Starting phenix.real_space_refine
on Wed Mar 12 18:50:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9em9_19814/03_2025/9em9_19814.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9em9_19814/03_2025/9em9_19814.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9em9_19814/03_2025/9em9_19814.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9em9_19814/03_2025/9em9_19814.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9em9_19814/03_2025/9em9_19814.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9em9_19814/03_2025/9em9_19814.cif"
  }
  resolution = 3.76
  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=   0.003 sd=   0.066
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       6      5.49       5
     Mg      2      5.21       5
     S      24      5.16       5
     C    5110      2.51       5
     N    1430      2.21       5
     O    1610      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8182
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 4058
          Classifications: {'peptide': 512}
          Link IDs: {'PTRANS': 14, 'TRANS': 497}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GNP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 11.15, per 1000 atoms: 1.36
  Number of scatterers: 8182
  At special positions: 0
  Unit cell: (128.112, 99.552, 102.816, 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      24     16.00
     P       6     15.00
     Mg      2     11.99
     O    1610      8.00
     N    1430      7.00
     C    5110      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   8 " - pdb=" SG  CYS A 763 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   8 " - pdb=" SG  CYS B 763 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.58
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1936

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 5 sheets defined
      65.4% alpha, 7.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 24
      removed outlier: 4.298A  pdb=" N   ARG A  12 " --> pdb=" O   CYS A   8 " (cutoff:3.500A)
      removed outlier: 5.250A  pdb=" N   GLU A  13 " --> pdb=" O   GLN A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 32
    Processing helix  chain 'A' and resid 33 through 46
      removed outlier: 4.003A  pdb=" N   VAL A  37 " --> pdb=" O   ASP A  33 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER A  46 " --> pdb=" O   GLY A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 70
    Processing helix  chain 'A' and resid 92 through 95
    Processing helix  chain 'A' and resid 104 through 120
    Processing helix  chain 'A' and resid 130 through 149
    Processing helix  chain 'A' and resid 154 through 174
    Processing helix  chain 'A' and resid 195 through 203
      removed outlier: 3.544A  pdb=" N   ARG A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 225
      removed outlier: 3.801A  pdb=" N   LYS A 224 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ASP A 225 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 220 through 225'
    Processing helix  chain 'A' and resid 239 through 252
    Processing helix  chain 'A' and resid 263 through 268
    Processing helix  chain 'A' and resid 271 through 284
      removed outlier: 3.614A  pdb=" N   ASN A 284 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 290
      removed outlier: 3.847A  pdb=" N   ASP A 289 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 304
      removed outlier: 3.883A  pdb=" N   TRP A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   TYR A 303 " --> pdb=" O   ASP A 299 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASN A 304 " --> pdb=" O   ASP A 300 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 298 through 304'
    Processing helix  chain 'A' and resid 304 through 319
    Processing helix  chain 'A' and resid 329 through 342
      removed outlier: 3.812A  pdb=" N   TYR A 335 " --> pdb=" O   LEU A 331 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN A 341 " --> pdb=" O   SER A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 359
      removed outlier: 4.112A  pdb=" N   LYS A 359 " --> pdb=" O   ALA A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 379
      removed outlier: 4.284A  pdb=" N   TYR A 377 " --> pdb=" O   GLU A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 387
    Processing helix  chain 'A' and resid 400 through 423
      removed outlier: 3.719A  pdb=" N   ILE A 406 " --> pdb=" O   ASN A 402 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLU A 409 " --> pdb=" O   ARG A 405 " (cutoff:3.500A)
      removed outlier: 7.963A  pdb=" N   ILE A 412 " --> pdb=" O   SER A 408 " (cutoff:3.500A)
      Proline residue:  A 413  - end of helix
      removed outlier: 3.746A  pdb=" N   ASP A 416 " --> pdb=" O   ILE A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 437
      removed outlier: 3.562A  pdb=" N   SER A 429 " --> pdb=" O   GLU A 425 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA A 436 " --> pdb=" O   GLY A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 472
      Proline residue:  A 453  - end of helix
    Processing helix  chain 'A' and resid 736 through 767
    Processing helix  chain 'B' and resid 5 through 24
