e-01 3.91e+01
  angle pdb=" PB  ANP A 600 "
        pdb=" N3B ANP A 600 "
        pdb=" PG  ANP A 600 "
      ideal   model   delta    sigma   weight residual
     126.95  108.20   18.75 3.00e+00 1.11e-01 3.91e+01
  angle pdb=" N   THR A 197 "
        pdb=" CA  THR A 197 "
        pdb=" C   THR A 197 "
      ideal   model   delta    sigma   weight residual
     111.71  105.46    6.25 1.15e+00 7.56e-01 2.95e+01
  angle pdb=" N   THR B 197 "
        pdb=" CA  THR B 197 "
        pdb=" C   THR B 197 "
      ideal   model   delta    sigma   weight residual
     111.71  105.47    6.24 1.15e+00 7.56e-01 2.94e+01
  ... (remaining 10140 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.74: 4322
       23.74 -    47.48: 162
       47.48 -    71.22: 46
       71.22 -    94.96: 27
       94.96 -   118.70: 3
  Dihedral angle restraints: 4560
    sinusoidal: 1926
      harmonic: 2634
  Sorted by residual:
  dihedral pdb=" CA  CYS C 319 "
           pdb=" C   CYS C 319 "
           pdb=" N   LEU C 320 "
           pdb=" CA  LEU C 320 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.98  -23.02     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  CYS B 319 "
           pdb=" C   CYS B 319 "
           pdb=" N   LEU B 320 "
           pdb=" CA  LEU B 320 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.98  -23.02     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  CYS A 319 "
           pdb=" C   CYS A 319 "
           pdb=" N   LEU A 320 "
           pdb=" CA  LEU A 320 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.99  -23.01     0      5.00e+00 4.00e-02 2.12e+01
  ... (remaining 4557 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 888
       0.064 -    0.129: 244
       0.129 -    0.193: 23
       0.193 -    0.257: 0
       0.257 -    0.321: 3
  Chirality restraints: 1158
  Sorted by residual:
  chirality pdb=" C3' ANP C 600 "
            pdb=" C2' ANP C 600 "
            pdb=" C4' ANP C 600 "
            pdb=" O3' ANP C 600 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.68    0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" C3' ANP B 600 "
            pdb=" C2' ANP B 600 "
            pdb=" C4' ANP B 600 "
            pdb=" O3' ANP B 600 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.68    0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" C3' ANP A 600 "
            pdb=" C2' ANP A 600 "
            pdb=" C4' ANP A 600 "
            pdb=" O3' ANP A 600 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.67    0.32 2.00e-01 2.50e+01 2.50e+00
  ... (remaining 1155 not shown)

  Planarity restraints: 1272
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 246 "   -0.011 2.00e-02 2.50e+03   2.27e-02 5.15e+00
        pdb=" C   ALA A 246 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ALA A 246 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ARG A 247 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 246 "   -0.011 2.00e-02 2.50e+03   2.25e-02 5.06e+00
        pdb=" C   ALA B 246 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ALA B 246 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ARG B 247 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA C 246 "   -0.011 2.00e-02 2.50e+03   2.24e-02 5.00e+00
        pdb=" C   ALA C 246 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ALA C 246 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ARG C 247 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1269 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.18: 46
        2.18 -     2.86: 3020
        2.86 -     3.54: 11307
        3.54 -     4.22: 18610
        4.22 -     4.90: 29872
  Nonbonded interactions: 62855
  Sorted by model distance:
  nonbonded pdb=" CB  ALA A 271 "
            pdb=" OP2  DT D   4 "
     model   vdw
     1.503 3.460
  nonbonded pdb=" CA  ALA A 271 "
            pdb=" OP2  DT D   4 "
     model   vdw
     1.572 3.470
  nonbonded pdb=" N   ALA A 271 "
            pdb=" OP2  DT D   4 "
     model   vdw
     1.580 3.120
  nonbonded pdb=" OH  TYR B 159 "
            pdb=" OD2 ASP B 222 "
     model   vdw
     1.586 3.040
  nonbonded pdb=" OH  TYR A 159 "
            pdb=" OD2 ASP A 222 "
     model   vdw
     1.586 3.040
  ... (remaining 62850 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.370
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.080
  Find NCS groups from input model:        0.110
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7180
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      :  0.011   0.150   7484  Z= 0.675
  Angle     :  1.411  18.767  10145  Z= 0.917
  Chirality :  0.056   0.321   1158
  Planarity :  0.005   0.034   1272
  Dihedral  : 16.126 118.695   2874
  Min Nonbonded Distance : 1.503

Molprobity Statistics.
