Starting phenix.real_space_refine
on Mon Nov 17 23:38:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6d7l_7823/11_2025/6d7l_7823.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6d7l_7823/11_2025/6d7l_7823.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6d7l_7823/11_2025/6d7l_7823.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6d7l_7823/11_2025/6d7l_7823.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6d7l_7823/11_2025/6d7l_7823.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6d7l_7823/11_2025/6d7l_7823.cif"
  }
  resolution = 4.0
  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=   0.005
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      56      5.16       5
     C    5760      2.51       5
     N    1584      2.21       5
     O    1772      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9172
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 288, 2293
          Classifications: {'peptide': 288}
          Link IDs: {'PTRANS': 7, 'TRANS': 280}
          Chain breaks: 2
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 1.93, per 1000 atoms: 0.21
  Number of scatterers: 9172
  At special positions: 0
  Unit cell: (108.504, 108.504, 78.912, 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      56     16.00
     O    1772      8.00
     N    1584      7.00
     C    5760      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: 0.73
  Conformation dependent library (CDL) restraints added in 511.3 milliseconds
  

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2208

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 0 sheets defined
      69.5% alpha, 0.0% 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 37 through 49
      removed outlier: 3.847A  pdb=" N   TYR A  49 " --> pdb=" O   ASP A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 61
    Processing helix  chain 'A' and resid 85 through 94
      removed outlier: 3.859A  pdb=" N   VAL A  89 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LEU A  94 " --> pdb=" O   THR A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 112
      removed outlier: 3.604A  pdb=" N   ALA A 105 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 124
      removed outlier: 3.828A  pdb=" N   HIS A 124 " --> pdb=" O   ALA A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 170
      removed outlier: 3.761A  pdb=" N   CYS A 170 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 182
      removed outlier: 3.537A  pdb=" N   VAL A 176 " --> pdb=" O   LYS A 172 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LYS A 182 " --> pdb=" O   MET A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
      removed outlier: 3.542A  pdb=" N   LYS A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   HIS A 205 " --> pdb=" O   GLU A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 221
    Processing helix  chain 'A' and resid 225 through 229
    Processing helix  chain 'A' and resid 233 through 252
      removed outlier: 3.567A  pdb=" N   THR A 237 " --> pdb=" O   ASP A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 275
      removed outlier: 3.729A  pdb=" N   TYR A 259 " --> pdb=" O   PHE A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 292
      removed outlier: 3.554A  pdb=" N   GLU A 292 " --> pdb=" O   ASN A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 774 through 796
    Processing helix  chain 'A' and resid 800 through 823
      removed outlier: 3.569A  pdb=" N   LEU A 804 " --> pdb=" O   ASN A 800 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 49
      removed outlier: 3.846A  pdb=" N   TYR B  49 " --> pdb=" O   ASP B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 61
    Processing helix  chain 'B' and resid 85 through 94
      removed outlier: 3.859A  pdb=" N   VAL B  89 " --> pdb=" O   GLU B  85 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU B  94 " --> pdb=" O   THR B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 112
      removed outlier: 3.605A  pdb=" N   ALA B 105 " --> pdb=" O   ARG B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 124
      removed outlier: 3.828A  pdb=" N   HIS B 124 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 170
      removed outlier: 3.761A  pdb=" N   CYS B 170 " --> pdb=" O   LEU B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 182
      removed outlier: 3.535A  pdb=" N   VAL B 176 " --> pdb=" O   LYS B 172 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LYS B 182 " --> pdb=" O   MET B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 205
      removed outlier: 3.541A  pdb=" N   LYS B 202 " --> pdb=" O   ASP B 198 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   HIS B 205 " --> pdb=" O   GLU B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 221
    Processing helix  chain 'B' and resid 225 through 229
    Processing helix  chain 'B' and resid 233 through 252
      removed outlier: 3.567A  pdb=" N   THR B 237 " --> pdb=" O   ASP B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 275
      removed outlier: 3.729A  pdb=" N   TYR B 259 " --> pdb=" O   PHE B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 292
      removed outlier: 3.554A  pdb=" N   GLU B 292 " --> pdb=" O   ASN B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 774 through 796
    Processing helix  chain 'B' and resid 800 through 823
      removed outlier: 3.568A  pdb=" N   LEU B 804 " --> pdb=" O   ASN B 800 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 38 through 49
      removed outlier: 3.847A  pdb=" N   TYR C  49 " --> pdb=" O   ASP C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 61
    Processing helix  chain 'C' and resid 85 through 94