      removed outlier: 4.299A  pdb=" N   ARG B  12 " --> pdb=" O   CYS B   8 " (cutoff:3.500A)
      removed outlier: 5.250A  pdb=" N   GLU B  13 " --> pdb=" O   GLN B   9 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 32
    Processing helix  chain 'B' and resid 33 through 46
      removed outlier: 4.002A  pdb=" N   VAL B  37 " --> pdb=" O   ASP B  33 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   SER B  46 " --> pdb=" O   GLY B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 70
    Processing helix  chain 'B' and resid 92 through 95
    Processing helix  chain 'B' and resid 104 through 120
    Processing helix  chain 'B' and resid 130 through 149
    Processing helix  chain 'B' and resid 154 through 174
    Processing helix  chain 'B' and resid 195 through 203
      removed outlier: 3.544A  pdb=" N   ARG B 203 " --> pdb=" O   ALA B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 225
      removed outlier: 3.801A  pdb=" N   LYS B 224 " --> pdb=" O   HIS B 220 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ASP B 225 " --> pdb=" O   SER B 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 220 through 225'
    Processing helix  chain 'B' and resid 239 through 252
    Processing helix  chain 'B' and resid 263 through 268
    Processing helix  chain 'B' and resid 271 through 284
      removed outlier: 3.614A  pdb=" N   ASN B 284 " --> pdb=" O   ARG B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 290
      removed outlier: 3.847A  pdb=" N   ASP B 289 " --> pdb=" O   GLY B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 304
      removed outlier: 3.884A  pdb=" N   TRP B 302 " --> pdb=" O   ILE B 298 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   TYR B 303 " --> pdb=" O   ASP B 299 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ASN B 304 " --> pdb=" O   ASP B 300 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 298 through 304'
    Processing helix  chain 'B' and resid 304 through 319
    Processing helix  chain 'B' and resid 329 through 342
      removed outlier: 3.813A  pdb=" N   TYR B 335 " --> pdb=" O   LEU B 331 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN B 341 " --> pdb=" O   SER B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 359
      removed outlier: 4.113A  pdb=" N   LYS B 359 " --> pdb=" O   ALA B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 379
      removed outlier: 4.285A  pdb=" N   TYR B 377 " --> pdb=" O   GLU B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 387
    Processing helix  chain 'B' and resid 400 through 423
      removed outlier: 3.719A  pdb=" N   ILE B 406 " --> pdb=" O   ASN B 402 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLU B 409 " --> pdb=" O   ARG B 405 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   ILE B 412 " --> pdb=" O   SER B 408 " (cutoff:3.500A)
      Proline residue:  B 413  - end of helix
      removed outlier: 3.746A  pdb=" N   ASP B 416 " --> pdb=" O   ILE B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 437
      removed outlier: 3.562A  pdb=" N   SER B 429 " --> pdb=" O   GLU B 425 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA B 436 " --> pdb=" O   GLY B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 472
      Proline residue:  B 453  - end of helix
    Processing helix  chain 'B' and resid 736 through 767
    Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52
      removed outlier: 6.083A  pdb=" N   PHE A  49 " --> pdb=" O   VAL A 228 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   VAL A 230 " --> pdb=" O   PHE A  49 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   ILE A  51 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      removed outlier: 8.418A  pdb=" N   ASN A 227 " --> pdb=" O   TYR A  90 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   TYR A  90 " --> pdb=" O   ASN A 227 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ARG A 213 " --> pdb=" O   THR A 101 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ARG A  97 " --> pdb=" O   PHE A 217 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   TYR A 185 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 262
      removed outlier: 6.121A  pdb=" N   CYS A 260 " --> pdb=" O   VAL A 294 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 394
    Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 52
      removed outlier: 6.084A  pdb=" N   PHE B  49 " --> pdb=" O   VAL B 228 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   VAL B 230 " --> pdb=" O   PHE B  49 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   ILE B  51 " --> pdb=" O   VAL B 230 " (cutoff:3.500A)
      removed outlier: 8.417A  pdb=" N   ASN B 227 " --> pdb=" O   TYR B  90 " (cutoff:3.500A)
      removed outlier: 5.066A  pdb=" N   TYR B  90 " --> pdb=" O   ASN B 227 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ARG B 213 " --> pdb=" O   THR B 101 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ARG B  97 " --> pdb=" O   PHE B 217 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   TYR B 185 " --> pdb=" O   LEU B 100 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 259 through 262
      removed outlier: 6.121A  pdb=" N   CYS B 260 " --> pdb=" O   VAL B 294 " (cutoff:3.500A)

    464 hydrogen bonds defined for protein.
