Starting phenix.real_space_refine
on Wed Sep 17 09:10:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ztw_60475/09_2025/8ztw_60475.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ztw_60475/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ztw_60475/09_2025/8ztw_60475.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ztw_60475/09_2025/8ztw_60475.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ztw_60475/09_2025/8ztw_60475.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ztw_60475/09_2025/8ztw_60475.map"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.020
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.22, per 1000 atoms: 0.29
  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: 0.63
  Conformation dependent library (CDL) restraints added in 469.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.28
  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: 1.33

  Time building geometry restraints manager: 0.87 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: 0.02
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:             4.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.780
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.720
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.52 (0.28), 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
 ARG   0.005   0.000   ARG A 305 
 TYR   0.018   0.002   TYR B 366 
 PHE   0.015   0.002   PHE A 297 
 TRP   0.020   0.002   TRP A 131 
 HIS   0.010   0.001   HIS B 177 

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

*********************** 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  : 0.300 
Fit side-chains
REVERT: B  297 PHE cc_start: 0.6704 (m-10) cc_final: 0.6322 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.4567
  time to fit residues: 43.2972
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  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.4584

-------------------------------------------------------------------------------
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 = 0.4751 r_free = 0.4751 target = 0.252414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.231702 restraints weight = 8199.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.4572 rms_B_bonded: 1.90
r_work: 0.4466 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.4466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6163
moved from start:          0.1438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7804  Z= 0.206
  Angle     :  0.635   6.023  10574  Z= 0.347
  Chirality :  0.046   0.150   1072
  Planarity :  0.005   0.042   1358
  Dihedral  :  5.019  19.027   1000
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 16.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  8.73 %
    Favored  : 90.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.65 (0.27), residues: 904
  helix:  0.27 (0.24), residues: 422
  sheet: -0.27 (0.57), residues: 74
  loop : -1.16 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  81 
 TYR   0.020   0.002   TYR B 366 
 PHE   0.033   0.003   PHE B   7 
 TRP   0.021   0.002   TRP A 347 
 HIS   0.012   0.002   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 7804)
  covalent geometry    : angle       0.63513 (10574)
  hydrogen bonds       : bond        0.06037 (  305)
  hydrogen bonds       : angle       5.43139 (  888)

*********************** 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
  79 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  272 GLN cc_start: 0.4610 (pt0) cc_final: 0.3211 (mm110)
REVERT: A  412 ASN cc_start: 0.6138 (p0) cc_final: 0.5751 (p0)
REVERT: B  297 PHE cc_start: 0.6658 (m-10) cc_final: 0.5912 (m-10)
  outliers start: 6
  outliers final: 0
  residues processed: 74
  average time/residue: 0.4252
  time to fit residues: 34.3129
Evaluate side-chains
  66 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 58 optimal weight:    0.4980
   chunk 19 optimal weight:    0.5980
   chunk 68 optimal weight:    0.0470
   chunk 35 optimal weight:    8.9990
   chunk 6 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.0282

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4771 r_free = 0.4771 target = 0.255015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.234271 restraints weight = 8107.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.4591 rms_B_bonded: 1.89
r_work: 0.4483 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.4483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6129
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7804  Z= 0.162
  Angle     :  0.566   6.166  10574  Z= 0.311
  Chirality :  0.043   0.138   1072
  Planarity :  0.004   0.043   1358
  Dihedral  :  4.856  18.561   1000
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 10.22 %
    Favored  : 88.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.27), residues: 904
  helix:  0.44 (0.24), residues: 422
  sheet: -0.43 (0.56), residues: 74
  loop : -1.19 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 321 
 TYR   0.020   0.002   TYR A  98 
 PHE   0.025   0.002   PHE B   7 
 TRP   0.015   0.002   TRP A 347 
 HIS   0.007   0.001   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 7804)
  covalent geometry    : angle       0.56649 (10574)
  hydrogen bonds       : bond        0.04990 (  305)
  hydrogen bonds       : angle       5.18741 (  888)

