Starting phenix.real_space_refine
on Tue Sep 24 08:10:14 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/09_2024/5h1b_9566.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/09_2024/5h1b_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/09_2024/5h1b_9566.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/09_2024/5h1b_9566.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/09_2024/5h1b_9566.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1b_9566/09_2024/5h1b_9566.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 4.73, per 1000 atoms: 0.64
  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: 1.69
  Conformation dependent library (CDL) restraints added in 841.1 milliseconds
  

  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: 0.75
  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: 1.81

  Time building geometry restraints manager: 1.95 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:             0.810
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     18.390
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.700
-------------------------------------------------------------------------------
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      :  0.010   0.150   7481  Z= 0.667
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (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
 HIS   0.009   0.002   HIS C 138 
 PHE   0.018   0.003   PHE C  86 
 TYR   0.019   0.002   TYR A 315 
 ARG   0.010   0.002   ARG C 215 

*********************** 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 fitting.
    rotamer outliers: 42
    poor density    : 98
  time to evaluate  : 0.917 
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: 0.6302 (mp)
REVERT: A  265 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8424 (mm)
REVERT: B   62 ASN cc_start: 0.7700 (m-40) cc_final: 0.7444 (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: 0.8012 (mm)
  outliers start: 42
  outliers final: 13
  residues processed: 132
  average time/residue: 0.2937
  time to fit residues: 47.7154
Evaluate side-chains
  72 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 54
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 68 optimal weight:    5.9990
   chunk 37 optimal weight:    9.9990
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    8.9990
   chunk 36 optimal weight:    6.9990
   chunk 70 optimal weight:    3.9990
   chunk 27 optimal weight:   20.0000
   chunk 42 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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**
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.4034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7481  Z= 0.287
  Angle     :  0.777   7.710  10145  Z= 0.412
  Chirality :  0.044   0.167   1158
  Planarity :  0.005   0.042   1272
  Dihedral  : 13.507 111.171   1191
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 18.10
  Ramachandran Plot:
    Outliers :  1.32 %
    Allowed  :  4.28 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  0.94 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.27), residues: 912
  helix: -0.30 (0.23), residues: 429
  sheet: -0.58 (0.40), residues: 168
  loop :  0.45 (0.37), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B 294 
 PHE   0.019   0.002   PHE B 126 
 TYR   0.018   0.002   TYR B 315 
 ARG   0.007   0.001   ARG B 193 

*********************** 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
  72 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.798 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 ILE cc_start: 0.6115 (OUTLIER) cc_final: 0.5871 (mt)
REVERT: C  251 MET cc_start: 0.7689 (tpt) cc_final: 0.7389 (tpt)
REVERT: C  301 TYR cc_start: 0.7594 (t80) cc_final: 0.7387 (t80)
  outliers start: 4
  outliers final: 0
  residues processed: 72
  average time/residue: 0.2152
  time to fit residues: 20.9573
Evaluate side-chains
  42 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 45 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 68 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 81 optimal weight:    8.9990
   chunk 88 optimal weight:    6.9990
   chunk 72 optimal weight:    8.9990
   chunk 27 optimal weight:    8.9990
   chunk 65 optimal weight:    7.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 199 HIS
C 267 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.4915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7481  Z= 0.307
  Angle     :  0.703   7.483  10145  Z= 0.373
  Chirality :  0.041   0.168   1158
  Planarity :  0.004   0.038   1272
  Dihedral  : 12.623 107.355   1191
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 16.53
  Ramachandran Plot:
    Outliers :  1.32 %
    Allowed  :  5.37 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  2.02 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.27), residues: 912
  helix:  0.39 (0.23), residues: 447
  sheet: -0.73 (0.39), residues: 168
  loop :  0.02 (0.37), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 294 
 PHE   0.020   0.002   PHE B  86 
 TYR   0.021   0.001   TYR C 315 
 ARG   0.004   0.001   ARG B 193 