    1362 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.58

  Time building geometry restraints manager: 2.99 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2782
        1.34 -     1.46: 1387
        1.46 -     1.58: 4101
        1.58 -     1.70: 6
        1.70 -     1.82: 34
  Bond restraints: 8310
  Sorted by residual:
  bond pdb=" N3B GNP A 801 "
       pdb=" PG  GNP A 801 "
    ideal  model  delta    sigma   weight residual
    1.801  1.705  0.096 2.00e-02 2.50e+03 2.31e+01
  bond pdb=" N3B GNP B 801 "
       pdb=" PG  GNP B 801 "
    ideal  model  delta    sigma   weight residual
    1.801  1.705  0.096 2.00e-02 2.50e+03 2.31e+01
  bond pdb=" O5' GNP A 801 "
       pdb=" PA  GNP A 801 "
    ideal  model  delta    sigma   weight residual
    1.660  1.565  0.095 2.00e-02 2.50e+03 2.26e+01
  bond pdb=" O5' GNP B 801 "
       pdb=" PA  GNP B 801 "
    ideal  model  delta    sigma   weight residual
    1.660  1.566  0.094 2.00e-02 2.50e+03 2.23e+01
  bond pdb=" O3A GNP A 801 "
       pdb=" PB  GNP A 801 "
    ideal  model  delta    sigma   weight residual
    1.687  1.635  0.052 2.00e-02 2.50e+03 6.87e+00
  ... (remaining 8305 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 11008
        2.05 -     4.11: 180
        4.11 -     6.16: 40
        6.16 -     8.21: 10
        8.21 -    10.27: 6
  Bond angle restraints: 11244
  Sorted by residual:
  angle pdb=" N   LYS B 263 "
        pdb=" CA  LYS B 263 "
        pdb=" C   LYS B 263 "
      ideal   model   delta    sigma   weight residual
     109.81  120.08  -10.27 2.21e+00 2.05e-01 2.16e+01
  angle pdb=" N   LYS A 263 "
        pdb=" CA  LYS A 263 "
        pdb=" C   LYS A 263 "
      ideal   model   delta    sigma   weight residual
     109.81  120.06  -10.25 2.21e+00 2.05e-01 2.15e+01
  angle pdb=" CA  TYR B 466 "
        pdb=" CB  TYR B 466 "
        pdb=" CG  TYR B 466 "
      ideal   model   delta    sigma   weight residual
     113.90  107.60    6.30 1.80e+00 3.09e-01 1.22e+01
  angle pdb=" CA  TYR A 466 "
        pdb=" CB  TYR A 466 "
        pdb=" CG  TYR A 466 "
      ideal   model   delta    sigma   weight residual
     113.90  107.61    6.29 1.80e+00 3.09e-01 1.22e+01
  angle pdb=" O1B GNP A 801 "
        pdb=" PB  GNP A 801 "
        pdb=" O2B GNP A 801 "
      ideal   model   delta    sigma   weight residual
     119.66  110.05    9.61 3.00e+00 1.11e-01 1.03e+01
  ... (remaining 11239 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.10: 4572
       16.10 -    32.21: 392
       32.21 -    48.31: 76
       48.31 -    64.41: 46
       64.41 -    80.51: 22
  Dihedral angle restraints: 5108
    sinusoidal: 2112
      harmonic: 2996
  Sorted by residual:
  dihedral pdb=" CA  SER B 256 "
           pdb=" C   SER B 256 "
           pdb=" N   ALA B 257 "
           pdb=" CA  ALA B 257 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.18   29.82     0      5.00e+00 4.00e-02 3.56e+01
  dihedral pdb=" CA  SER A 256 "
           pdb=" C   SER A 256 "
           pdb=" N   ALA A 257 "
           pdb=" CA  ALA A 257 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.21   29.79     0      5.00e+00 4.00e-02 3.55e+01
  dihedral pdb=" CA  THR B 255 "
           pdb=" C   THR B 255 "
           pdb=" N   SER B 256 "
           pdb=" CA  SER B 256 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.19   28.81     0      5.00e+00 4.00e-02 3.32e+01
  ... (remaining 5105 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 926
       0.044 -    0.088: 256
       0.088 -    0.132: 59
       0.132 -    0.176: 13
       0.176 -    0.220: 2
  Chirality restraints: 1256
  Sorted by residual:
  chirality pdb=" CA  TYR A 466 "
            pdb=" N   TYR A 466 "
            pdb=" C   TYR A 466 "
            pdb=" CB  TYR A 466 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  TYR B 466 "
            pdb=" N   TYR B 466 "
            pdb=" C   TYR B 466 "
            pdb=" CB  TYR B 466 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  LYS B 263 "
            pdb=" N   LYS B 263 "
            pdb=" C   LYS B 263 "
            pdb=" CB  LYS B 263 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.20e-01
  ... (remaining 1253 not shown)

  Planarity restraints: 1474
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 290 "   -0.409 9.50e-02 1.11e+02   1.85e-01 2.58e+01
        pdb=" NE  ARG A 290 "    0.038 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 290 "   -0.035 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 290 "    0.016 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 290 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 290 "    0.409 9.50e-02 1.11e+02   1.85e-01 2.58e+01