  All-atom Clashscore : 54.25
  Ramachandran Plot:
    Outliers :  2.63 %
    Allowed  :  6.25 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  :  2.43 %
    Favored  : 91.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    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: -1.51 (0.27), residues: 912
  helix: -2.43 (0.18), residues: 378
  sheet: -0.80 (0.40), residues: 159
  loop :  0.92 (0.36), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.002   ARG C 215 
 TYR   0.019   0.002   TYR A 315 
 PHE   0.018   0.003   PHE C  86 
 HIS   0.009   0.002   HIS C 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.01014 ( 7481)
  covalent geometry    : angle       1.41058 (10145)
  hydrogen bonds       : bond        0.21876 (  334)
  hydrogen bonds       : angle      10.51666 (  918)
  Misc. bond           : bond        0.14875 (    3)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 98
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ILE cc_start: 0.6707 (OUTLIER) cc_final: 0.6299 (mp)
REVERT: A  265 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8383 (mm)
REVERT: B   62 ASN cc_start: 0.7700 (m-40) cc_final: 0.7437 (m110)
REVERT: B   99 ILE cc_start: 0.6839 (OUTLIER) cc_final: 0.6453 (mp)
REVERT: B  170 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.6648 (mpt180)
REVERT: B  265 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8016 (mm)
  outliers start: 42
  outliers final: 12
  residues processed: 132
  average time/residue: 0.1436
  time to fit residues: 23.3836
Evaluate side-chains
  70 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    5.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  34 ASN
A 138 HIS
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 138 HIS
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  34 ASN
C  93 HIS
C 138 HIS
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.039170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.033726 restraints weight = 53670.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.034782 restraints weight = 29705.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.035550 restraints weight = 18812.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.036059 restraints weight = 13037.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.036420 restraints weight = 9744.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.4053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   7484  Z= 0.256
  Angle     :  0.811   7.712  10145  Z= 0.429
  Chirality :  0.045   0.177   1158
  Planarity :  0.005   0.046   1272
  Dihedral  : 13.758 113.214   1191
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 19.47
  Ramachandran Plot:
    Outliers :  1.32 %
    Allowed  :  4.50 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  0.94 %
    Favored  : 98.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    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: -0.55 (0.27), residues: 912
  helix: -0.34 (0.23), residues: 429
  sheet: -0.83 (0.40), residues: 162
  loop :  0.24 (0.37), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 193 
 TYR   0.015   0.002   TYR B 301 
 PHE   0.020   0.002   PHE B 126 
 HIS   0.005   0.001   HIS B 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00550 ( 7481)
  covalent geometry    : angle       0.81101 (10145)
  hydrogen bonds       : bond        0.05109 (  334)
  hydrogen bonds       : angle       6.18403 (  918)
  Misc. bond           : bond        0.00126 (    3)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ASN cc_start: 0.8739 (m-40) cc_final: 0.8375 (m110)
REVERT: A  125 MET cc_start: 0.8817 (mmt) cc_final: 0.8533 (mmp)
REVERT: A  137 CYS cc_start: 0.8976 (m) cc_final: 0.8740 (m)
REVERT: B   62 ASN cc_start: 0.8831 (m-40) cc_final: 0.8458 (m110)
REVERT: B  137 CYS cc_start: 0.9189 (m) cc_final: 0.8989 (m)
REVERT: B  248 PHE cc_start: 0.9355 (t80) cc_final: 0.9050 (t80)
REVERT: B  251 MET cc_start: 0.9157 (tpt) cc_final: 0.8913 (tpt)
REVERT: C   62 ASN cc_start: 0.8756 (m-40) cc_final: 0.8373 (p0)
REVERT: C   99 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7755 (mt)
REVERT: C  251 MET cc_start: 0.9097 (tpt) cc_final: 0.8515 (tpt)
REVERT: C  301 TYR cc_start: 0.8945 (t80) cc_final: 0.8718 (t80)
  outliers start: 5
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1013
  time to fit residues: 9.7415
Evaluate side-chains
  46 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 41 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 ASN
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 267 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.040481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.035254 restraints weight = 51595.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.036370 restraints weight = 28853.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.037143 restraints weight = 18276.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.037675 restraints weight = 12582.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.038050 restraints weight = 9295.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.4962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7484  Z= 0.148
