Starting phenix.real_space_refine
on Fri Jul 25 11:40:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ztw_60475/07_2025/8ztw_60475.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ztw_60475/07_2025/8ztw_60475.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ztw_60475/07_2025/8ztw_60475.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ztw_60475/07_2025/8ztw_60475.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ztw_60475/07_2025/8ztw_60475.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ztw_60475/07_2025/8ztw_60475.cif"
  }
  resolution = 2.6
  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=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      22      5.16       5
     C    4932      2.51       5
     N    1250      2.21       5
     O    1376      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7580
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 3790
          Classifications: {'peptide': 454}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 436}
    Chain: "B"
      Number of atoms: 3790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 3790
          Classifications: {'peptide': 454}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 436}
  Time building chain proxies: 5.65, per 1000 atoms: 0.75
  Number of scatterers: 7580
  At special positions: 0
  Unit cell: (74.9233, 113.23, 69.29, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      22     16.00
     O    1376      8.00
     N    1250      7.00
     C    4932      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.98
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1688

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 7 sheets defined
      51.8% alpha, 9.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 19
      removed outlier: 3.551A  pdb=" N   ILE A  18 " --> pdb=" O   ALA A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 27
      removed outlier: 4.116A  pdb=" N   GLY A  26 " --> pdb=" O   ASN A  23 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 38
      removed outlier: 3.542A  pdb=" N   ARG A  34 " --> pdb=" O   SER A  30 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLN A  38 " --> pdb=" O   ARG A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 46
      removed outlier: 3.663A  pdb=" N   HIS A  46 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 69
    Processing helix  chain 'A' and resid 78 through 83
    Processing helix  chain 'A' and resid 91 through 108
      removed outlier: 3.814A  pdb=" N   ASN A 108 " --> pdb=" O   GLU A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 128
    Processing helix  chain 'A' and resid 135 through 152
    Processing helix  chain 'A' and resid 163 through 169
    Processing helix  chain 'A' and resid 184 through 208
    Processing helix  chain 'A' and resid 225 through 231
    Processing helix  chain 'A' and resid 235 through 250
      removed outlier: 3.593A  pdb=" N   ARG A 239 " --> pdb=" O   SER A 235 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   LEU A 244 " --> pdb=" O   GLU A 240 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   SER A 245 " --> pdb=" O   MET A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 259
      Proline residue:  A 256  - end of helix
    Processing helix  chain 'A' and resid 263 through 273
    Processing helix  chain 'A' and resid 277 through 292
    Processing helix  chain 'A' and resid 338 through 352
      removed outlier: 3.696A  pdb=" N   PHE A 342 " --> pdb=" O   PRO A 338 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   LYS A 349 " --> pdb=" O   LEU A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 397
      removed outlier: 3.722A  pdb=" N   VAL A 381 " --> pdb=" O   ASP A 377 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ALA A 394 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 418
    Processing helix  chain 'A' and resid 438 through 452
    Processing helix  chain 'B' and resid 14 through 19
    Processing helix  chain 'B' and resid 23 through 27
      removed outlier: 3.934A  pdb=" N   GLY B  26 " --> pdb=" O   ASN B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 38
      removed outlier: 3.560A  pdb=" N   ARG B  34 " --> pdb=" O   SER B  30 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLN B  38 " --> pdb=" O   ARG B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 46
      removed outlier: 3.619A  pdb=" N   GLY B  45 " --> pdb=" O   ILE B  42 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   HIS B  46 " --> pdb=" O   LEU B  43 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 42 through 46'
    Processing helix  chain 'B' and resid 57 through 69
    Processing helix  chain 'B' and resid 78 through 83
    Processing helix  chain 'B' and resid 91 through 108
      removed outlier: 3.814A  pdb=" N   ASN B 108 " --> pdb=" O   GLU B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 128
    Processing helix  chain 'B' and resid 135 through 152
    Processing helix  chain 'B' and resid 163 through 169
    Processing helix  chain 'B' and resid 184 through 208
    Processing helix  chain 'B' and resid 225 through 231