        pdb=" NE  ARG B 290 "   -0.038 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 290 "    0.035 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 290 "   -0.016 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 290 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 372 "    0.017 2.00e-02 2.50e+03   3.44e-02 1.19e+01
        pdb=" C   SER B 372 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   SER B 372 "    0.022 2.00e-02 2.50e+03
        pdb=" N   GLU B 373 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1471 not shown)

  Histogram of nonbonded interaction distances:
        1.85 -     2.46: 28
        2.46 -     3.07: 5636
        3.07 -     3.68: 12218
        3.68 -     4.29: 17778
        4.29 -     4.90: 29257
  Nonbonded interactions: 64917
  Sorted by model distance:
  nonbonded pdb=" O2B GNP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     1.853 2.170
  nonbonded pdb=" O2B GNP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     1.853 2.170
  nonbonded pdb=" OG1 THR B  82 "
            pdb="MG    MG B 802 "
     model   vdw
     1.883 2.170
  nonbonded pdb=" OG1 THR A  82 "
            pdb="MG    MG A 802 "
     model   vdw
     1.885 2.170
  nonbonded pdb=" O1G GNP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     1.937 2.170
  ... (remaining 64912 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             8.130
  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:             0.020
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.120
  Process input model:                     30.370
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
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      :  0.004   0.096   8310  Z= 0.246
  Angle     :  0.754  10.266  11244  Z= 0.419
  Chirality :  0.044   0.220   1256
  Planarity :  0.011   0.185   1474
  Dihedral  : 14.920  80.515   3166
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.71 (0.24), residues: 1016
  helix: -0.27 (0.19), residues: 600
  sheet: -0.10 (0.41), residues: 118
  loop : -0.68 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 302 
 HIS   0.004   0.001   HIS B 164 
 PHE   0.019   0.002   PHE B 348 
 TYR   0.028   0.005   TYR B 466 
 ARG   0.040   0.004   ARG A 290 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 MET cc_start: 0.4999 (mmt) cc_final: 0.4727 (mtt)
REVERT: A  444 PHE cc_start: 0.7811 (m-80) cc_final: 0.7586 (m-10)
REVERT: A  447 LEU cc_start: 0.8910 (tp) cc_final: 0.8672 (tt)
REVERT: B  187 MET cc_start: 0.4964 (mmt) cc_final: 0.4708 (mtt)
REVERT: B  444 PHE cc_start: 0.7943 (m-80) cc_final: 0.7713 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.2501
  time to fit residues: 47.9281
Evaluate side-chains
  76 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 77 optimal weight:    0.5980
   chunk 42 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
A  10 ASN
A  92 ASN
A 276 GLN
A 309 GLN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 417 GLN
B   9 GLN
B  10 ASN
B 276 GLN
B 309 GLN
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 417 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.121191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.097356 restraints weight = 24303.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.096695 restraints weight = 20578.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.097577 restraints weight = 21852.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8310  Z= 0.250
  Angle     :  0.675   9.429  11244  Z= 0.349
  Chirality :  0.043   0.277   1256
  Planarity :  0.005   0.061   1474
  Dihedral  : 10.776  62.326   1186
  Min Nonbonded Distance : 1.791

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.07 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  :  8.94 %
    Favored  : 88.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.26), residues: 1016
  helix:  0.94 (0.20), residues: 604
  sheet:  0.04 (0.44), residues: 122
  loop : -0.02 (0.40), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 302 
 HIS   0.006   0.001   HIS B 164 
 PHE   0.013   0.002   PHE A 319 
 TYR   0.037   0.003   TYR B 201 
 ARG   0.006   0.001   ARG B 738 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 80
  time to evaluate  : 1.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   38 GLU cc_start: 0.9044 (tt0) cc_final: 0.8715 (tm-30)
  outliers start: 26
  outliers final: 19
  residues processed: 94
  average time/residue: 0.2145
  time to fit residues: 27.8907
Evaluate side-chains
  72 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 53
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 GLN
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain B residue  451 LEU
Chi-restraints excluded: chain B residue  461 PHE
Chi-restraints excluded: chain B residue  753 TYR