      removed outlier: 3.860A  pdb=" N   VAL C  89 " --> pdb=" O   GLU C  85 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LEU C  94 " --> pdb=" O   THR C  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 112
      removed outlier: 3.605A  pdb=" N   ALA C 105 " --> pdb=" O   ARG C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 124
      removed outlier: 3.828A  pdb=" N   HIS C 124 " --> pdb=" O   ALA C 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 162 through 170
      removed outlier: 3.761A  pdb=" N   CYS C 170 " --> pdb=" O   LEU C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 182
      removed outlier: 3.536A  pdb=" N   VAL C 176 " --> pdb=" O   LYS C 172 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LYS C 182 " --> pdb=" O   MET C 178 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 198 through 205
      removed outlier: 3.541A  pdb=" N   LYS C 202 " --> pdb=" O   ASP C 198 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   HIS C 205 " --> pdb=" O   GLU C 201 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 221
    Processing helix  chain 'C' and resid 225 through 229
    Processing helix  chain 'C' and resid 233 through 252
      removed outlier: 3.567A  pdb=" N   THR C 237 " --> pdb=" O   ASP C 233 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 255 through 275
      removed outlier: 3.729A  pdb=" N   TYR C 259 " --> pdb=" O   PHE C 255 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 283 through 292
      removed outlier: 3.555A  pdb=" N   GLU C 292 " --> pdb=" O   ASN C 288 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 774 through 796
    Processing helix  chain 'C' and resid 800 through 823
      removed outlier: 3.569A  pdb=" N   LEU C 804 " --> pdb=" O   ASN C 800 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 38 through 49
      removed outlier: 3.846A  pdb=" N   TYR D  49 " --> pdb=" O   ASP D  45 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 51 through 61
    Processing helix  chain 'D' and resid 85 through 94
      removed outlier: 3.859A  pdb=" N   VAL D  89 " --> pdb=" O   GLU D  85 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LEU D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 112
      removed outlier: 3.605A  pdb=" N   ALA D 105 " --> pdb=" O   ARG D 101 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 115 through 124
      removed outlier: 3.827A  pdb=" N   HIS D 124 " --> pdb=" O   ALA D 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 162 through 170
      removed outlier: 3.761A  pdb=" N   CYS D 170 " --> pdb=" O   LEU D 166 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 172 through 182
      removed outlier: 3.535A  pdb=" N   VAL D 176 " --> pdb=" O   LYS D 172 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LYS D 182 " --> pdb=" O   MET D 178 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 205
      removed outlier: 3.542A  pdb=" N   LYS D 202 " --> pdb=" O   ASP D 198 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   HIS D 205 " --> pdb=" O   GLU D 201 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 221
    Processing helix  chain 'D' and resid 225 through 229
    Processing helix  chain 'D' and resid 233 through 252
      removed outlier: 3.566A  pdb=" N   THR D 237 " --> pdb=" O   ASP D 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 275
      removed outlier: 3.729A  pdb=" N   TYR D 259 " --> pdb=" O   PHE D 255 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 283 through 292
      removed outlier: 3.555A  pdb=" N   GLU D 292 " --> pdb=" O   ASN D 288 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 774 through 796
    Processing helix  chain 'D' and resid 800 through 823
      removed outlier: 3.568A  pdb=" N   LEU D 804 " --> pdb=" O   ASN D 800 " (cutoff:3.500A)

    509 hydrogen bonds defined for protein.
    1503 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: 1.37

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3084
        1.34 -     1.46: 1532
        1.46 -     1.58: 4588
        1.58 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 9288
  Sorted by residual:
  bond pdb=" C   SER A 158 "
       pdb=" N   PRO A 159 "
    ideal  model  delta    sigma   weight residual
    1.326  1.355 -0.029 1.44e-02 4.82e+03 4.09e+00
  bond pdb=" C   SER C 158 "
       pdb=" N   PRO C 159 "
    ideal  model  delta    sigma   weight residual
    1.326  1.355 -0.029 1.44e-02 4.82e+03 4.09e+00
  bond pdb=" C   SER D 158 "
       pdb=" N   PRO D 159 "
    ideal  model  delta    sigma   weight residual
    1.326  1.355 -0.029 1.44e-02 4.82e+03 4.09e+00
  bond pdb=" C   SER B 158 "
       pdb=" N   PRO B 159 "
    ideal  model  delta    sigma   weight residual
    1.326  1.355 -0.029 1.44e-02 4.82e+03 3.94e+00
  bond pdb=" N   PRO C 224 "
       pdb=" CD  PRO C 224 "
    ideal  model  delta    sigma   weight residual
    1.473  1.495 -0.022 1.40e-02 5.10e+03 2.44e+00
  ... (remaining 9283 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 11848
        1.72 -     3.45: 496
        3.45 -     5.17: 100
        5.17 -     6.89: 24
        6.89 -     8.62: 12
  Bond angle restraints: 12480
  Sorted by residual:
  angle pdb=" C   GLU B 232 "
        pdb=" N   ASP B 233 "
        pdb=" CA  ASP B 233 "
      ideal   model   delta    sigma   weight residual
     122.83  127.55   -4.72 1.08e+00 8.57e-01 1.91e+01
  angle pdb=" C   GLU D 232 "
        pdb=" N   ASP D 233 "
        pdb=" CA  ASP D 233 "
      ideal   model   delta    sigma   weight residual
     122.83  127.52   -4.69 1.08e+00 8.57e-01 1.89e+01
  angle pdb=" C   GLU A 232 "
        pdb=" N   ASP A 233 "
        pdb=" CA  ASP A 233 "