*********************** 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
  92 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.287 
Fit side-chains
REVERT: A  272 GLN cc_start: 0.4567 (pt0) cc_final: 0.3194 (mm110)
REVERT: A  412 ASN cc_start: 0.6038 (p0) cc_final: 0.5619 (p0)
REVERT: B  264 GLN cc_start: 0.4636 (tt0) cc_final: 0.4330 (mm-40)
REVERT: B  297 PHE cc_start: 0.6644 (m-10) cc_final: 0.5850 (m-10)
REVERT: B  321 ARG cc_start: 0.4252 (ptm160) cc_final: 0.3680 (ptm160)
REVERT: B  412 ASN cc_start: 0.6100 (OUTLIER) cc_final: 0.5738 (p0)
REVERT: B  419 TYR cc_start: 0.3356 (m-10) cc_final: 0.3107 (m-80)
  outliers start: 13
  outliers final: 1
  residues processed: 82
  average time/residue: 0.4448
  time to fit residues: 39.5101
Evaluate side-chains
  70 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 68
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 LEU
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 60 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 75 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9980
   chunk 55 optimal weight:    5.9990
   chunk 80 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 78 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    1.7586

-------------------------------------------------------------------------------
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
A 412 ASN
B 451 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4725 r_free = 0.4725 target = 0.249324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.228333 restraints weight = 8307.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.4544 rms_B_bonded: 1.91
r_work: 0.4432 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.4432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6237
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   7804  Z= 0.229
  Angle     :  0.661   7.197  10574  Z= 0.360
  Chirality :  0.046   0.143   1072
  Planarity :  0.005   0.041   1358
  Dihedral  :  5.308  22.539   1000
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 17.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 12.34 %
    Favored  : 85.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.04 (0.26), residues: 904
  helix:  0.03 (0.24), residues: 424
  sheet: -0.74 (0.56), residues: 74
  loop : -1.41 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  81 
 TYR   0.023   0.002   TYR A  98 
 PHE   0.025   0.003   PHE B   7 
 TRP   0.012   0.002   TRP A  32 
 HIS   0.008   0.002   HIS B 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 ( 7804)
  covalent geometry    : angle       0.66084 (10574)
  hydrogen bonds       : bond        0.05718 (  305)
  hydrogen bonds       : angle       5.37620 (  888)

*********************** 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
  91 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.296 
Fit side-chains
REVERT: B  297 PHE cc_start: 0.6991 (m-10) cc_final: 0.5976 (m-10)
REVERT: B  321 ARG cc_start: 0.4394 (ptm160) cc_final: 0.3707 (ptm160)
REVERT: B  412 ASN cc_start: 0.6217 (OUTLIER) cc_final: 0.5812 (p0)
REVERT: B  419 TYR cc_start: 0.3316 (m-10) cc_final: 0.2912 (m-80)
  outliers start: 15
  outliers final: 6
  residues processed: 81
  average time/residue: 0.4061
  time to fit residues: 36.0022
Evaluate side-chains
  77 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
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  211 ASP
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 46 optimal weight:    0.7980
   chunk 5 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.8982

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4763 r_free = 0.4763 target = 0.254071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.233330 restraints weight = 8209.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.4587 rms_B_bonded: 1.89
r_work: 0.4478 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.4478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6145
moved from start:          0.2082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7804  Z= 0.154
  Angle     :  0.566   6.438  10574  Z= 0.310
  Chirality :  0.043   0.142   1072
  Planarity :  0.004   0.042   1358
  Dihedral  :  4.962  20.162   1000
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 14.96 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.79 (0.27), residues: 904
  helix:  0.36 (0.24), residues: 422
  sheet: -1.02 (0.56), residues: 74
  loop : -1.34 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  81 
 TYR   0.021   0.002   TYR B  98 
 PHE   0.028   0.002   PHE B   7 
 TRP   0.010   0.002   TRP A  32 
 HIS   0.005   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7804)
  covalent geometry    : angle       0.56596 (10574)
  hydrogen bonds       : bond        0.04628 (  305)
  hydrogen bonds       : angle       5.17807 (  888)