Chi-restraints excluded: chain B residue  759 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   chunk 49 optimal weight:    4.9990
   chunk 59 optimal weight:    0.3980
   chunk 95 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 94 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  16 ASN
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 380 ASN ** 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 = 0.4166 r_free = 0.4166 target = 0.121745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.092662 restraints weight = 25234.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.094746 restraints weight = 15995.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.096116 restraints weight = 12044.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.3492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8310  Z= 0.243
  Angle     :  0.678  11.349  11244  Z= 0.343
  Chirality :  0.042   0.222   1256
  Planarity :  0.004   0.048   1474
  Dihedral  :  9.277  50.616   1186
  Min Nonbonded Distance : 1.823

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  :  9.84 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.26), residues: 1016
  helix:  0.77 (0.20), residues: 608
  sheet: -0.31 (0.44), residues: 124
  loop : -0.21 (0.40), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 410 
 HIS   0.005   0.001   HIS B 164 
 PHE   0.015   0.001   PHE A 319 
 TYR   0.044   0.002   TYR B 201 
 ARG   0.004   0.000   ARG B 204 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 GLU cc_start: 0.9518 (tt0) cc_final: 0.9289 (tp30)
REVERT: A  454 LEU cc_start: 0.9504 (tp) cc_final: 0.9272 (pp)
REVERT: B   38 GLU cc_start: 0.9518 (tt0) cc_final: 0.8950 (tm-30)
  outliers start: 27
  outliers final: 15
  residues processed: 86
  average time/residue: 0.2121
  time to fit residues: 26.9463
Evaluate side-chains
  75 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  255 THR
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  753 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 0 optimal weight:    9.9990
   chunk 93 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   chunk 15 optimal weight:    7.9990
   chunk 73 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 8 optimal weight:    0.4980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A   9 GLN
A  10 ASN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   9 GLN
B  10 ASN
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.120487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.091738 restraints weight = 26247.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.094048 restraints weight = 15937.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.095593 restraints weight = 11601.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.4095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8310  Z= 0.256
  Angle     :  0.687  10.752  11244  Z= 0.342
  Chirality :  0.043   0.265   1256
  Planarity :  0.005   0.056   1474
  Dihedral  :  7.246  43.458   1186
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 11.09 %
    Favored  : 85.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.26), residues: 1016
  helix:  0.90 (0.21), residues: 590
  sheet: -0.64 (0.44), residues: 122
  loop : -0.26 (0.38), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 410 
 HIS   0.001   0.000   HIS B 164 
 PHE   0.015   0.002   PHE B 319 
 TYR   0.037   0.002   TYR A 201 
 ARG   0.003   0.001   ARG B 741 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 68
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 GLU cc_start: 0.9560 (tt0) cc_final: 0.9311 (tp30)
REVERT: A  197 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7802 (tm-30)
REVERT: B   38 GLU cc_start: 0.9559 (tt0) cc_final: 0.8895 (tm-30)
REVERT: B  115 LEU cc_start: 0.9106 (mm) cc_final: 0.8836 (mm)
REVERT: B  197 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7522 (tm-30)
  outliers start: 27
  outliers final: 22
  residues processed: 89
  average time/residue: 0.1867
  time to fit residues: 24.1930
Evaluate side-chains
  88 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 CYS
Chi-restraints excluded: chain A residue    9 GLN
Chi-restraints excluded: chain A residue   65 ILE
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain B residue    9 GLN
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  753 TYR
Chi-restraints excluded: chain B residue  759 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 82 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 57 optimal weight:    0.3980
   chunk 46 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 HIS