      ideal   model   delta    sigma   weight residual
     122.83  127.52   -4.69 1.08e+00 8.57e-01 1.89e+01
  angle pdb=" C   GLU C 232 "
        pdb=" N   ASP C 233 "
        pdb=" CA  ASP C 233 "
      ideal   model   delta    sigma   weight residual
     122.83  127.50   -4.67 1.08e+00 8.57e-01 1.87e+01
  angle pdb=" N   HIS D 124 "
        pdb=" CA  HIS D 124 "
        pdb=" C   HIS D 124 "
      ideal   model   delta    sigma   weight residual
     109.81  118.43   -8.62 2.21e+00 2.05e-01 1.52e+01
  ... (remaining 12475 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.43: 5112
        9.43 -    18.85: 644
       18.85 -    28.28: 24
       28.28 -    37.71: 12
       37.71 -    47.14: 12
  Dihedral angle restraints: 5804
    sinusoidal: 2412
      harmonic: 3392
  Sorted by residual:
  dihedral pdb=" CA  SER C 158 "
           pdb=" C   SER C 158 "
           pdb=" N   PRO C 159 "
           pdb=" CA  PRO C 159 "
      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  SER D 158 "
           pdb=" C   SER D 158 "
           pdb=" N   PRO D 159 "
           pdb=" CA  PRO D 159 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.29   20.71     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" CA  SER A 158 "
           pdb=" C   SER A 158 "
           pdb=" N   PRO A 159 "
           pdb=" CA  PRO A 159 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.29   20.71     0      5.00e+00 4.00e-02 1.72e+01
  ... (remaining 5801 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 925
       0.044 -    0.088: 382
       0.088 -    0.132: 82
       0.132 -    0.177: 25
       0.177 -    0.221: 6
  Chirality restraints: 1420
  Sorted by residual:
  chirality pdb=" CA  HIS C 124 "
            pdb=" N   HIS C 124 "
            pdb=" C   HIS C 124 "
            pdb=" CB  HIS C 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CA  HIS A 124 "
            pdb=" N   HIS A 124 "
            pdb=" C   HIS A 124 "
            pdb=" CB  HIS A 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  HIS B 124 "
            pdb=" N   HIS B 124 "
            pdb=" C   HIS B 124 "
            pdb=" CB  HIS B 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  ... (remaining 1417 not shown)

  Planarity restraints: 1612
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 158 "    0.032 5.00e-02 4.00e+02   4.83e-02 3.73e+00
        pdb=" N   PRO B 159 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B 159 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 159 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 233 "   -0.032 5.00e-02 4.00e+02   4.82e-02 3.72e+00
        pdb=" N   PRO D 234 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO D 234 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO D 234 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 158 "   -0.032 5.00e-02 4.00e+02   4.82e-02 3.71e+00
        pdb=" N   PRO C 159 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO C 159 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 159 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1609 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2323
        2.80 -     3.32: 8416
        3.32 -     3.85: 13449
        3.85 -     4.37: 16353
        4.37 -     4.90: 26973
  Nonbonded interactions: 67514
  Sorted by model distance:
  nonbonded pdb=" O   VAL C  82 "
            pdb=" OH  TYR C 114 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   VAL B  82 "
            pdb=" OH  TYR B 114 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   VAL A  82 "
            pdb=" OH  TYR A 114 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" O   VAL D  82 "
            pdb=" OH  TYR D 114 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" NZ  LYS A 808 "
            pdb=" OE1 GLU D 806 "
     model   vdw
     2.299 3.120
  ... (remaining 67509 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'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.440
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7301
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   9288  Z= 0.203
  Angle     :  0.861   8.617  12480  Z= 0.488
  Chirality :  0.052   0.221   1420
  Planarity :  0.005   0.048   1612
  Dihedral  :  7.646  47.136   3596
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -3.90 (0.18), residues: 1128
  helix: -1.64 (0.14), residues: 780
  sheet:  None (None), residues: 0
  loop : -4.70 (0.21), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 785 
 TYR   0.014   0.002   TYR C 218 
 PHE   0.010   0.002   PHE A 193 
 HIS   0.005   0.002   HIS A 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 9288)
  covalent geometry    : angle       0.86103 (12480)
  hydrogen bonds       : bond        0.07609 (  509)
  hydrogen bonds       : angle       5.44504 ( 1503)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  416 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 416
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 LEU cc_start: 0.7402 (mt) cc_final: 0.6855 (mp)
REVERT: A   72 TYR cc_start: 0.6654 (m-80) cc_final: 0.5769 (m-80)
REVERT: A  221 LEU cc_start: 0.8458 (mt) cc_final: 0.8241 (tp)
REVERT: A  245 LEU cc_start: 0.9360 (mt) cc_final: 0.9147 (mt)
REVERT: A  793 ASP cc_start: 0.8786 (m-30) cc_final: 0.8447 (t0)
REVERT: A  822 LYS cc_start: 0.8562 (mttt) cc_final: 0.8319 (tppt)
REVERT: B   65 LEU cc_start: 0.7305 (mt) cc_final: 0.6748 (mp)
REVERT: B   72 TYR cc_start: 0.6631 (m-80) cc_final: 0.6168 (m-80)
REVERT: B  221 LEU cc_start: 0.8465 (mt) cc_final: 0.8212 (tp)
REVERT: B  245 LEU cc_start: 0.9361 (mt) cc_final: 0.9145 (mt)
REVERT: B  793 ASP cc_start: 0.8783 (m-30) cc_final: 0.8454 (t0)
REVERT: C   65 LEU cc_start: 0.7303 (mt) cc_final: 0.6752 (mp)