    Processing helix  chain 'B' and resid 235 through 250
      removed outlier: 3.625A  pdb=" N   ARG B 239 " --> pdb=" O   SER B 235 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   LEU B 244 " --> pdb=" O   GLU B 240 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   SER B 245 " --> pdb=" O   MET B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 259
      removed outlier: 3.684A  pdb=" N   LEU B 254 " --> pdb=" O   ASN B 250 " (cutoff:3.500A)
      Proline residue:  B 256  - end of helix
    Processing helix  chain 'B' and resid 263 through 273
    Processing helix  chain 'B' and resid 277 through 292
    Processing helix  chain 'B' and resid 338 through 352
      removed outlier: 3.812A  pdb=" N   PHE B 342 " --> pdb=" O   PRO B 338 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   LYS B 349 " --> pdb=" O   LEU B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 397
      removed outlier: 3.719A  pdb=" N   VAL B 381 " --> pdb=" O   ASP B 377 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ALA B 391 " --> pdb=" O   HIS B 387 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ALA B 394 " --> pdb=" O   ALA B 390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 418
    Processing helix  chain 'B' and resid 438 through 452
    Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12
      removed outlier: 5.984A  pdb=" N   ALA A  11 " --> pdb=" O   ARG A  74 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   TYR A  73 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   THR A 115 " --> pdb=" O   TYR A  73 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   PHE A  75 " --> pdb=" O   THR A 115 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   ILE A 159 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   VAL A 114 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 7.316A  pdb=" N   PHE A 161 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   THR A 217 " --> pdb=" O   THR A 160 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   ASN A 162 " --> pdb=" O   THR A 217 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   PHE A 297 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   LEU A 298 " --> pdb=" O   TYR A 358 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   ILE A 357 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   GLY A 403 " --> pdb=" O   ILE A 357 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   GLY A  10 " --> pdb=" O   VAL A 406 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224
      removed outlier: 3.814A  pdb=" N   TYR A 224 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 327 through 329
    Processing sheet with id=AA4, first strand: chain 'A' and resid 426 through 428
    Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12
      removed outlier: 5.956A  pdb=" N   ALA B  11 " --> pdb=" O   ARG B  74 " (cutoff:3.500A)
      removed outlier: 8.059A  pdb=" N   SER B  76 " --> pdb=" O   ALA B  11 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   TYR B  73 " --> pdb=" O   VAL B 113 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   THR B 115 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   PHE B  75 " --> pdb=" O   THR B 115 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   ILE B 159 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   VAL B 114 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   PHE B 161 " --> pdb=" O   VAL B 114 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   THR B 217 " --> pdb=" O   THR B 160 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   ASN B 162 " --> pdb=" O   THR B 217 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   PHE B 297 " --> pdb=" O   ILE B 214 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   LEU B 298 " --> pdb=" O   TYR B 358 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ILE B 357 " --> pdb=" O   LEU B 401 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   GLY B 403 " --> pdb=" O   ILE B 357 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   GLY B  10 " --> pdb=" O   VAL B 406 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 223 through 224
      removed outlier: 6.105A  pdb=" N   TYR B 224 " --> pdb=" O   ARG B 308 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LEU B 309 " --> pdb=" O   ARG B 321 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ARG B 321 " --> pdb=" O   LEU B 309 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'B' and resid 426 through 428

    305 hydrogen bonds defined for protein.
    888 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: 2.17

  Time building geometry restraints manager: 2.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2097
        1.33 -     1.45: 1532
        1.45 -     1.57: 4135
        1.57 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 7804
  Sorted by residual:
  bond pdb=" N   PHE B 318 "
       pdb=" CA  PHE B 318 "
    ideal  model  delta    sigma   weight residual
    1.463  1.448  0.015 1.22e-02 6.72e+03 1.49e+00
  bond pdb=" N   PHE A 318 "
       pdb=" CA  PHE A 318 "