  Angle     :  0.655   7.461  10145  Z= 0.346
  Chirality :  0.040   0.154   1158
  Planarity :  0.004   0.051   1272
  Dihedral  : 12.404 107.849   1191
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 15.58
  Ramachandran Plot:
    Outliers :  1.21 %
    Allowed  :  4.28 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  1.89 %
    Favored  : 97.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    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:  0.17 (0.28), residues: 912
  helix:  0.63 (0.24), residues: 429
  sheet: -0.77 (0.39), residues: 165
  loop :  0.17 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 250 
 TYR   0.009   0.001   TYR C 205 
 PHE   0.015   0.002   PHE B 126 
 HIS   0.004   0.001   HIS B 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7481)
  covalent geometry    : angle       0.65495 (10145)
  hydrogen bonds       : bond        0.04285 (  334)
  hydrogen bonds       : angle       5.40360 (  918)
  Misc. bond           : bond        0.00161 (    3)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 65
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.8861 (pttp) cc_final: 0.8523 (ptpt)
REVERT: A   62 ASN cc_start: 0.8557 (m-40) cc_final: 0.8298 (p0)
REVERT: A  137 CYS cc_start: 0.9083 (m) cc_final: 0.8846 (m)
REVERT: B   62 ASN cc_start: 0.8720 (m-40) cc_final: 0.8329 (m110)
REVERT: B  243 MET cc_start: 0.8552 (tmm) cc_final: 0.8275 (tmm)
REVERT: B  248 PHE cc_start: 0.9358 (t80) cc_final: 0.9002 (t80)
REVERT: C   62 ASN cc_start: 0.8780 (m-40) cc_final: 0.8468 (p0)
REVERT: C  137 CYS cc_start: 0.9147 (m) cc_final: 0.8947 (m)
REVERT: C  206 GLN cc_start: 0.9019 (mt0) cc_final: 0.8803 (tt0)
REVERT: C  225 THR cc_start: 0.9092 (p) cc_final: 0.8556 (p)
REVERT: C  251 MET cc_start: 0.9067 (tpt) cc_final: 0.8805 (tpt)
  outliers start: 3
  outliers final: 1
  residues processed: 68
  average time/residue: 0.0895
  time to fit residues: 8.5243
Evaluate side-chains
  46 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 26 optimal weight:    0.0060
   chunk 86 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 41 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   chunk 9 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   overall best weight:    1.3400

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 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 = 0.2934 r_free = 0.2934 target = 0.040844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.035623 restraints weight = 53930.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.036766 restraints weight = 29705.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.037584 restraints weight = 18572.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.038106 restraints weight = 12494.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.038508 restraints weight = 9169.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.5534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7484  Z= 0.124
  Angle     :  0.612   8.109  10145  Z= 0.321
  Chirality :  0.039   0.152   1158
  Planarity :  0.003   0.053   1272
  Dihedral  : 12.065 101.833   1191
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  1.21 %
    Allowed  :  3.51 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.29 %
    Favored  : 97.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    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:  0.72 (0.27), residues: 912
  helix:  1.32 (0.25), residues: 411
  sheet: -0.68 (0.37), residues: 165
  loop :  0.22 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 193 
 TYR   0.014   0.001   TYR B 301 
 PHE   0.014   0.002   PHE B 126 
 HIS   0.003   0.001   HIS B 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7481)
  covalent geometry    : angle       0.61221 (10145)
  hydrogen bonds       : bond        0.03851 (  334)
  hydrogen bonds       : angle       4.94794 (  918)
  Misc. bond           : bond        0.00087 (    3)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.8845 (pttp) cc_final: 0.8522 (ptpt)
REVERT: A   62 ASN cc_start: 0.8581 (m-40) cc_final: 0.8287 (p0)
REVERT: A  137 CYS cc_start: 0.9182 (m) cc_final: 0.8949 (m)
REVERT: A  267 ASN cc_start: 0.9005 (p0) cc_final: 0.8447 (t0)
REVERT: B   62 ASN cc_start: 0.8605 (m-40) cc_final: 0.8234 (m110)
REVERT: B  158 MET cc_start: 0.8119 (pmm) cc_final: 0.7534 (mpp)
REVERT: B  243 MET cc_start: 0.8427 (tmm) cc_final: 0.8137 (tmm)
REVERT: B  248 PHE cc_start: 0.9282 (t80) cc_final: 0.8972 (t80)