REVERT: C   72 TYR cc_start: 0.6668 (m-80) cc_final: 0.6106 (m-80)
REVERT: C  221 LEU cc_start: 0.8462 (mt) cc_final: 0.8244 (tp)
REVERT: C  245 LEU cc_start: 0.9382 (mt) cc_final: 0.9167 (mt)
REVERT: C  793 ASP cc_start: 0.8782 (m-30) cc_final: 0.8424 (t0)
REVERT: D   65 LEU cc_start: 0.7403 (mt) cc_final: 0.6855 (mp)
REVERT: D   72 TYR cc_start: 0.6656 (m-80) cc_final: 0.6123 (m-80)
REVERT: D  221 LEU cc_start: 0.8459 (mt) cc_final: 0.8238 (tp)
REVERT: D  245 LEU cc_start: 0.9362 (mt) cc_final: 0.9146 (mt)
REVERT: D  793 ASP cc_start: 0.8780 (m-30) cc_final: 0.8451 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 416
  average time/residue: 0.1307
  time to fit residues: 69.5318
Evaluate side-chains
  231 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 231
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    0.0970
   chunk 106 optimal weight:    4.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 124 HIS
A 177 HIS
B  66 ASN
B  75 GLN
** B  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 124 HIS
B 177 HIS
C  66 ASN
C  75 GLN
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 124 HIS
C 177 HIS
D  75 GLN
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 124 HIS
D 177 HIS

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.102852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.090708 restraints weight = 33827.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.092298 restraints weight = 24335.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.093487 restraints weight = 18845.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.094380 restraints weight = 15359.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.095046 restraints weight = 13029.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.4352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9288  Z= 0.152
  Angle     :  0.742   6.265  12480  Z= 0.386
  Chirality :  0.043   0.139   1420
  Planarity :  0.004   0.034   1612
  Dihedral  :  5.694  20.033   1248
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 16.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 10.73 %
    Favored  : 86.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -2.17 (0.22), residues: 1128
  helix: -0.08 (0.17), residues: 784
  sheet:  None (None), residues: 0
  loop : -4.76 (0.20), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 116 
 TYR   0.010   0.001   TYR C 192 
 PHE   0.007   0.001   PHE D  43 
 HIS   0.005   0.001   HIS D 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 9288)
  covalent geometry    : angle       0.74239 (12480)
  hydrogen bonds       : bond        0.03457 (  509)
  hydrogen bonds       : angle       4.51551 ( 1503)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 227
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 GLU cc_start: 0.6956 (tp30) cc_final: 0.6657 (tp30)
REVERT: A  245 LEU cc_start: 0.9264 (mt) cc_final: 0.9064 (mt)
REVERT: A  793 ASP cc_start: 0.8706 (m-30) cc_final: 0.8474 (t0)
REVERT: A  817 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8112 (mt-10)
REVERT: B  174 GLU cc_start: 0.6922 (tp30) cc_final: 0.6613 (tp30)
REVERT: B  779 MET cc_start: 0.8971 (tpp) cc_final: 0.8547 (tpp)
REVERT: B  793 ASP cc_start: 0.8676 (m-30) cc_final: 0.8459 (t0)
REVERT: B  817 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8106 (mt-10)
REVERT: C  174 GLU cc_start: 0.6903 (tp30) cc_final: 0.6590 (tp30)
REVERT: C  793 ASP cc_start: 0.8690 (m-30) cc_final: 0.8464 (t0)
REVERT: D  174 GLU cc_start: 0.6951 (tp30) cc_final: 0.6715 (tp30)
REVERT: D  245 LEU cc_start: 0.9254 (mt) cc_final: 0.9051 (mt)
REVERT: D  779 MET cc_start: 0.8976 (tpp) cc_final: 0.8552 (tpp)
REVERT: D  793 ASP cc_start: 0.8706 (m-30) cc_final: 0.8482 (t0)
  outliers start: 33
  outliers final: 11
  residues processed: 253
  average time/residue: 0.1056
  time to fit residues: 35.7092
Evaluate side-chains
  165 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 154
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  119 GLU
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  119 GLU
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  119 GLU
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain D residue   92 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0770
   chunk 45 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 80 optimal weight:    5.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.2146

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  66 ASN
B  75 GLN
** B  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  66 ASN
C  75 GLN
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  66 ASN
D  75 GLN
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.102522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.090703 restraints weight = 33641.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.092594 restraints weight = 22607.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.093943 restraints weight = 16546.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.094923 restraints weight = 12873.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.095579 restraints weight = 10535.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.5399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9288  Z= 0.161
  Angle     :  0.821  12.884  12480  Z= 0.408
  Chirality :  0.046   0.262   1420
  Planarity :  0.005   0.058   1612
  Dihedral  :  5.472  20.029   1248
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 17.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.66 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 11.81 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -1.50 (0.23), residues: 1128