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 380 ASN ** 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 = 0.4154 r_free = 0.4154 target = 0.120511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.097836 restraints weight = 25483.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.097750 restraints weight = 22992.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.098173 restraints weight = 22526.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.4339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8310  Z= 0.217
  Angle     :  0.693  15.805  11244  Z= 0.331
  Chirality :  0.043   0.344   1256
  Planarity :  0.004   0.045   1474
  Dihedral  :  6.163  39.993   1186
  Min Nonbonded Distance : 1.821

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 12.10 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.26), residues: 1016
  helix:  0.95 (0.21), residues: 598
  sheet: -0.54 (0.45), residues: 122
  loop : -0.33 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 410 
 HIS   0.002   0.000   HIS B 164 
 PHE   0.015   0.001   PHE B 319 
 TYR   0.035   0.002   TYR B 201 
 ARG   0.004   0.000   ARG B  12 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 MET cc_start: 0.4641 (mtt) cc_final: 0.4438 (mtm)
REVERT: A  197 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7895 (tm-30)
REVERT: B   38 GLU cc_start: 0.8853 (tt0) cc_final: 0.8510 (tm-30)
REVERT: B  115 LEU cc_start: 0.8846 (mm) cc_final: 0.8595 (mm)
  outliers start: 21
  outliers final: 16
  residues processed: 83
  average time/residue: 0.1860
  time to fit residues: 22.3631
Evaluate side-chains
  78 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain B residue   65 ILE
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  408 SER
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  753 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 51 optimal weight:    9.9990
   chunk 88 optimal weight:    0.1980
   chunk 99 optimal weight:    0.4980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 111 GLN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 772 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.121124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.097898 restraints weight = 25395.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.097293 restraints weight = 22135.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.097820 restraints weight = 22202.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.4587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8310  Z= 0.188
  Angle     :  0.678  12.678  11244  Z= 0.326
  Chirality :  0.044   0.342   1256
  Planarity :  0.004   0.044   1474
  Dihedral  :  5.698  36.794   1186
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.46 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.26), residues: 1016
  helix:  1.02 (0.21), residues: 598
  sheet: -0.61 (0.45), residues: 122
  loop : -0.36 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 410 
 HIS   0.001   0.000   HIS B 164 
 PHE   0.012   0.001   PHE A 319 
 TYR   0.038   0.002   TYR B 201 
 ARG   0.004   0.000   ARG B  12 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7900 (tm-30)
REVERT: A  201 TYR cc_start: 0.5972 (p90) cc_final: 0.5690 (p90)
REVERT: A  462 TYR cc_start: 0.8060 (t80) cc_final: 0.7775 (t80)
REVERT: B   38 GLU cc_start: 0.8985 (tt0) cc_final: 0.8732 (tp30)
REVERT: B  115 LEU cc_start: 0.8936 (mm) cc_final: 0.8675 (mm)
REVERT: B  440 TYR cc_start: 0.6942 (t80) cc_final: 0.6685 (t80)
REVERT: B  749 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8218 (tttt)
  outliers start: 16
  outliers final: 14
  residues processed: 76
  average time/residue: 0.2241
  time to fit residues: 24.2967
Evaluate side-chains
  76 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  749 LYS
Chi-restraints excluded: chain B residue  753 TYR
Chi-restraints excluded: chain B residue  759 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 99 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0020
   chunk 63 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 41 optimal weight:    0.4980
   chunk 54 optimal weight:    8.9990
   chunk 13 optimal weight:    0.7980
   chunk 87 optimal weight:    0.0170
   chunk 96 optimal weight:    0.7980
   overall best weight:    0.3626

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  92 ASN
** B 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 452 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.121088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.097945 restraints weight = 24898.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.097339 restraints weight = 21664.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.097903 restraints weight = 21190.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.4796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8310  Z= 0.159
  Angle     :  0.680  13.229  11244  Z= 0.321