REVERT: C   58 LYS cc_start: 0.9046 (pttp) cc_final: 0.8778 (ptpt)
REVERT: C   62 ASN cc_start: 0.8775 (m-40) cc_final: 0.8533 (p0)
REVERT: C  137 CYS cc_start: 0.9108 (m) cc_final: 0.8871 (m)
REVERT: C  206 GLN cc_start: 0.9055 (mt0) cc_final: 0.8754 (tt0)
REVERT: C  243 MET cc_start: 0.8269 (tmm) cc_final: 0.7981 (tmm)
REVERT: C  251 MET cc_start: 0.9023 (tpt) cc_final: 0.8769 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 66
  average time/residue: 0.0969
  time to fit residues: 8.8339
Evaluate side-chains
  45 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 58 optimal weight:    8.9990
   chunk 49 optimal weight:    7.9990
   chunk 62 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 80 optimal weight:    8.9990
   chunk 31 optimal weight:    9.9990
   chunk 11 optimal weight:   10.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 199 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.039029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.033686 restraints weight = 53553.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.034801 restraints weight = 29741.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.035577 restraints weight = 18822.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.036121 restraints weight = 12986.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.036500 restraints weight = 9622.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.5764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7484  Z= 0.190
  Angle     :  0.652   7.512  10145  Z= 0.343
  Chirality :  0.040   0.163   1158
  Planarity :  0.004   0.057   1272
  Dihedral  : 12.326 107.523   1191
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  1.21 %
    Allowed  :  4.93 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    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:  0.52 (0.27), residues: 912
  helix:  1.17 (0.24), residues: 429
  sheet: -0.79 (0.37), residues: 162
  loop :  0.05 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  96 
 TYR   0.019   0.001   TYR B 191 
 PHE   0.015   0.002   PHE C  86 
 HIS   0.003   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 7481)
  covalent geometry    : angle       0.65163 (10145)
  hydrogen bonds       : bond        0.04039 (  334)
  hydrogen bonds       : angle       4.89534 (  918)
  Misc. bond           : bond        0.00129 (    3)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.8853 (pttp) cc_final: 0.8512 (ptpt)
REVERT: A   62 ASN cc_start: 0.8633 (m-40) cc_final: 0.8354 (p0)
REVERT: A  137 CYS cc_start: 0.9080 (m) cc_final: 0.8819 (m)
REVERT: A  251 MET cc_start: 0.9086 (tpt) cc_final: 0.8415 (tpt)
REVERT: B   62 ASN cc_start: 0.8663 (m-40) cc_final: 0.8328 (m110)
REVERT: B  225 THR cc_start: 0.9249 (p) cc_final: 0.8744 (p)
REVERT: B  248 PHE cc_start: 0.9329 (t80) cc_final: 0.9015 (t80)
REVERT: B  301 TYR cc_start: 0.8582 (t80) cc_final: 0.8187 (t80)
REVERT: C   62 ASN cc_start: 0.8824 (m-40) cc_final: 0.8550 (p0)
REVERT: C  137 CYS cc_start: 0.9148 (m) cc_final: 0.8853 (m)
REVERT: C  206 GLN cc_start: 0.9215 (mt0) cc_final: 0.8752 (tt0)
REVERT: C  251 MET cc_start: 0.8977 (tpt) cc_final: 0.8420 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0944
  time to fit residues: 7.7551
Evaluate side-chains
  46 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 73 optimal weight:    0.4980
   chunk 83 optimal weight:   10.0000
   chunk 61 optimal weight:    3.9990
   chunk 22 optimal weight:    7.9990
   chunk 72 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    3.6988

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 ASN
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 HIS
C 135 GLN
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 242 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.039102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.033764 restraints weight = 53750.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.034876 restraints weight = 29751.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.035666 restraints weight = 18796.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.036183 restraints weight = 13050.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.036574 restraints weight = 9678.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.6039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7484  Z= 0.180
  Angle     :  0.653   9.235  10145  Z= 0.338
  Chirality :  0.040   0.175   1158
  Planarity :  0.004   0.050   1272
  Dihedral  : 12.286 110.098   1191
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  1.21 %
    Allowed  :  4.39 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.81 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    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:  0.57 (0.27), residues: 912
  helix:  1.23 (0.24), residues: 429
  sheet: -0.58 (0.40), residues: 141