*********************** 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
  83 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A   65 MET cc_start: 0.6556 (mmt) cc_final: 0.5511 (mmt)
REVERT: A  412 ASN cc_start: 0.5880 (OUTLIER) cc_final: 0.5523 (p0)
REVERT: B   38 GLN cc_start: 0.6462 (mm110) cc_final: 0.6210 (mp10)
REVERT: B  110 ILE cc_start: 0.7221 (mt) cc_final: 0.7020 (mt)
REVERT: B  297 PHE cc_start: 0.6761 (m-10) cc_final: 0.5693 (m-10)
REVERT: B  321 ARG cc_start: 0.4366 (ptm160) cc_final: 0.3806 (ptm160)
REVERT: B  412 ASN cc_start: 0.6037 (OUTLIER) cc_final: 0.5668 (p0)
REVERT: B  419 TYR cc_start: 0.3318 (m-10) cc_final: 0.2936 (m-80)
  outliers start: 9
  outliers final: 2
  residues processed: 75
  average time/residue: 0.4182
  time to fit residues: 34.1234
Evaluate side-chains
  74 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  344 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 2 optimal weight:    0.4980
   chunk 36 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 56 optimal weight:    0.0170
   overall best weight:    1.3024

-------------------------------------------------------------------------------
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 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 291 ASN
** B 301 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 = 0.4742 r_free = 0.4742 target = 0.251772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.230961 restraints weight = 8231.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.4565 rms_B_bonded: 1.89
r_work: 0.4458 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.4458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6192
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7804  Z= 0.185
  Angle     :  0.599   6.576  10574  Z= 0.327
  Chirality :  0.044   0.144   1072
  Planarity :  0.005   0.043   1358
  Dihedral  :  5.092  20.294   1000
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.34 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.27), residues: 904
  helix:  0.24 (0.24), residues: 422
  sheet: -1.10 (0.56), residues: 74
  loop : -1.39 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 305 
 TYR   0.021   0.002   TYR A  98 
 PHE   0.028   0.003   PHE B   7 
 TRP   0.011   0.002   TRP A  32 
 HIS   0.007   0.002   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 7804)
  covalent geometry    : angle       0.59945 (10574)
  hydrogen bonds       : bond        0.04970 (  305)
  hydrogen bonds       : angle       5.25223 (  888)

*********************** 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
  90 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.289 
Fit side-chains
REVERT: B   38 GLN cc_start: 0.6474 (mm110) cc_final: 0.6227 (mp10)
REVERT: B  321 ARG cc_start: 0.4445 (ptm160) cc_final: 0.4097 (ptm160)
REVERT: B  412 ASN cc_start: 0.6164 (OUTLIER) cc_final: 0.5781 (p0)
REVERT: B  419 TYR cc_start: 0.3405 (m-10) cc_final: 0.2961 (m-80)
  outliers start: 17
  outliers final: 4
  residues processed: 80
  average time/residue: 0.3988
  time to fit residues: 34.8759
Evaluate side-chains
  73 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain B residue  337 PHE
Chi-restraints excluded: chain B residue  344 LEU
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 42 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0870
   chunk 86 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 74 optimal weight:    0.6980
   chunk 31 optimal weight:    0.3980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 250 ASN
B 291 ASN
** B 301 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 = 0.4789 r_free = 0.4789 target = 0.257707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.237066 restraints weight = 8160.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.4617 rms_B_bonded: 1.89
r_work: 0.4513 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.4513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6060
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7804  Z= 0.124
  Angle     :  0.523   6.917  10574  Z= 0.288
  Chirality :  0.042   0.157   1072
  Planarity :  0.004   0.045   1358
  Dihedral  :  4.709  24.458   1000
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 16.46 %
    Favored  : 82.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.27), residues: 904
  helix:  0.63 (0.25), residues: 422
  sheet: -0.15 (0.63), residues: 68
  loop : -1.42 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 305 
 TYR   0.017   0.001   TYR A  98 
 PHE   0.029   0.002   PHE A   7 
 TRP   0.009   0.001   TRP A  32 
 HIS   0.004   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 7804)
  covalent geometry    : angle       0.52332 (10574)
  hydrogen bonds       : bond        0.04026 (  305)
  hydrogen bonds       : angle       5.01209 (  888)