  helix:  0.49 (0.18), residues: 784
  sheet:  None (None), residues: 0
  loop : -4.71 (0.19), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 815 
 TYR   0.018   0.001   TYR A  49 
 PHE   0.004   0.001   PHE B 193 
 HIS   0.003   0.001   HIS D 177 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 9288)
  covalent geometry    : angle       0.82118 (12480)
  hydrogen bonds       : bond        0.03609 (  509)
  hydrogen bonds       : angle       4.46751 ( 1503)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 178
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8271 (pp30)
REVERT: A  174 GLU cc_start: 0.7250 (tp30) cc_final: 0.6705 (tp30)
REVERT: A  264 MET cc_start: 0.8607 (mmm) cc_final: 0.8229 (mmm)
REVERT: A  793 ASP cc_start: 0.8730 (m-30) cc_final: 0.8373 (t0)
REVERT: B  174 GLU cc_start: 0.7209 (tp30) cc_final: 0.6697 (tp30)
REVERT: B  264 MET cc_start: 0.8586 (mmm) cc_final: 0.8211 (mmm)
REVERT: B  793 ASP cc_start: 0.8712 (m-30) cc_final: 0.8365 (t0)
REVERT: C  174 GLU cc_start: 0.7197 (tp30) cc_final: 0.6688 (tp30)
REVERT: C  264 MET cc_start: 0.8612 (mmm) cc_final: 0.8241 (mmm)
REVERT: C  793 ASP cc_start: 0.8722 (m-30) cc_final: 0.8364 (t0)
REVERT: D  174 GLU cc_start: 0.7158 (tp30) cc_final: 0.6737 (tp30)
REVERT: D  178 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7930 (ptm)
REVERT: D  264 MET cc_start: 0.8608 (mmm) cc_final: 0.8233 (mmm)
REVERT: D  793 ASP cc_start: 0.8727 (m-30) cc_final: 0.8378 (t0)
  outliers start: 30
  outliers final: 8
  residues processed: 198
  average time/residue: 0.0769
  time to fit residues: 22.7987
Evaluate side-chains
  160 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 151
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  178 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 101 optimal weight:    0.0770
   chunk 8 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 3 optimal weight:    0.4980
   chunk 63 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 108 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0170
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.4376

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  66 ASN
B  75 GLN
** B  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  66 ASN
C  75 GLN
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  75 GLN
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.103041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.091264 restraints weight = 33111.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.093034 restraints weight = 23065.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.094324 restraints weight = 17249.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.095281 restraints weight = 13656.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.095882 restraints weight = 11305.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.5709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9288  Z= 0.132
  Angle     :  0.772  11.413  12480  Z= 0.385
  Chirality :  0.043   0.227   1420
  Planarity :  0.005   0.065   1612
  Dihedral  :  5.242  19.062   1248
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 12.60 %
    Favored  : 85.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -1.06 (0.24), residues: 1128
  helix:  0.88 (0.18), residues: 776
  sheet:  None (None), residues: 0
  loop : -4.58 (0.21), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 116 
 TYR   0.015   0.001   TYR C  72 
 PHE   0.004   0.001   PHE D 193 
 HIS   0.004   0.001   HIS A 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9288)
  covalent geometry    : angle       0.77155 (12480)
  hydrogen bonds       : bond        0.03438 (  509)
  hydrogen bonds       : angle       4.37782 ( 1503)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 178
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  174 GLU cc_start: 0.7216 (tp30) cc_final: 0.6619 (tp30)
REVERT: A  793 ASP cc_start: 0.8642 (m-30) cc_final: 0.8312 (t0)
REVERT: A  794 LYS cc_start: 0.8897 (tptp) cc_final: 0.8501 (tppp)
REVERT: B  174 GLU cc_start: 0.7162 (tp30) cc_final: 0.6576 (tp30)
REVERT: B  245 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8957 (mm)
REVERT: B  779 MET cc_start: 0.8961 (tpp) cc_final: 0.8642 (mpp)
REVERT: B  793 ASP cc_start: 0.8606 (m-30) cc_final: 0.8360 (t0)
REVERT: B  794 LYS cc_start: 0.8882 (tptp) cc_final: 0.8511 (tppp)
REVERT: C  174 GLU cc_start: 0.7166 (tp30) cc_final: 0.6583 (tp30)
REVERT: C  245 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8961 (mm)
REVERT: C  779 MET cc_start: 0.8954 (tpp) cc_final: 0.8638 (mpp)
REVERT: C  793 ASP cc_start: 0.8629 (m-30) cc_final: 0.8371 (t0)
REVERT: C  794 LYS cc_start: 0.8892 (tptp) cc_final: 0.8505 (tppp)
REVERT: D  116 ARG cc_start: 0.6734 (OUTLIER) cc_final: 0.6477 (tpp80)
REVERT: D  174 GLU cc_start: 0.7111 (tp30) cc_final: 0.6583 (tp30)
REVERT: D  779 MET cc_start: 0.8938 (tpp) cc_final: 0.8645 (mpp)
REVERT: D  793 ASP cc_start: 0.8670 (m-30) cc_final: 0.8400 (t0)
REVERT: D  794 LYS cc_start: 0.8903 (tptp) cc_final: 0.8511 (tppp)
  outliers start: 22
  outliers final: 11
  residues processed: 197
  average time/residue: 0.0778
  time to fit residues: 22.7326
Evaluate side-chains
  172 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 158
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  788 LEU
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  788 LEU
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain D residue   91 GLU
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  116 ARG
Chi-restraints excluded: chain D residue  178 MET
Chi-restraints excluded: chain D residue  788 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 99 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 85 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 106 optimal weight:    0.0270