    ideal  model  delta    sigma   weight residual
    1.463  1.448  0.015 1.22e-02 6.72e+03 1.44e+00
  bond pdb=" CB  GLU B 361 "
       pdb=" CG  GLU B 361 "
    ideal  model  delta    sigma   weight residual
    1.520  1.490  0.030 3.00e-02 1.11e+03 9.71e-01
  bond pdb=" CB  THR B 217 "
       pdb=" CG2 THR B 217 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.35e-01
  bond pdb=" CB  GLN B  17 "
       pdb=" CG  GLN B  17 "
    ideal  model  delta    sigma   weight residual
    1.520  1.494  0.026 3.00e-02 1.11e+03 7.40e-01
  ... (remaining 7799 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 10351
        1.70 -     3.40: 197
        3.40 -     5.10: 23
        5.10 -     6.80: 1
        6.80 -     8.50: 2
  Bond angle restraints: 10574
  Sorted by residual:
  angle pdb=" CB  MET B  65 "
        pdb=" CG  MET B  65 "
        pdb=" SD  MET B  65 "
      ideal   model   delta    sigma   weight residual
     112.70  121.20   -8.50 3.00e+00 1.11e-01 8.03e+00
  angle pdb=" CB  MET A  65 "
        pdb=" CG  MET A  65 "
        pdb=" SD  MET A  65 "
      ideal   model   delta    sigma   weight residual
     112.70  121.18   -8.48 3.00e+00 1.11e-01 7.98e+00
  angle pdb=" C   ASN B 412 "
        pdb=" CA  ASN B 412 "
        pdb=" CB  ASN B 412 "
      ideal   model   delta    sigma   weight residual
     111.91  116.42   -4.51 2.06e+00 2.36e-01 4.78e+00
  angle pdb=" C   PHE A 337 "
        pdb=" N   PRO A 338 "
        pdb=" CA  PRO A 338 "
      ideal   model   delta    sigma   weight residual
     118.97  121.13   -2.16 1.04e+00 9.25e-01 4.32e+00
  angle pdb=" N   ASN B 412 "
        pdb=" CA  ASN B 412 "
        pdb=" CB  ASN B 412 "
      ideal   model   delta    sigma   weight residual
     111.24  108.02    3.22 1.58e+00 4.01e-01 4.16e+00
  ... (remaining 10569 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.05: 4014
       15.05 -    30.10: 392
       30.10 -    45.16: 96
       45.16 -    60.21: 24
       60.21 -    75.26: 4
  Dihedral angle restraints: 4530
    sinusoidal: 1876
      harmonic: 2654
  Sorted by residual:
  dihedral pdb=" CA  ASP B 411 "
           pdb=" C   ASP B 411 "
           pdb=" N   ASN B 412 "
           pdb=" CA  ASN B 412 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.28  -20.72     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" CA  GLU A  19 "
           pdb=" C   GLU A  19 "
           pdb=" N   GLY A  20 "
           pdb=" CA  GLY A  20 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.48  -16.52     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  ASN B 412 "
           pdb=" C   ASN B 412 "
           pdb=" N   PHE B 413 "
           pdb=" CA  PHE B 413 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.62  -16.38     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 4527 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 650
       0.032 -    0.064: 271
       0.064 -    0.096: 102
       0.096 -    0.128: 40
       0.128 -    0.159: 9
  Chirality restraints: 1072
  Sorted by residual:
  chirality pdb=" CB  VAL B 281 "
            pdb=" CA  VAL B 281 "
            pdb=" CG1 VAL B 281 "
            pdb=" CG2 VAL B 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.36e-01
  chirality pdb=" CB  THR A 217 "
            pdb=" CA  THR A 217 "
            pdb=" OG1 THR A 217 "
            pdb=" CG2 THR A 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.46e-01
  chirality pdb=" CB  VAL A 281 "
            pdb=" CA  VAL A 281 "
            pdb=" CG1 VAL A 281 "
            pdb=" CG2 VAL A 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.39e-01
  ... (remaining 1069 not shown)

  Planarity restraints: 1358
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 412 "   -0.011 2.00e-02 2.50e+03   2.12e-02 4.50e+00
        pdb=" CG  ASN B 412 "    0.037 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 412 "   -0.014 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 412 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 143 "    0.010 2.00e-02 2.50e+03   1.93e-02 3.71e+00
        pdb=" C   TYR A 143 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   TYR A 143 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ALA A 144 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 143 "   -0.010 2.00e-02 2.50e+03   1.90e-02 3.61e+00
        pdb=" C   TYR B 143 "    0.033 2.00e-02 2.50e+03
        pdb=" O   TYR B 143 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ALA B 144 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1355 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 158
        2.68 -     3.24: 7567
        3.24 -     3.79: 12847
        3.79 -     4.35: 18263
        4.35 -     4.90: 28286
  Nonbonded interactions: 67121
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 302 "
            pdb=" ND2 ASN B 362 "
     model   vdw
     2.131 3.120
  nonbonded pdb=" OD1 ASP B  99 "
            pdb=" OH  TYR B 151 "
     model   vdw
     2.134 3.040
  nonbonded pdb=" OD1 ASP A  99 "
            pdb=" OH  TYR A 151 "
     model   vdw
     2.137 3.040
  nonbonded pdb=" O   TYR A 302 "
            pdb=" ND2 ASN A 362 "
     model   vdw