*********************** 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
  86 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  103 ASN cc_start: 0.5470 (m110) cc_final: 0.5163 (t0)
REVERT: A  412 ASN cc_start: 0.5797 (p0) cc_final: 0.5516 (p0)
REVERT: B  103 ASN cc_start: 0.5576 (m110) cc_final: 0.5166 (t0)
REVERT: B  264 GLN cc_start: 0.4665 (tt0) cc_final: 0.4370 (mm-40)
REVERT: B  321 ARG cc_start: 0.4360 (ptm160) cc_final: 0.4039 (ptm160)
REVERT: B  412 ASN cc_start: 0.5864 (OUTLIER) cc_final: 0.5528 (p0)
REVERT: B  419 TYR cc_start: 0.3317 (m-10) cc_final: 0.2991 (m-80)
  outliers start: 9
  outliers final: 3
  residues processed: 79
  average time/residue: 0.3875
  time to fit residues: 33.5590
Evaluate side-chains
  74 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  357 ILE
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 50 optimal weight:    9.9990
   chunk 11 optimal weight:    0.2980
   chunk 16 optimal weight:    0.8980
   chunk 66 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 69 optimal weight:    6.9990
   chunk 80 optimal weight:    0.5980
   chunk 26 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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
** B 301 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 = 0.4803 r_free = 0.4803 target = 0.259485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4630 r_free = 0.4630 target = 0.238807 restraints weight = 8240.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.4617 rms_B_bonded: 1.90
r_work: 0.4513 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.4513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6066
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      :  0.003   0.042   7804  Z= 0.127
  Angle     :  0.523   6.158  10574  Z= 0.287
  Chirality :  0.042   0.140   1072
  Planarity :  0.004   0.045   1358
  Dihedral  :  4.649  27.465   1000
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 16.21 %
    Favored  : 82.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.27), residues: 904
  helix:  0.76 (0.25), residues: 422
  sheet: -0.22 (0.63), residues: 68
  loop : -1.37 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 305 
 TYR   0.018   0.001   TYR A  98 
 PHE   0.037   0.002   PHE A   7 
 TRP   0.009   0.001   TRP A  32 
 HIS   0.004   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7804)
  covalent geometry    : angle       0.52291 (10574)
  hydrogen bonds       : bond        0.03978 (  305)
  hydrogen bonds       : angle       4.95058 (  888)

*********************** 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
  89 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A  103 ASN cc_start: 0.5497 (m110) cc_final: 0.5173 (t0)
REVERT: A  412 ASN cc_start: 0.5783 (p0) cc_final: 0.5511 (p0)
REVERT: B   38 GLN cc_start: 0.6053 (mp10) cc_final: 0.5534 (mt0)
REVERT: B  103 ASN cc_start: 0.5648 (m110) cc_final: 0.5248 (t0)
REVERT: B  264 GLN cc_start: 0.4694 (tt0) cc_final: 0.4404 (mm-40)
REVERT: B  321 ARG cc_start: 0.4382 (ptm160) cc_final: 0.4049 (ptm160)
REVERT: B  412 ASN cc_start: 0.5891 (OUTLIER) cc_final: 0.5561 (p0)
REVERT: B  419 TYR cc_start: 0.3297 (m-10) cc_final: 0.2962 (m-80)
  outliers start: 11
  outliers final: 5
  residues processed: 82
  average time/residue: 0.4004
  time to fit residues: 35.9190
Evaluate side-chains
  79 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  344 LEU
Chi-restraints excluded: chain A residue  357 ILE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 8 optimal weight:    0.4980
   chunk 35 optimal weight:    0.8980
   chunk 64 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0070
   chunk 21 optimal weight:    0.0040
   chunk 43 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 78 optimal weight:    0.2980
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.2810

-------------------------------------------------------------------------------
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
** B 301 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 = 0.4848 r_free = 0.4848 target = 0.264499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4683 r_free = 0.4683 target = 0.244188 restraints weight = 8221.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.4687 rms_B_bonded: 1.88
r_work: 0.4584 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.4584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5931
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7804  Z= 0.101
  Angle     :  0.481   5.957  10574  Z= 0.263
  Chirality :  0.041   0.142   1072
  Planarity :  0.004   0.047   1358
  Dihedral  :  4.334  30.324   1000
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 16.71 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.18 (0.27), residues: 904
  helix:  1.02 (0.25), residues: 428
  sheet: -0.12 (0.64), residues: 68
  loop : -1.37 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 305 
 TYR   0.013   0.001   TYR A  98 
 PHE   0.029   0.001   PHE A   7 
 TRP   0.012   0.001   TRP A 407 
 HIS   0.008   0.001   HIS B 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 7804)
  covalent geometry    : angle       0.48108 (10574)
  hydrogen bonds       : bond        0.03392 (  305)
  hydrogen bonds       : angle       4.75656 (  888)