  Chirality :  0.044   0.321   1256
  Planarity :  0.004   0.036   1474
  Dihedral  :  5.443  36.839   1186
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.35 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.62 (0.26), residues: 1016
  helix:  1.03 (0.21), residues: 602
  sheet: -0.53 (0.46), residues: 122
  loop : -0.26 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 410 
 HIS   0.001   0.000   HIS A 164 
 PHE   0.009   0.001   PHE A 319 
 TYR   0.039   0.002   TYR B 201 
 ARG   0.004   0.000   ARG B  12 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7603 (tm-30)
REVERT: A  201 TYR cc_start: 0.6215 (p90) cc_final: 0.5900 (p90)
REVERT: A  462 TYR cc_start: 0.7891 (t80) cc_final: 0.7673 (t80)
REVERT: B  115 LEU cc_start: 0.8880 (mm) cc_final: 0.8633 (mm)
  outliers start: 21
  outliers final: 17
  residues processed: 82
  average time/residue: 0.2375
  time to fit residues: 27.4138
Evaluate side-chains
  80 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 1.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  447 LEU
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  753 TYR
Chi-restraints excluded: chain B residue  759 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 99 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 37 optimal weight:    0.1980
   chunk 34 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0980
   chunk 55 optimal weight:    2.9990
   chunk 88 optimal weight:    0.4980
   chunk 21 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 63 optimal weight:    0.0470
   overall best weight:    0.3078

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

Flipped N/Q/H residues before XYZ refinement:
A  80 HIS
A 276 GLN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 HIS
** B 380 ASN ** 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 = 0.4164 r_free = 0.4164 target = 0.121078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.097416 restraints weight = 24607.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.097354 restraints weight = 19761.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.097996 restraints weight = 19841.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.5021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8310  Z= 0.155
  Angle     :  0.662  12.442  11244  Z= 0.320
  Chirality :  0.044   0.350   1256
  Planarity :  0.003   0.033   1474
  Dihedral  :  5.317  39.131   1186
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 14.82 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.26), residues: 1016
  helix:  1.09 (0.21), residues: 602
  sheet: -0.44 (0.47), residues: 122
  loop : -0.28 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 410 
 HIS   0.001   0.000   HIS B 164 
 PHE   0.007   0.001   PHE A 292 
 TYR   0.033   0.002   TYR B 201 
 ARG   0.004   0.000   ARG A 390 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 1.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7474 (tm-30)
REVERT: A  201 TYR cc_start: 0.6133 (p90) cc_final: 0.5889 (p90)
REVERT: A  462 TYR cc_start: 0.8091 (t80) cc_final: 0.7855 (t80)
REVERT: A  742 LEU cc_start: 0.7885 (mt) cc_final: 0.7622 (tp)
REVERT: B  466 TYR cc_start: 0.4874 (t80) cc_final: 0.4589 (t80)
  outliers start: 14
  outliers final: 14
  residues processed: 75
  average time/residue: 0.2748
  time to fit residues: 29.7462
Evaluate side-chains
  81 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  753 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 85 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 52 optimal weight:    5.9990
   chunk 92 optimal weight:    0.2980
   chunk 14 optimal weight:   10.0000
   chunk 50 optimal weight:    0.9990
   chunk 41 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
A 120 ASN
A 276 GLN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 452 GLN
** B 380 ASN ** 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 = 0.4145 r_free = 0.4145 target = 0.118936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.095673 restraints weight = 24940.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.095587 restraints weight = 21616.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.096009 restraints weight = 20692.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.5133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8310  Z= 0.196
  Angle     :  0.680  12.808  11244  Z= 0.329
  Chirality :  0.044   0.348   1256
  Planarity :  0.004   0.039   1474
  Dihedral  :  5.397  41.101   1186
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 14.14 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.27), residues: 1016
  helix:  1.09 (0.21), residues: 604
  sheet: -0.49 (0.47), residues: 122