     2.162 3.120
  nonbonded pdb=" OH  TYR B 302 "
            pdb=" O   PHE B 337 "
     model   vdw
     2.168 3.040
  ... (remaining 67116 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: 0.03
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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.710
  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:13.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5885
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      :  0.003   0.032   7804  Z= 0.163
  Angle     :  0.588   8.502  10574  Z= 0.324
  Chirality :  0.044   0.159   1072
  Planarity :  0.005   0.044   1358
  Dihedral  : 13.088  75.261   2842
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 17.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    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: -0.52 (0.28), residues: 904
  helix:  0.23 (0.26), residues: 394
  sheet:  0.06 (0.58), residues: 76
  loop : -0.88 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 131 
 HIS   0.010   0.001   HIS B 177 
 PHE   0.015   0.002   PHE A 297 
 TYR   0.018   0.002   TYR B 366 
 ARG   0.005   0.000   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19734 (  305)
  hydrogen bonds       : angle       7.27182 (  888)
  covalent geometry    : bond        0.00349 ( 7804)
  covalent geometry    : angle       0.58849 (10574)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.882 
Fit side-chains
REVERT: B  297 PHE cc_start: 0.6704 (m-10) cc_final: 0.6310 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.9252
  time to fit residues: 88.2677
Evaluate side-chains
  67 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 68 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 70 optimal weight:    0.4980
   chunk 27 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A  17 GLN
A  37 HIS
A 108 ASN
A 250 ASN
A 324 HIS
B  17 GLN
B  37 HIS
** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4748 r_free = 0.4748 target = 0.252192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.231633 restraints weight = 8111.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.4571 rms_B_bonded: 1.88
r_work: 0.4463 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.4463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6165
moved from start:          0.1416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7804  Z= 0.209
  Angle     :  0.639   5.941  10574  Z= 0.349
  Chirality :  0.046   0.150   1072
  Planarity :  0.005   0.041   1358
  Dihedral  :  5.020  18.942   1000
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 16.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  8.35 %
    Favored  : 90.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    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 (0.27), residues: 904
  helix:  0.24 (0.24), residues: 422
  sheet: -0.27 (0.57), residues: 74
  loop : -1.15 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 347 
 HIS   0.011   0.002   HIS B 177 
 PHE   0.022   0.003   PHE A 342 
 TYR   0.020   0.002   TYR B 366 
 ARG   0.003   0.001   ARG B  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06029 (  305)
  hydrogen bonds       : angle       5.41923 (  888)
  covalent geometry    : bond        0.00461 ( 7804)
  covalent geometry    : angle       0.63854 (10574)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.856 
Fit side-chains
REVERT: A  272 GLN cc_start: 0.4585 (pt0) cc_final: 0.3180 (mm110)
REVERT: A  412 ASN cc_start: 0.6159 (p0) cc_final: 0.5767 (p0)
REVERT: B  297 PHE cc_start: 0.6663 (m-10) cc_final: 0.5925 (m-10)
  outliers start: 6
  outliers final: 0
  residues processed: 75
  average time/residue: 0.8753
  time to fit residues: 71.7158
Evaluate side-chains
  64 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 12 optimal weight:    0.0970
   chunk 47 optimal weight:    7.9990
   chunk 58 optimal weight:    0.6980
   chunk 24 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.0580

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
A 451 ASN
B 250 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4767 r_free = 0.4767 target = 0.254687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4590 r_free = 0.4590 target = 0.233936 restraints weight = 8151.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.4590 rms_B_bonded: 1.90
r_work: 0.4482 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.4482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6134
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7804  Z= 0.164
  Angle     :  0.571   6.175  10574  Z= 0.313
  Chirality :  0.043   0.138   1072
  Planarity :  0.004   0.043   1358
  Dihedral  :  4.874  18.606   1000
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 14.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 10.22 %
    Favored  : 88.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    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: -0.57 (0.27), residues: 904
  helix:  0.43 (0.24), residues: 422
  sheet: -0.41 (0.57), residues: 74
  loop : -1.20 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 347 