  loop : -0.15 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  96 
 TYR   0.013   0.001   TYR B 191 
 PHE   0.018   0.002   PHE C  86 
 HIS   0.003   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 7481)
  covalent geometry    : angle       0.65338 (10145)
  hydrogen bonds       : bond        0.03899 (  334)
  hydrogen bonds       : angle       4.86637 (  918)
  Misc. bond           : bond        0.00104 (    3)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.8850 (pttp) cc_final: 0.8351 (ptpt)
REVERT: A   62 ASN cc_start: 0.8637 (m-40) cc_final: 0.8266 (m110)
REVERT: A  251 MET cc_start: 0.9023 (tpt) cc_final: 0.8324 (tpt)
REVERT: B   62 ASN cc_start: 0.8606 (m-40) cc_final: 0.8246 (m110)
REVERT: B  137 CYS cc_start: 0.9302 (m) cc_final: 0.9070 (m)
REVERT: B  243 MET cc_start: 0.8374 (tmm) cc_final: 0.8152 (tmm)
REVERT: B  248 PHE cc_start: 0.9318 (t80) cc_final: 0.9024 (t80)
REVERT: B  301 TYR cc_start: 0.8786 (t80) cc_final: 0.8544 (t80)
REVERT: C  137 CYS cc_start: 0.9168 (m) cc_final: 0.8857 (m)
REVERT: C  251 MET cc_start: 0.8957 (tpt) cc_final: 0.8472 (tpt)
  outliers start: 1
  outliers final: 1
  residues processed: 59
  average time/residue: 0.0850
  time to fit residues: 7.0900
Evaluate side-chains
  45 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 73 optimal weight:    8.9990
   chunk 17 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 39 optimal weight:    0.0980
   chunk 85 optimal weight:    0.3980
   chunk 2 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 58 optimal weight:    9.9990
   chunk 67 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 135 GLN
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.039744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.034295 restraints weight = 53515.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.035416 restraints weight = 30012.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.036242 restraints weight = 19169.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.036793 restraints weight = 13125.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.037192 restraints weight = 9718.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.6300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7484  Z= 0.131
  Angle     :  0.621   8.380  10145  Z= 0.317
  Chirality :  0.039   0.194   1158
  Planarity :  0.003   0.041   1272
  Dihedral  : 11.948 103.260   1191
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  1.21 %
    Allowed  :  3.95 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    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:  0.75 (0.27), residues: 912
  helix:  1.41 (0.25), residues: 429
  sheet: -0.45 (0.42), residues: 132
  loop : -0.15 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  96 
 TYR   0.011   0.001   TYR B 191 
 PHE   0.019   0.002   PHE B  86 
 HIS   0.002   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7481)
  covalent geometry    : angle       0.62097 (10145)
  hydrogen bonds       : bond        0.03583 (  334)
  hydrogen bonds       : angle       4.75583 (  918)
  Misc. bond           : bond        0.00071 (    3)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.8844 (pttp) cc_final: 0.8450 (ptpt)
REVERT: A  125 MET cc_start: 0.8839 (mmm) cc_final: 0.8605 (mmm)
REVERT: A  158 MET cc_start: 0.8181 (ptp) cc_final: 0.7948 (pmm)
REVERT: A  251 MET cc_start: 0.9078 (tpt) cc_final: 0.8718 (tpp)
REVERT: B   62 ASN cc_start: 0.8687 (m-40) cc_final: 0.8326 (m110)
REVERT: B  248 PHE cc_start: 0.9254 (t80) cc_final: 0.8933 (t80)
REVERT: B  267 ASN cc_start: 0.8628 (p0) cc_final: 0.8344 (p0)
REVERT: C  137 CYS cc_start: 0.9188 (m) cc_final: 0.8923 (m)
REVERT: C  251 MET cc_start: 0.8972 (tpt) cc_final: 0.8451 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0800
  time to fit residues: 6.8658
Evaluate side-chains
  45 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 64 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0050
   chunk 16 optimal weight:    8.9990
   chunk 43 optimal weight:   10.0000
   chunk 79 optimal weight:    0.6980
   chunk 59 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   chunk 11 optimal weight:   10.0000
   overall best weight:    2.7400

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 267 ASN
B  47 HIS
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 196 ASN
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.039410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.034209 restraints weight = 54306.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.035305 restraints weight = 30390.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.036083 restraints weight = 19340.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.036613 restraints weight = 13287.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.036992 restraints weight = 9824.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.6465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7484  Z= 0.152