   chunk 65 optimal weight:    6.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    0.6238

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
** B  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  75 GLN
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  75 GLN
** D  76 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 = 0.3885 r_free = 0.3885 target = 0.102879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.090747 restraints weight = 33536.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.092682 restraints weight = 22992.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.094049 restraints weight = 17051.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.095014 restraints weight = 13428.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.095901 restraints weight = 11115.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.5955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9288  Z= 0.135
  Angle     :  0.753  11.232  12480  Z= 0.375
  Chirality :  0.043   0.192   1420
  Planarity :  0.004   0.038   1612
  Dihedral  :  5.108  18.790   1248
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.45 %
    Favored  : 82.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -0.65 (0.25), residues: 1128
  helix:  1.12 (0.19), residues: 784
  sheet:  None (None), residues: 0
  loop : -4.35 (0.22), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 815 
 TYR   0.016   0.001   TYR A  72 
 PHE   0.006   0.001   PHE C 193 
 HIS   0.003   0.001   HIS C 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9288)
  covalent geometry    : angle       0.75281 (12480)
  hydrogen bonds       : bond        0.03341 (  509)
  hydrogen bonds       : angle       4.36351 ( 1503)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 195
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 ILE cc_start: 0.9313 (mm) cc_final: 0.8834 (tt)
REVERT: A  174 GLU cc_start: 0.7206 (tp30) cc_final: 0.6875 (tp30)
REVERT: A  264 MET cc_start: 0.8380 (mmm) cc_final: 0.8071 (mmm)
REVERT: A  793 ASP cc_start: 0.8689 (m-30) cc_final: 0.8435 (t0)
REVERT: A  794 LYS cc_start: 0.8860 (tptp) cc_final: 0.8513 (tppp)
REVERT: B  165 ILE cc_start: 0.9320 (mm) cc_final: 0.8839 (tt)
REVERT: B  174 GLU cc_start: 0.7186 (tp30) cc_final: 0.6859 (tp30)
REVERT: B  264 MET cc_start: 0.8382 (mmm) cc_final: 0.8090 (mmm)
REVERT: B  793 ASP cc_start: 0.8652 (m-30) cc_final: 0.8405 (t0)
REVERT: B  794 LYS cc_start: 0.8838 (tptp) cc_final: 0.8519 (tppp)
REVERT: C  165 ILE cc_start: 0.9280 (mm) cc_final: 0.8796 (tt)
REVERT: C  174 GLU cc_start: 0.7165 (tp30) cc_final: 0.6853 (tp30)
REVERT: C  264 MET cc_start: 0.8403 (mmm) cc_final: 0.8104 (mmm)
REVERT: C  793 ASP cc_start: 0.8664 (m-30) cc_final: 0.8411 (t0)
REVERT: C  794 LYS cc_start: 0.8854 (tptp) cc_final: 0.8533 (tppp)
REVERT: D  165 ILE cc_start: 0.9309 (mm) cc_final: 0.8843 (tt)
REVERT: D  174 GLU cc_start: 0.7247 (tp30) cc_final: 0.6567 (tp30)
REVERT: D  264 MET cc_start: 0.8395 (mmm) cc_final: 0.8090 (mmm)
REVERT: D  793 ASP cc_start: 0.8694 (m-30) cc_final: 0.8430 (t0)
REVERT: D  794 LYS cc_start: 0.8871 (tptp) cc_final: 0.8518 (tppp)
  outliers start: 19
  outliers final: 10
  residues processed: 212
  average time/residue: 0.0755
  time to fit residues: 23.8938
Evaluate side-chains
  174 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 164
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  788 LEU
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  788 LEU
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain D residue   91 GLU
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  788 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0670
   chunk 109 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   chunk 90 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 86 optimal weight:    8.9990
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
** B  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  75 GLN
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  75 GLN
** D  76 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 = 0.3861 r_free = 0.3861 target = 0.101532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.089285 restraints weight = 33851.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.091125 restraints weight = 23362.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.092481 restraints weight = 17393.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.093523 restraints weight = 13693.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.094283 restraints weight = 11275.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.6279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9288  Z= 0.140
  Angle     :  0.791  12.853  12480  Z= 0.393
  Chirality :  0.045   0.245   1420
  Planarity :  0.004   0.034   1612
  Dihedral  :  4.997  18.614   1248
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 17.91 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -0.54 (0.25), residues: 1128
  helix:  1.22 (0.19), residues: 784
  sheet:  None (None), residues: 0
  loop : -4.38 (0.22), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 815 
 TYR   0.011   0.001   TYR B  72 
 PHE   0.004   0.001   PHE B 193 
 HIS   0.003   0.001   HIS C 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 9288)
  covalent geometry    : angle       0.79100 (12480)
  hydrogen bonds       : bond        0.03404 (  509)
  hydrogen bonds       : angle       4.34037 ( 1503)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 178
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 ILE cc_start: 0.9344 (mm) cc_final: 0.8890 (tt)