*********************** 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
  57 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
REVERT: A  251 MET cc_start: 0.7787 (tpt) cc_final: 0.7430 (tpt)
REVERT: B   84 MET cc_start: 0.7252 (mpp) cc_final: 0.6835 (mpp)
REVERT: B  225 THR cc_start: 0.8311 (p) cc_final: 0.7696 (p)
REVERT: B  248 PHE cc_start: 0.8694 (t80) cc_final: 0.8435 (t80)
REVERT: B  301 TYR cc_start: 0.7037 (t80) cc_final: 0.6813 (t80)
REVERT: C  251 MET cc_start: 0.7782 (tpt) cc_final: 0.7570 (tpt)
  outliers start: 2
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1570
  time to fit residues: 13.4969
Evaluate side-chains
  39 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 61 optimal weight:    0.4980
   chunk 42 optimal weight:    9.9990
   chunk 9 optimal weight:    6.9990
   chunk 39 optimal weight:    9.9990
   chunk 54 optimal weight:    9.9990
   chunk 82 optimal weight:    7.9990
   chunk 86 optimal weight:    3.9990
   chunk 77 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 72 optimal weight:    8.9990
   chunk 49 optimal weight:    7.9990
   overall best weight:    4.6988

-------------------------------------------------------------------------------
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**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 242 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.5472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7481  Z= 0.306
  Angle     :  0.696   9.265  10145  Z= 0.367
  Chirality :  0.041   0.179   1158
  Planarity :  0.004   0.053   1272
  Dihedral  : 12.699 109.377   1191
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  1.21 %
    Allowed  :  4.71 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.43 %
    Favored  : 97.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.27), residues: 912
  helix:  0.62 (0.23), residues: 447
  sheet: -0.79 (0.39), residues: 165
  loop : -0.13 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 294 
 PHE   0.018   0.002   PHE C 195 
 TYR   0.016   0.001   TYR C 315 
 ARG   0.004   0.001   ARG C  96 

*********************** 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
  53 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 52
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  158 MET cc_start: 0.7131 (pmm) cc_final: 0.6649 (mpp)
REVERT: B  267 ASN cc_start: 0.7936 (p0) cc_final: 0.7655 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 53
  average time/residue: 0.1734
  time to fit residues: 13.5913
Evaluate side-chains
  40 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 40
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 35 optimal weight:    7.9990
   chunk 74 optimal weight:    9.9990
   chunk 60 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 44 optimal weight:    7.9990
   chunk 78 optimal weight:    5.9990
   chunk 21 optimal weight:    0.8980
   chunk 29 optimal weight:    8.9990
   chunk 17 optimal weight:    8.9990
   overall best weight:    5.9788

-------------------------------------------------------------------------------
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  47 HIS
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  47 HIS
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.5849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   7481  Z= 0.362
  Angle     :  0.726   7.728  10145  Z= 0.382
  Chirality :  0.042   0.180   1158
  Planarity :  0.004   0.064   1272
  Dihedral  : 12.930 117.397   1191
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 16.05
  Ramachandran Plot:
    Outliers :  1.21 %
    Allowed  :  5.15 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.27), residues: 912
  helix:  0.74 (0.23), residues: 429
  sheet: -0.92 (0.37), residues: 159
  loop : -0.13 (0.35), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 138 
 PHE   0.021   0.002   PHE C 195 
 TYR   0.013   0.002   TYR B 315 
 ARG   0.009   0.001   ARG B  96 

*********************** 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
  48 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 LEU cc_start: 0.7741 (mp) cc_final: 0.7479 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.1760
  time to fit residues: 12.5545
Evaluate side-chains
  37 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 51 optimal weight:    0.0470
   chunk 21 optimal weight:    1.9990
   chunk 87 optimal weight:    7.9990
   chunk 72 optimal weight:    0.6980
   chunk 40 optimal weight:    5.9990
   chunk 7 optimal weight:    8.9990
   chunk 28 optimal weight:   10.0000
   chunk 45 optimal weight:   10.0000
   chunk 83 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   overall best weight:    2.1484