  Angle     :  0.644   8.045  10145  Z= 0.327
  Chirality :  0.040   0.171   1158
  Planarity :  0.003   0.040   1272
  Dihedral  : 11.887 105.759   1191
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  3.84 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.81 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    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:  0.69 (0.27), residues: 912
  helix:  1.36 (0.24), residues: 429
  sheet: -0.56 (0.41), residues: 141
  loop : -0.11 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  96 
 TYR   0.013   0.001   TYR B 191 
 PHE   0.021   0.002   PHE B  86 
 HIS   0.003   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7481)
  covalent geometry    : angle       0.64442 (10145)
  hydrogen bonds       : bond        0.03610 (  334)
  hydrogen bonds       : angle       4.73471 (  918)
  Misc. bond           : bond        0.00089 (    3)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.8834 (pttp) cc_final: 0.8322 (ptpt)
REVERT: A   62 ASN cc_start: 0.8658 (m-40) cc_final: 0.8348 (m110)
REVERT: A  137 CYS cc_start: 0.9154 (m) cc_final: 0.8943 (m)
REVERT: A  158 MET cc_start: 0.6961 (pmm) cc_final: 0.6573 (pmm)
REVERT: A  251 MET cc_start: 0.8889 (tpt) cc_final: 0.8413 (tpt)
REVERT: B   62 ASN cc_start: 0.8687 (m-40) cc_final: 0.8353 (m110)
REVERT: B  248 PHE cc_start: 0.9292 (t80) cc_final: 0.8944 (t80)
REVERT: B  267 ASN cc_start: 0.8610 (p0) cc_final: 0.8327 (p0)
REVERT: C   52 VAL cc_start: 0.9335 (t) cc_final: 0.9093 (p)
REVERT: C   58 LYS cc_start: 0.9148 (pttp) cc_final: 0.8930 (ptpt)
REVERT: C   84 MET cc_start: 0.7652 (mmm) cc_final: 0.7418 (mmt)
REVERT: C  137 CYS cc_start: 0.9176 (m) cc_final: 0.8916 (m)
REVERT: C  251 MET cc_start: 0.8972 (tpt) cc_final: 0.8451 (tpt)
  outliers start: 1
  outliers final: 1
  residues processed: 56
  average time/residue: 0.0985
  time to fit residues: 7.6253
Evaluate side-chains
  48 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   chunk 25 optimal weight:   20.0000
   chunk 57 optimal weight:    7.9990
   chunk 43 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 30 optimal weight:   10.0000
   chunk 12 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    7.9990
   chunk 85 optimal weight:    9.9990
   overall best weight:    5.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  47 HIS
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.038242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.033010 restraints weight = 53759.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.034105 restraints weight = 29908.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.034864 restraints weight = 18951.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.035394 restraints weight = 13115.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.035769 restraints weight = 9717.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.6431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   7484  Z= 0.240
  Angle     :  0.710   7.746  10145  Z= 0.363
  Chirality :  0.041   0.177   1158
  Planarity :  0.004   0.044   1272
  Dihedral  : 12.046 108.154   1191
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  4.82 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    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:  0.41 (0.27), residues: 912
  helix:  1.11 (0.24), residues: 429
  sheet: -0.65 (0.41), residues: 141
  loop : -0.24 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  96 
 TYR   0.020   0.001   TYR B 191 
 PHE   0.025   0.002   PHE B  86 
 HIS   0.004   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 7481)
  covalent geometry    : angle       0.71011 (10145)
  hydrogen bonds       : bond        0.04064 (  334)
  hydrogen bonds       : angle       5.02787 (  918)
  Misc. bond           : bond        0.00130 (    3)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   62 ASN cc_start: 0.8613 (m-40) cc_final: 0.8262 (m110)
REVERT: A  137 CYS cc_start: 0.9098 (m) cc_final: 0.8868 (m)
REVERT: A  251 MET cc_start: 0.9048 (tpt) cc_final: 0.8707 (tpp)
REVERT: B   36 ASN cc_start: 0.9203 (m110) cc_final: 0.8940 (m110)
REVERT: B   62 ASN cc_start: 0.8759 (m-40) cc_final: 0.8491 (m110)
REVERT: B  267 ASN cc_start: 0.8751 (p0) cc_final: 0.8448 (p0)
REVERT: C  137 CYS cc_start: 0.9164 (m) cc_final: 0.8901 (m)
REVERT: C  158 MET cc_start: 0.7937 (pmm) cc_final: 0.7721 (pmm)
REVERT: C  251 MET cc_start: 0.8930 (tpt) cc_final: 0.8388 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0746
  time to fit residues: 5.4288
Evaluate side-chains
  40 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 76 optimal weight:   10.0000
   chunk 85 optimal weight:    0.4980