REVERT: A  174 GLU cc_start: 0.7251 (tp30) cc_final: 0.6920 (tp30)
REVERT: A  264 MET cc_start: 0.8463 (mmm) cc_final: 0.8218 (mmm)
REVERT: A  793 ASP cc_start: 0.8714 (m-30) cc_final: 0.8450 (t0)
REVERT: A  794 LYS cc_start: 0.8796 (tptp) cc_final: 0.8532 (tppp)
REVERT: B  165 ILE cc_start: 0.9353 (mm) cc_final: 0.8890 (tt)
REVERT: B  174 GLU cc_start: 0.7219 (tp30) cc_final: 0.6901 (tp30)
REVERT: B  264 MET cc_start: 0.8457 (mmm) cc_final: 0.8217 (mmm)
REVERT: B  793 ASP cc_start: 0.8652 (m-30) cc_final: 0.8431 (t0)
REVERT: C  165 ILE cc_start: 0.9352 (mm) cc_final: 0.8889 (tt)
REVERT: C  174 GLU cc_start: 0.7221 (tp30) cc_final: 0.6914 (tp30)
REVERT: C  264 MET cc_start: 0.8478 (mmm) cc_final: 0.8214 (mmm)
REVERT: C  793 ASP cc_start: 0.8676 (m-30) cc_final: 0.8433 (t0)
REVERT: D  165 ILE cc_start: 0.9340 (mm) cc_final: 0.8896 (tt)
REVERT: D  174 GLU cc_start: 0.7260 (tp30) cc_final: 0.6837 (tp30)
REVERT: D  264 MET cc_start: 0.8459 (mmm) cc_final: 0.8220 (mmm)
REVERT: D  793 ASP cc_start: 0.8716 (m-30) cc_final: 0.8460 (t0)
  outliers start: 30
  outliers final: 13
  residues processed: 198
  average time/residue: 0.0798
  time to fit residues: 23.5753
Evaluate side-chains
  176 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 163
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  788 LEU
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  788 LEU
Chi-restraints excluded: chain D residue   91 GLU
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  116 ARG
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  788 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 32 optimal weight:    0.0870
   chunk 71 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0970
   chunk 65 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0270
   chunk 56 optimal weight:    5.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.3214

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  84 ASN
** C  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 ASN
D  75 GLN
** D  76 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 = 0.3888 r_free = 0.3888 target = 0.102849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.090754 restraints weight = 33946.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.092681 restraints weight = 23006.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.094083 restraints weight = 16990.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.095057 restraints weight = 13336.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.095824 restraints weight = 10971.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.6463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9288  Z= 0.140
  Angle     :  0.813  13.835  12480  Z= 0.404
  Chirality :  0.044   0.176   1420
  Planarity :  0.004   0.033   1612
  Dihedral  :  4.892  19.018   1248
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.69 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 18.01 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -0.50 (0.25), residues: 1128
  helix:  1.28 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop : -4.37 (0.21), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 116 
 TYR   0.018   0.001   TYR A  72 
 PHE   0.007   0.001   PHE B 193 
 HIS   0.003   0.001   HIS C 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9288)
  covalent geometry    : angle       0.81331 (12480)
  hydrogen bonds       : bond        0.03235 (  509)
  hydrogen bonds       : angle       4.29789 ( 1503)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 182
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 ILE cc_start: 0.9369 (mm) cc_final: 0.8886 (tt)
REVERT: A  174 GLU cc_start: 0.7323 (tp30) cc_final: 0.6926 (tp30)
REVERT: A  264 MET cc_start: 0.8424 (mmm) cc_final: 0.8212 (mmm)
REVERT: A  793 ASP cc_start: 0.8682 (m-30) cc_final: 0.8407 (t0)
REVERT: A  794 LYS cc_start: 0.8836 (tptp) cc_final: 0.8469 (tppp)
REVERT: A  795 GLU cc_start: 0.8283 (mp0) cc_final: 0.7912 (mp0)
REVERT: B  165 ILE cc_start: 0.9354 (mm) cc_final: 0.8886 (tt)
REVERT: B  174 GLU cc_start: 0.7333 (tp30) cc_final: 0.6935 (tp30)
REVERT: B  264 MET cc_start: 0.8402 (mmm) cc_final: 0.8162 (mmm)
REVERT: B  793 ASP cc_start: 0.8638 (m-30) cc_final: 0.8370 (t0)
REVERT: B  794 LYS cc_start: 0.8910 (tptp) cc_final: 0.8416 (tppp)
REVERT: B  795 GLU cc_start: 0.8307 (mp0) cc_final: 0.7842 (mp0)
REVERT: C  165 ILE cc_start: 0.9366 (mm) cc_final: 0.8899 (tt)
REVERT: C  174 GLU cc_start: 0.7350 (tp30) cc_final: 0.6941 (tp30)
REVERT: C  264 MET cc_start: 0.8461 (mmm) cc_final: 0.8246 (mmm)
REVERT: C  793 ASP cc_start: 0.8638 (m-30) cc_final: 0.8364 (t0)
REVERT: C  794 LYS cc_start: 0.8913 (tptp) cc_final: 0.8396 (tppp)
REVERT: C  795 GLU cc_start: 0.8310 (mp0) cc_final: 0.7839 (mp0)
REVERT: D  165 ILE cc_start: 0.9367 (mm) cc_final: 0.8884 (tt)
REVERT: D  174 GLU cc_start: 0.7292 (tp30) cc_final: 0.6955 (tp30)
REVERT: D  264 MET cc_start: 0.8445 (mmm) cc_final: 0.8235 (mmm)
REVERT: D  793 ASP cc_start: 0.8649 (m-30) cc_final: 0.8372 (t0)
REVERT: D  794 LYS cc_start: 0.8915 (tptp) cc_final: 0.8393 (tppp)
REVERT: D  795 GLU cc_start: 0.8313 (mp0) cc_final: 0.7843 (mp0)
  outliers start: 24
  outliers final: 14
  residues processed: 199
  average time/residue: 0.0847
  time to fit residues: 24.3555
Evaluate side-chains
  178 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 164
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain B residue   84 ASN
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain C residue   84 ASN
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain D residue   91 GLU