  loop : -0.20 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 410 
 HIS   0.002   0.000   HIS B 164 
 PHE   0.012   0.001   PHE B 319 
 TYR   0.033   0.002   TYR B 201 
 ARG   0.004   0.000   ARG B 204 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 1.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  197 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7451 (tm-30)
REVERT: A  742 LEU cc_start: 0.7796 (mt) cc_final: 0.7542 (tp)
REVERT: B  452 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8033 (mm-40)
  outliers start: 18
  outliers final: 15
  residues processed: 76
  average time/residue: 0.2028
  time to fit residues: 22.5481
Evaluate side-chains
  76 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  753 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 28 optimal weight:    0.3980
   chunk 57 optimal weight:    0.5980
   chunk 59 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0770
   chunk 101 optimal weight:    0.6980
   chunk 88 optimal weight:    0.2980
   chunk 85 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
A 120 ASN
A 276 GLN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 452 GLN
B 111 GLN
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.119853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.096664 restraints weight = 24710.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.096336 restraints weight = 22146.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.096851 restraints weight = 21205.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.5281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8310  Z= 0.172
  Angle     :  0.698  13.412  11244  Z= 0.336
  Chirality :  0.045   0.358   1256
  Planarity :  0.003   0.036   1474
  Dihedral  :  5.293  42.154   1186
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 15.05 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.73 (0.27), residues: 1016
  helix:  1.11 (0.21), residues: 602
  sheet: -0.52 (0.48), residues: 122
  loop : -0.17 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 410 
 HIS   0.002   0.000   HIS B 164 
 PHE   0.009   0.001   PHE B 319 
 TYR   0.037   0.002   TYR A 201 
 ARG   0.004   0.000   ARG B  12 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  742 LEU cc_start: 0.7737 (mt) cc_final: 0.7495 (tp)
REVERT: B  452 GLN cc_start: 0.8294 (mm-40) cc_final: 0.7984 (mm-40)
  outliers start: 17
  outliers final: 15
  residues processed: 72
  average time/residue: 0.1832
  time to fit residues: 19.6394
Evaluate side-chains
  78 residues out of total 884 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  380 ASN
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  753 TYR
Chi-restraints excluded: chain A residue  759 SER
Chi-restraints excluded: chain B residue  270 MET
Chi-restraints excluded: chain B residue  367 THR
Chi-restraints excluded: chain B residue  380 ASN
Chi-restraints excluded: chain B residue  391 VAL
Chi-restraints excluded: chain B residue  431 ILE
Chi-restraints excluded: chain B residue  753 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 77 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0770
   chunk 78 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0770
   chunk 82 optimal weight:    0.5980
   chunk 49 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 92 optimal weight:    0.5980
   overall best weight:    0.4096

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

Flipped N/Q/H residues before XYZ refinement:
A 276 GLN
** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 772 GLN
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.120797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.097148 restraints weight = 24830.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.096291 restraints weight = 21177.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.096969 restraints weight = 19607.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.5366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8310  Z= 0.171
  Angle     :  0.700  13.540  11244  Z= 0.335
  Chirality :  0.044   0.359   1256
  Planarity :  0.004   0.035   1474
  Dihedral  :  5.265  42.900   1186
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 14.93 %
    Favored  : 83.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.27), residues: 1016
  helix:  1.11 (0.21), residues: 604
  sheet: -0.58 (0.48), residues: 122
  loop : -0.23 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 410 
 HIS   0.003   0.000   HIS B 164 
 PHE   0.009   0.001   PHE A 319 
 TYR   0.044   0.002   TYR A 462 
 ARG   0.004   0.000   ARG A 390 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2990.81 seconds
wall clock time: 54 minutes 41.31 seconds (3281.31 seconds total)