 HIS   0.007   0.001   HIS B 177 
 PHE   0.019   0.002   PHE B   7 
 TYR   0.020   0.002   TYR B  98 
 ARG   0.003   0.000   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05025 (  305)
  hydrogen bonds       : angle       5.19377 (  888)
  covalent geometry    : bond        0.00361 ( 7804)
  covalent geometry    : angle       0.57099 (10574)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A  272 GLN cc_start: 0.4574 (pt0) cc_final: 0.3198 (mm110)
REVERT: A  412 ASN cc_start: 0.6058 (p0) cc_final: 0.5633 (p0)
REVERT: B  264 GLN cc_start: 0.4629 (tt0) cc_final: 0.4316 (mm-40)
REVERT: B  297 PHE cc_start: 0.6635 (m-10) cc_final: 0.5850 (m-10)
REVERT: B  321 ARG cc_start: 0.4265 (ptm160) cc_final: 0.3691 (ptm160)
REVERT: B  412 ASN cc_start: 0.6124 (OUTLIER) cc_final: 0.5762 (p0)
REVERT: B  419 TYR cc_start: 0.3363 (m-10) cc_final: 0.3112 (m-80)
  outliers start: 11
  outliers final: 2
  residues processed: 79
  average time/residue: 0.8979
  time to fit residues: 77.3520
Evaluate side-chains
  70 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain B residue  241 MET
Chi-restraints excluded: chain B residue  412 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 37 optimal weight:    0.8980
   chunk 77 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
** B 301 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 = 0.4781 r_free = 0.4781 target = 0.256212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.235437 restraints weight = 8116.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.4604 rms_B_bonded: 1.89
r_work: 0.4496 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.4496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6099
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7804  Z= 0.143
  Angle     :  0.537   5.946  10574  Z= 0.294
  Chirality :  0.043   0.137   1072
  Planarity :  0.004   0.043   1358
  Dihedral  :  4.744  18.440   1000
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 11.85 %
    Favored  : 87.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    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: -0.48 (0.27), residues: 904
  helix:  0.62 (0.25), residues: 422
  sheet: -0.65 (0.55), residues: 74
  loop : -1.22 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 347 
 HIS   0.005   0.001   HIS A  54 
 PHE   0.031   0.002   PHE A   7 
 TYR   0.019   0.002   TYR A  98 
 ARG   0.003   0.000   ARG B  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04500 (  305)
  hydrogen bonds       : angle       5.02001 (  888)
  covalent geometry    : bond        0.00316 ( 7804)
  covalent geometry    : angle       0.53711 (10574)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.886 
Fit side-chains
REVERT: A  272 GLN cc_start: 0.4584 (pt0) cc_final: 0.3240 (mm110)
REVERT: A  412 ASN cc_start: 0.5991 (p0) cc_final: 0.5579 (p0)
REVERT: B   65 MET cc_start: 0.6811 (OUTLIER) cc_final: 0.5772 (mtt)
REVERT: B  264 GLN cc_start: 0.4698 (tt0) cc_final: 0.4391 (mm-40)
REVERT: B  297 PHE cc_start: 0.6642 (m-10) cc_final: 0.5817 (m-10)
REVERT: B  321 ARG cc_start: 0.4264 (ptm160) cc_final: 0.3736 (ptm160)
REVERT: B  412 ASN cc_start: 0.6012 (OUTLIER) cc_final: 0.5654 (p0)
REVERT: B  419 TYR cc_start: 0.3368 (m-10) cc_final: 0.3091 (m-80)
  outliers start: 8
  outliers final: 1
  residues processed: 80
  average time/residue: 0.9237
  time to fit residues: 80.1789
Evaluate side-chains
  73 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 70
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain B residue   65 MET
Chi-restraints excluded: chain B residue  412 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 50 optimal weight:    9.9990
   chunk 74 optimal weight:    0.8980
   chunk 41 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 88 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 20 optimal weight:    5.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
A 291 ASN
** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 354 GLN
B 451 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4753 r_free = 0.4753 target = 0.252577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4573 r_free = 0.4573 target = 0.231775 restraints weight = 8120.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.4575 rms_B_bonded: 1.88
r_work: 0.4465 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.4465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6168
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7804  Z= 0.181
  Angle     :  0.590   6.526  10574  Z= 0.322
  Chirality :  0.044   0.140   1072
  Planarity :  0.005   0.042   1358
  Dihedral  :  4.977  19.380   1000
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 14.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 14.46 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    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: 904
  helix:  0.46 (0.24), residues: 422
  sheet: -0.96 (0.55), residues: 74
  loop : -1.30 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  32 
 HIS   0.007   0.002   HIS A  54 
 PHE   0.034   0.003   PHE A   7 
 TYR   0.020   0.002   TYR A  98 