   chunk 86 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 58 optimal weight:    9.9990
   chunk 87 optimal weight:    8.9990
   chunk 56 optimal weight:    7.9990
   chunk 47 optimal weight:    6.9990
   chunk 70 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   overall best weight:    5.2988

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 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 = 0.2831 r_free = 0.2831 target = 0.038129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.032863 restraints weight = 54478.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.033976 restraints weight = 30165.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.034742 restraints weight = 19075.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.035248 restraints weight = 13224.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.035628 restraints weight = 9836.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.6560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   7484  Z= 0.235
  Angle     :  0.733  11.513  10145  Z= 0.370
  Chirality :  0.041   0.182   1158
  Planarity :  0.004   0.045   1272
  Dihedral  : 12.060 107.177   1191
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  5.04 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    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:  0.21 (0.27), residues: 912
  helix:  0.95 (0.24), residues: 429
  sheet: -0.59 (0.43), residues: 135
  loop : -0.44 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  96 
 TYR   0.017   0.002   TYR B 191 
 PHE   0.029   0.002   PHE C  86 
 HIS   0.004   0.001   HIS C 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 7481)
  covalent geometry    : angle       0.73259 (10145)
  hydrogen bonds       : bond        0.04132 (  334)
  hydrogen bonds       : angle       5.08463 (  918)
  Misc. bond           : bond        0.00141 (    3)

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

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

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1824 Ramachandran restraints generated.
    912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A   62 ASN cc_start: 0.8625 (m-40) cc_final: 0.8259 (m110)
REVERT: A  137 CYS cc_start: 0.9175 (m) cc_final: 0.8934 (m)
REVERT: A  158 MET cc_start: 0.7663 (pmm) cc_final: 0.7208 (pmm)
REVERT: A  251 MET cc_start: 0.9082 (tpt) cc_final: 0.8441 (tpt)
REVERT: B   62 ASN cc_start: 0.8587 (m-40) cc_final: 0.8319 (m-40)
REVERT: B  137 CYS cc_start: 0.9280 (m) cc_final: 0.9036 (m)
REVERT: B  243 MET cc_start: 0.8380 (tmm) cc_final: 0.8178 (tmm)
REVERT: B  267 ASN cc_start: 0.8820 (p0) cc_final: 0.8526 (p0)
REVERT: C  137 CYS cc_start: 0.9192 (m) cc_final: 0.8916 (m)
REVERT: C  158 MET cc_start: 0.8018 (pmm) cc_final: 0.7790 (pmm)
REVERT: C  251 MET cc_start: 0.8949 (tpt) cc_final: 0.8376 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.0766
  time to fit residues: 5.1976
Evaluate side-chains
  39 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 73 optimal weight:   20.0000
   chunk 63 optimal weight:    8.9990
   chunk 87 optimal weight:    9.9990
   chunk 27 optimal weight:    7.9990
   chunk 58 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 196 ASN
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.038868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.033552 restraints weight = 53219.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.034672 restraints weight = 29881.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.035434 restraints weight = 18959.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.035965 restraints weight = 13150.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.036346 restraints weight = 9740.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.6678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7484  Z= 0.174
  Angle     :  0.682   7.999  10145  Z= 0.343
  Chirality :  0.040   0.175   1158
  Planarity :  0.004   0.092   1272
  Dihedral  : 11.945 104.843   1191
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  4.28 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    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:  0.37 (0.28), residues: 912
  helix:  1.14 (0.24), residues: 429
  sheet: -0.62 (0.43), residues: 138
  loop : -0.39 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  96 
 TYR   0.014   0.001   TYR B 191 
 PHE   0.021   0.002   PHE B  86 
 HIS   0.002   0.001   HIS C 138 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 7481)
  covalent geometry    : angle       0.68177 (10145)
  hydrogen bonds       : bond        0.03835 (  334)
  hydrogen bonds       : angle       4.88053 (  918)
  Misc. bond           : bond        0.00098 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1038.25 seconds
wall clock time: 18 minutes 54.59 seconds (1134.59 seconds total)