-------------------------------------------------------------------------------
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**
** 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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.6148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7481  Z= 0.193
  Angle     :  0.645  10.991  10145  Z= 0.329
  Chirality :  0.040   0.183   1158
  Planarity :  0.003   0.052   1272
  Dihedral  : 12.598 115.999   1191
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  1.21 %
    Allowed  :  4.28 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.27), residues: 912
  helix:  1.25 (0.24), residues: 429
  sheet: -0.53 (0.40), residues: 141
  loop : -0.08 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 294 
 PHE   0.014   0.002   PHE B  86 
 TYR   0.010   0.001   TYR C 216 
 ARG   0.005   0.001   ARG B  96 

*********************** 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
  57 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
REVERT: B  267 ASN cc_start: 0.7940 (p0) cc_final: 0.7738 (p0)
REVERT: C  251 MET cc_start: 0.7717 (tpt) cc_final: 0.7365 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1808
  time to fit residues: 14.8337
Evaluate side-chains
  41 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 49 optimal weight:    7.9990
   chunk 73 optimal weight:   20.0000
   chunk 48 optimal weight:    1.9990
   chunk 86 optimal weight:    0.2980
   chunk 54 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 40 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 34 optimal weight:    8.9990
   chunk 51 optimal weight:    9.9990
   overall best weight:    2.6386

-------------------------------------------------------------------------------
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**
B  93 HIS
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.6399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7481  Z= 0.211
  Angle     :  0.649   7.583  10145  Z= 0.333
  Chirality :  0.040   0.162   1158
  Planarity :  0.004   0.081   1272
  Dihedral  : 12.296 108.456   1191
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  1.21 %
    Allowed  :  4.50 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.27), residues: 912
  helix:  1.28 (0.24), residues: 429
  sheet: -0.42 (0.42), residues: 135
  loop : -0.05 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 294 
 PHE   0.014   0.002   PHE B  86 
 TYR   0.015   0.001   TYR B 216 
 ARG   0.005   0.000   ARG A 167 

*********************** 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
  55 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  267 ASN cc_start: 0.7815 (p0) cc_final: 0.7588 (p0)
REVERT: C  251 MET cc_start: 0.7718 (tpt) cc_final: 0.7379 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.1785
  time to fit residues: 14.2256
Evaluate side-chains
  38 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 26 optimal weight:    0.0270
   chunk 17 optimal weight:    6.9990
   chunk 16 optimal weight:   10.0000
   chunk 55 optimal weight:    0.0770
   chunk 59 optimal weight:    8.9990
   chunk 42 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 78 optimal weight:    7.9990
   chunk 83 optimal weight:    4.9990
   chunk 75 optimal weight:   10.0000
   overall best weight:    1.1800

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

Flipped N/Q/H residues before XYZ refinement:
A  62 ASN
** 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**
B 196 ASN
** 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: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.6730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7481  Z= 0.160
  Angle     :  0.617   7.955  10145  Z= 0.315
  Chirality :  0.039   0.158   1158
  Planarity :  0.004   0.058   1272
  Dihedral  : 12.058 106.618   1191
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  1.10 %
    Allowed  :  4.06 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.54 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.27), residues: 912
  helix:  1.48 (0.24), residues: 426
  sheet: -0.42 (0.41), residues: 144
  loop :  0.06 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 244 
 PHE   0.016   0.001   PHE C  86 
 TYR   0.015   0.001   TYR C 216 
 ARG   0.007   0.000   ARG B 167 

*********************** 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
  58 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 MET cc_start: 0.7762 (tpt) cc_final: 0.7560 (tpt)
REVERT: B  267 ASN cc_start: 0.7690 (p0) cc_final: 0.7482 (p0)
REVERT: C  251 MET cc_start: 0.7767 (tpt) cc_final: 0.7451 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 58
  average time/residue: 0.2037
  time to fit residues: 16.6817
Evaluate side-chains
  41 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 80 optimal weight:    9.9990
   chunk 83 optimal weight:    8.9990
   chunk 48 optimal weight:   10.0000
   chunk 35 optimal weight:    7.9990
   chunk 63 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 73 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 85 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    4.7988