 ARG   0.003   0.000   ARG A  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04919 (  305)
  hydrogen bonds       : angle       5.12628 (  888)
  covalent geometry    : bond        0.00402 ( 7804)
  covalent geometry    : angle       0.58987 (10574)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 74
  time to evaluate  : 0.904 
Fit side-chains
REVERT: A  412 ASN cc_start: 0.6127 (OUTLIER) cc_final: 0.5658 (p0)
REVERT: B  297 PHE cc_start: 0.6825 (m-10) cc_final: 0.5850 (m-10)
REVERT: B  321 ARG cc_start: 0.4380 (ptm160) cc_final: 0.3718 (ptm160)
REVERT: B  412 ASN cc_start: 0.6154 (OUTLIER) cc_final: 0.5771 (p0)
REVERT: B  419 TYR cc_start: 0.3272 (m-10) cc_final: 0.2911 (m-80)
  outliers start: 12
  outliers final: 4
  residues processed: 79
  average time/residue: 0.8204
  time to fit residues: 71.0514
Evaluate side-chains
  73 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 67
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  412 ASN
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  357 ILE
Chi-restraints excluded: chain B residue  412 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 57 optimal weight:    0.5980
   chunk 89 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
A 291 ASN
B 291 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4763 r_free = 0.4763 target = 0.254294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.233463 restraints weight = 8120.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.4590 rms_B_bonded: 1.89
r_work: 0.4482 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.4482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6136
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7804  Z= 0.157
  Angle     :  0.563   7.043  10574  Z= 0.308
  Chirality :  0.043   0.144   1072
  Planarity :  0.004   0.042   1358
  Dihedral  :  4.873  21.651   1000
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 14.96 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    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: 904
  helix:  0.53 (0.24), residues: 422
  sheet: -1.02 (0.56), residues: 74
  loop : -1.28 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  32 
 HIS   0.006   0.001   HIS A  54 
 PHE   0.029   0.002   PHE A   7 
 TYR   0.020   0.002   TYR A  98 
 ARG   0.003   0.000   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04539 (  305)
  hydrogen bonds       : angle       5.05986 (  888)
  covalent geometry    : bond        0.00348 ( 7804)
  covalent geometry    : angle       0.56346 (10574)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.854 
Fit side-chains
REVERT: A  412 ASN cc_start: 0.6072 (OUTLIER) cc_final: 0.5612 (p0)
REVERT: B  297 PHE cc_start: 0.6747 (m-10) cc_final: 0.5750 (m-10)
REVERT: B  321 ARG cc_start: 0.4364 (ptm160) cc_final: 0.3727 (ptm160)
REVERT: B  412 ASN cc_start: 0.6012 (OUTLIER) cc_final: 0.5657 (p0)
REVERT: B  419 TYR cc_start: 0.3324 (m-10) cc_final: 0.2955 (m-80)
  outliers start: 12
  outliers final: 4
  residues processed: 75
  average time/residue: 0.8385
  time to fit residues: 69.0001
Evaluate side-chains
  74 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  412 ASN
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  357 ILE
Chi-restraints excluded: chain B residue  412 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 37 optimal weight:    0.4980
   chunk 3 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   chunk 83 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  37 HIS
A 250 ASN
A 291 ASN
B 291 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4780 r_free = 0.4780 target = 0.256327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.235477 restraints weight = 8057.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.4607 rms_B_bonded: 1.88
r_work: 0.4502 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.4502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6095
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7804  Z= 0.138
  Angle     :  0.539   6.601  10574  Z= 0.295
  Chirality :  0.043   0.163   1072
  Planarity :  0.004   0.043   1358
  Dihedral  :  4.755  24.950   1000
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 15.09 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    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: -0.51 (0.27), residues: 904
  helix:  0.65 (0.25), residues: 422
  sheet: -0.22 (0.63), residues: 68
  loop : -1.40 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  32 
 HIS   0.005   0.001   HIS A  54 
 PHE   0.032   0.002   PHE A   7 
 TYR   0.018   0.002   TYR A  98 
 ARG   0.002   0.000   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04229 (  305)
  hydrogen bonds       : angle       4.99300 (  888)
  covalent geometry    : bond        0.00303 ( 7804)
  covalent geometry    : angle       0.53857 (10574)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.812 
Fit side-chains
REVERT: A  103 ASN cc_start: 0.5558 (m110) cc_final: 0.5219 (t0)
REVERT: A  412 ASN cc_start: 0.5988 (OUTLIER) cc_final: 0.5547 (p0)
REVERT: B  103 ASN cc_start: 0.5579 (m110) cc_final: 0.5206 (t0)
REVERT: B  264 GLN cc_start: 0.4726 (tt0) cc_final: 0.4434 (mm-40)