*********************** 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
  92 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.318 
Fit side-chains
REVERT: A  412 ASN cc_start: 0.5347 (p0) cc_final: 0.5097 (p0)
REVERT: B   38 GLN cc_start: 0.5867 (mp10) cc_final: 0.5522 (mt0)
REVERT: B  103 ASN cc_start: 0.5469 (m110) cc_final: 0.5180 (t0)
REVERT: B  264 GLN cc_start: 0.4746 (tt0) cc_final: 0.4466 (mm-40)
REVERT: B  321 ARG cc_start: 0.4293 (ptm160) cc_final: 0.3956 (ptm160)
REVERT: B  412 ASN cc_start: 0.5541 (OUTLIER) cc_final: 0.5229 (p0)
  outliers start: 9
  outliers final: 1
  residues processed: 85
  average time/residue: 0.4000
  time to fit residues: 37.1189
Evaluate side-chains
  76 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A 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 62 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 5 optimal weight:    9.9990
   chunk 30 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 1 optimal weight:    4.9990
   overall best weight:    1.0982

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.255158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.234185 restraints weight = 8147.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.4591 rms_B_bonded: 1.90
r_work: 0.4483 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.4483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6130
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      :  0.004   0.041   7804  Z= 0.168
  Angle     :  0.577   5.999  10574  Z= 0.316
  Chirality :  0.044   0.141   1072
  Planarity :  0.004   0.044   1358
  Dihedral  :  4.821  33.739   1000
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 18.20 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.27), residues: 904
  helix:  0.73 (0.25), residues: 434
  sheet: -1.71 (0.58), residues: 74
  loop : -1.35 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 305 
 TYR   0.019   0.002   TYR B  98 
 PHE   0.040   0.003   PHE A   7 
 TRP   0.011   0.002   TRP A  32 
 HIS   0.006   0.002   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 7804)
  covalent geometry    : angle       0.57720 (10574)
  hydrogen bonds       : bond        0.04463 (  305)
  hydrogen bonds       : angle       4.96718 (  888)

********************** 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
  74 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A  412 ASN cc_start: 0.5961 (OUTLIER) cc_final: 0.5656 (p0)
REVERT: B  264 GLN cc_start: 0.4674 (tt0) cc_final: 0.4371 (mm-40)
REVERT: B  321 ARG cc_start: 0.4399 (ptm160) cc_final: 0.4097 (ptm160)
REVERT: B  412 ASN cc_start: 0.6007 (OUTLIER) cc_final: 0.5674 (p0)
  outliers start: 6
  outliers final: 2
  residues processed: 71
  average time/residue: 0.4239
  time to fit residues: 32.7879
Evaluate side-chains
  71 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  412 ASN
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 8 optimal weight:    3.9990
   chunk 27 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 79 optimal weight:    0.6980
   chunk 45 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A  92 GLN
A 250 ASN
B 250 ASN
B 291 ASN
** B 301 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 = 0.4778 r_free = 0.4778 target = 0.256245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.235880 restraints weight = 8141.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.4597 rms_B_bonded: 1.84
r_work: 0.4495 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work (final): 0.4495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6111
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7804  Z= 0.155
  Angle     :  0.567   7.238  10574  Z= 0.311
  Chirality :  0.044   0.189   1072
  Planarity :  0.004   0.041   1358
  Dihedral  :  4.839  35.734   1000
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 18.20 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.23 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.61 (0.27), residues: 904
  helix:  0.62 (0.25), residues: 434
  sheet: -0.87 (0.71), residues: 56
  loop : -1.44 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 305 
 TYR   0.019   0.002   TYR A  98 
 PHE   0.034   0.002   PHE A   7 
 TRP   0.010   0.002   TRP A  32 
 HIS   0.005   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7804)
  covalent geometry    : angle       0.56698 (10574)
  hydrogen bonds       : bond        0.04332 (  305)
  hydrogen bonds       : angle       4.97647 (  888)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2183.90 seconds
wall clock time: 38 minutes 23.31 seconds (2303.31 seconds total)