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

Flipped N/Q/H residues before XYZ refinement:
A  62 ASN
** 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**
** 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: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.6630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027   7481  Z= 0.305
  Angle     :  0.696   7.711  10145  Z= 0.355
  Chirality :  0.041   0.176   1158
  Planarity :  0.005   0.080   1272
  Dihedral  : 12.181 109.916   1191
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  5.37 %
    Favored  : 93.75 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.27), residues: 912
  helix:  1.24 (0.24), residues: 420
  sheet: -0.41 (0.41), residues: 141
  loop : -0.12 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 294 
 PHE   0.027   0.002   PHE C  86 
 TYR   0.014   0.002   TYR B 301 
 ARG   0.004   0.001   ARG A 130 

*********************** 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
  50 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
REVERT: B   62 ASN cc_start: 0.6504 (p0) cc_final: 0.6173 (p0)
REVERT: C  251 MET cc_start: 0.7778 (tpt) cc_final: 0.7460 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.1818
  time to fit residues: 13.2755
Evaluate side-chains
  39 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 59 optimal weight:    6.9990
   chunk 89 optimal weight:    6.9990
   chunk 82 optimal weight:    4.9990
   chunk 71 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 55 optimal weight:    0.4980
   chunk 43 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9990
   chunk 76 optimal weight:   20.0000
   chunk 21 optimal weight:    8.9990
   overall best weight:    3.4988

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.6711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   7481  Z= 0.243
  Angle     :  0.653   7.987  10145  Z= 0.334
  Chirality :  0.040   0.174   1158
  Planarity :  0.005   0.076   1272
  Dihedral  : 12.057 108.255   1191
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  4.50 %
    Favored  : 94.63 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.28), residues: 912
  helix:  1.33 (0.24), residues: 420
  sheet: -0.43 (0.42), residues: 141
  loop : -0.13 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 294 
 PHE   0.021   0.002   PHE C  86 
 TYR   0.013   0.001   TYR B 301 
 ARG   0.003   0.000   ARG A 130 

********************** 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
  51 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   62 ASN cc_start: 0.6522 (p0) cc_final: 0.6254 (p0)
REVERT: B  158 MET cc_start: 0.7702 (mpp) cc_final: 0.7469 (mpp)
REVERT: C  251 MET cc_start: 0.7789 (tpt) cc_final: 0.7503 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 51
  average time/residue: 0.1680
  time to fit residues: 12.6906
Evaluate side-chains
  38 residues out of total 741 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 19 optimal weight:   10.0000
   chunk 71 optimal weight:    6.9990
   chunk 29 optimal weight:   20.0000
   chunk 73 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 62 optimal weight:    6.9990
   chunk 4 optimal weight:    0.0170
   chunk 51 optimal weight:    7.9990
   overall best weight:    2.1422

-------------------------------------------------------------------------------
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 = 0.2891 r_free = 0.2891 target = 0.039926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.034680 restraints weight = 52367.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.035771 restraints weight = 29727.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.036574 restraints weight = 19111.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.6865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7481  Z= 0.186
  Angle     :  0.625   8.105  10145  Z= 0.318
  Chirality :  0.039   0.169   1158
  Planarity :  0.004   0.062   1272
  Dihedral  : 11.904 107.896   1191
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.88 %
    Allowed  :  4.17 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.67 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.28), residues: 912
  helix:  1.55 (0.24), residues: 417
  sheet: -0.32 (0.43), residues: 141
  loop : -0.11 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 294 
 PHE   0.017   0.001   PHE C  86 
 TYR   0.013   0.001   TYR C 216 
 ARG   0.003   0.000   ARG A 130 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1326.61 seconds
wall clock time: 24 minutes 46.80 seconds (1486.80 seconds total)