REVERT: B  297 PHE cc_start: 0.6682 (m-10) cc_final: 0.5641 (m-10)
REVERT: B  321 ARG cc_start: 0.4379 (ptm160) cc_final: 0.4056 (ptm160)
REVERT: B  412 ASN cc_start: 0.5953 (OUTLIER) cc_final: 0.5600 (p0)
REVERT: B  419 TYR cc_start: 0.3289 (m-10) cc_final: 0.2937 (m-80)
  outliers start: 14
  outliers final: 5
  residues processed: 81
  average time/residue: 0.8131
  time to fit residues: 72.4657
Evaluate side-chains
  78 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  412 ASN
Chi-restraints excluded: chain B residue  337 PHE
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  357 ILE
Chi-restraints excluded: chain B residue  412 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 73 optimal weight:    5.9990
   chunk 6 optimal weight:    0.2980
   chunk 4 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
A 291 ASN
B 250 ASN
B 291 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4795 r_free = 0.4795 target = 0.258435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.237367 restraints weight = 8178.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.4615 rms_B_bonded: 1.90
r_work: 0.4508 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.4508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6072
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7804  Z= 0.129
  Angle     :  0.523   6.490  10574  Z= 0.287
  Chirality :  0.042   0.143   1072
  Planarity :  0.004   0.043   1358
  Dihedral  :  4.666  28.430   1000
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.71 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    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: -0.40 (0.27), residues: 904
  helix:  0.76 (0.25), residues: 422
  sheet: -0.23 (0.63), residues: 68
  loop : -1.34 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  32 
 HIS   0.005   0.001   HIS A  54 
 PHE   0.035   0.002   PHE A   7 
 TYR   0.017   0.002   TYR A  98 
 ARG   0.002   0.000   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04025 (  305)
  hydrogen bonds       : angle       4.92036 (  888)
  covalent geometry    : bond        0.00284 ( 7804)
  covalent geometry    : angle       0.52317 (10574)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 ASN cc_start: 0.5587 (m110) cc_final: 0.5233 (t0)
REVERT: A  412 ASN cc_start: 0.5930 (OUTLIER) cc_final: 0.5506 (p0)
REVERT: B   38 GLN cc_start: 0.6071 (mp10) cc_final: 0.5559 (mt0)
REVERT: B  103 ASN cc_start: 0.5664 (m110) cc_final: 0.5261 (t0)
REVERT: B  264 GLN cc_start: 0.4712 (tt0) cc_final: 0.4416 (mm-40)
REVERT: B  297 PHE cc_start: 0.6614 (m-10) cc_final: 0.5494 (m-10)
REVERT: B  321 ARG cc_start: 0.4392 (ptm160) cc_final: 0.4061 (ptm160)
REVERT: B  412 ASN cc_start: 0.5903 (OUTLIER) cc_final: 0.5572 (p0)
REVERT: B  419 TYR cc_start: 0.3289 (m-10) cc_final: 0.2966 (m-80)
  outliers start: 12
  outliers final: 4
  residues processed: 82
  average time/residue: 0.8485
  time to fit residues: 76.2286
Evaluate side-chains
  80 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  342 PHE
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  412 ASN
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  412 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 68 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0980
   chunk 46 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 76 optimal weight:    0.0670
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
A 291 ASN
B 250 ASN
B 291 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4807 r_free = 0.4807 target = 0.259841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.238659 restraints weight = 8253.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.4650 rms_B_bonded: 1.92
r_work: 0.4544 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.4544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6043
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7804  Z= 0.120
  Angle     :  0.508   6.341  10574  Z= 0.279
  Chirality :  0.042   0.141   1072
  Planarity :  0.004   0.045   1358
  Dihedral  :  4.590  29.858   1000
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 16.58 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    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: -0.29 (0.27), residues: 904
  helix:  0.88 (0.25), residues: 422
  sheet: -0.25 (0.63), residues: 68
  loop : -1.32 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  32 
 HIS   0.006   0.001   HIS B 172 
 PHE   0.034   0.002   PHE A   7 
 TYR   0.017   0.001   TYR A  98 
 ARG   0.002   0.000   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03856 (  305)
  hydrogen bonds       : angle       4.87495 (  888)
  covalent geometry    : bond        0.00266 ( 7804)
  covalent geometry    : angle       0.50812 (10574)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.867 
Fit side-chains
REVERT: A  103 ASN cc_start: 0.5482 (m110) cc_final: 0.5171 (t0)
REVERT: A  412 ASN cc_start: 0.5837 (OUTLIER) cc_final: 0.5429 (p0)
REVERT: B   38 GLN cc_start: 0.6133 (mp10) cc_final: 0.5602 (mt0)
REVERT: B  103 ASN cc_start: 0.5619 (m110) cc_final: 0.5239 (t0)
REVERT: B  264 GLN cc_start: 0.4754 (tt0) cc_final: 0.4443 (mm-40)
REVERT: B  297 PHE cc_start: 0.6543 (m-10) cc_final: 0.5438 (m-10)
REVERT: B  321 ARG cc_start: 0.4365 (ptm160) cc_final: 0.4042 (ptm160)
REVERT: B  412 ASN cc_start: 0.5856 (OUTLIER) cc_final: 0.5511 (p0)
REVERT: B  419 TYR cc_start: 0.3289 (m-10) cc_final: 0.2967 (m-80)
  outliers start: 10
  outliers final: 3
  residues processed: 78
  average time/residue: 0.8980
  time to fit residues: 76.9397
Evaluate side-chains
  78 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  412 ASN
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  357 ILE
Chi-restraints excluded: chain B residue  412 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 87 optimal weight:    0.4980
   chunk 30 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
B 250 ASN
B 291 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4772 r_free = 0.4772 target = 0.255439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.234253 restraints weight = 8221.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.4596 rms_B_bonded: 1.91
r_work: 0.4486 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.4486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6131
moved from start:          0.2390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7804  Z= 0.162
  Angle     :  0.562   6.437  10574  Z= 0.308
  Chirality :  0.044   0.146   1072
  Planarity :  0.004   0.042   1358
  Dihedral  :  4.869  33.011   1000
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 16.83 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    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: -0.47 (0.27), residues: 904
  helix:  0.69 (0.25), residues: 422
  sheet: -0.28 (0.63), residues: 68
  loop : -1.38 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  32 
 HIS   0.006   0.001   HIS A  54 
 PHE   0.041   0.003   PHE A   7 
 TYR   0.020   0.002   TYR A  98 
 ARG   0.003   0.000   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04461 (  305)
  hydrogen bonds       : angle       5.01626 (  888)
  covalent geometry    : bond        0.00365 ( 7804)
  covalent geometry    : angle       0.56196 (10574)

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

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

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1808 Ramachandran restraints generated.
    904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.799 
Fit side-chains
REVERT: A  103 ASN cc_start: 0.5710 (m110) cc_final: 0.5325 (t0)
REVERT: A  412 ASN cc_start: 0.6077 (OUTLIER) cc_final: 0.5613 (p0)
REVERT: B  264 GLN cc_start: 0.4678 (tt0) cc_final: 0.4350 (mm-40)
REVERT: B  297 PHE cc_start: 0.6759 (m-10) cc_final: 0.5615 (m-10)
REVERT: B  321 ARG cc_start: 0.4394 (ptm160) cc_final: 0.4079 (ptm160)
REVERT: B  412 ASN cc_start: 0.6094 (OUTLIER) cc_final: 0.5734 (p0)
REVERT: B  419 TYR cc_start: 0.3348 (m-10) cc_final: 0.2947 (m-80)
  outliers start: 9
  outliers final: 3
  residues processed: 74
  average time/residue: 0.8542
  time to fit residues: 69.0352
Evaluate side-chains
  72 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  412 ASN
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  357 ILE
Chi-restraints excluded: chain B residue  412 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 87 optimal weight:    0.2980
   chunk 37 optimal weight:    0.5980
   chunk 67 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 78 optimal weight:    0.0170
   chunk 68 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 80 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.5018

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
B  38 GLN
B 250 ASN
B 291 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4809 r_free = 0.4809 target = 0.260383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.239431 restraints weight = 8085.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.4656 rms_B_bonded: 1.90
r_work: 0.4549 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.4549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6023
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7804  Z= 0.117
  Angle     :  0.498   6.215  10574  Z= 0.274
  Chirality :  0.042   0.191   1072
  Planarity :  0.004   0.043   1358
  Dihedral  :  4.573  34.140   1000
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 17.33 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    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: -0.38 (0.27), residues: 904
  helix:  0.81 (0.25), residues: 428
  sheet: -0.32 (0.62), residues: 68
  loop : -1.40 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  32 
 HIS   0.004   0.001   HIS B 172 
 PHE   0.031   0.002   PHE A   7 
 TYR   0.017   0.001   TYR A  98 
 ARG   0.002   0.000   ARG A 305 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03778 (  305)
  hydrogen bonds       : angle       4.84875 (  888)
  covalent geometry    : bond        0.00257 ( 7804)
  covalent geometry    : angle       0.49846 (10574)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4685.63 seconds
wall clock time: 80 minutes 58.21 seconds (4858.21 seconds total)