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  788 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 88 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 100 optimal weight:    0.0010
   chunk 36 optimal weight:    0.9980
   chunk 0 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 44 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0870
   chunk 40 optimal weight:    0.1980
   overall best weight:    0.3764

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  75 GLN
** D  76 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 = 0.3894 r_free = 0.3894 target = 0.103472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.091921 restraints weight = 32889.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.093673 restraints weight = 23025.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.094943 restraints weight = 17391.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.095849 restraints weight = 13886.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.096551 restraints weight = 11570.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.6555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9288  Z= 0.141
  Angle     :  0.828  13.799  12480  Z= 0.409
  Chirality :  0.045   0.249   1420
  Planarity :  0.004   0.031   1612
  Dihedral  :  4.844  17.236   1248
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.16 %
    Favored  : 91.84 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 19.49 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -0.47 (0.25), residues: 1128
  helix:  1.29 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop : -4.33 (0.22), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 188 
 TYR   0.011   0.001   TYR C  72 
 PHE   0.004   0.001   PHE B 193 
 HIS   0.003   0.001   HIS C 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 9288)
  covalent geometry    : angle       0.82795 (12480)
  hydrogen bonds       : bond        0.03192 (  509)
  hydrogen bonds       : angle       4.27029 ( 1503)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 171
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 ILE cc_start: 0.9276 (mm) cc_final: 0.8852 (tt)
REVERT: A  174 GLU cc_start: 0.7201 (tp30) cc_final: 0.6859 (tp30)
REVERT: A  793 ASP cc_start: 0.8620 (m-30) cc_final: 0.8397 (t0)
REVERT: A  794 LYS cc_start: 0.8777 (tptp) cc_final: 0.8523 (tppp)
REVERT: B  165 ILE cc_start: 0.9276 (mm) cc_final: 0.8852 (tt)
REVERT: B  174 GLU cc_start: 0.7243 (tp30) cc_final: 0.6890 (tp30)
REVERT: B  793 ASP cc_start: 0.8563 (m-30) cc_final: 0.8347 (t0)
REVERT: B  794 LYS cc_start: 0.8829 (tptp) cc_final: 0.8457 (tppp)
REVERT: C  165 ILE cc_start: 0.9272 (mm) cc_final: 0.8844 (tt)
REVERT: C  174 GLU cc_start: 0.7234 (tp30) cc_final: 0.6879 (tp30)
REVERT: C  793 ASP cc_start: 0.8566 (m-30) cc_final: 0.8348 (t0)
REVERT: C  794 LYS cc_start: 0.8829 (tptp) cc_final: 0.8441 (tppp)
REVERT: D  165 ILE cc_start: 0.9272 (mm) cc_final: 0.8849 (tt)
REVERT: D  174 GLU cc_start: 0.7113 (tp30) cc_final: 0.6806 (tp30)
REVERT: D  793 ASP cc_start: 0.8584 (m-30) cc_final: 0.8359 (t0)
REVERT: D  794 LYS cc_start: 0.8858 (tptp) cc_final: 0.8468 (tppp)
  outliers start: 18
  outliers final: 16
  residues processed: 183
  average time/residue: 0.0818
  time to fit residues: 21.7174
Evaluate side-chains
  179 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 163
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain B residue   84 ASN
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue   88 GLU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain C residue   84 ASN
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain D residue   88 GLU
Chi-restraints excluded: chain D residue   91 GLU
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  788 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 76 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0060
   chunk 15 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 59 optimal weight:    6.9990
   chunk 101 optimal weight:    3.9990
   chunk 108 optimal weight:    0.9990
   overall best weight:    1.1800

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

Flipped N/Q/H residues before XYZ refinement:
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  75 GLN
** D  76 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 = 0.3829 r_free = 0.3829 target = 0.100217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.088127 restraints weight = 34457.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.089872 restraints weight = 24127.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.091136 restraints weight = 18221.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.092138 restraints weight = 14537.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.092857 restraints weight = 12017.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.6727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9288  Z= 0.160
  Angle     :  0.850  14.101  12480  Z= 0.424
  Chirality :  0.046   0.270   1420
  Planarity :  0.004   0.033   1612
  Dihedral  :  4.909  24.538   1248
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 21.16 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -0.38 (0.26), residues: 1128
  helix:  1.35 (0.19), residues: 788
  sheet:  None (None), residues: 0
  loop : -4.42 (0.22), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 188 
 TYR   0.014   0.001   TYR A  72 
 PHE   0.009   0.001   PHE A 193 
 HIS   0.004   0.001   HIS D 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 9288)
  covalent geometry    : angle       0.85006 (12480)
  hydrogen bonds       : bond        0.03420 (  509)
  hydrogen bonds       : angle       4.34094 ( 1503)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 167
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 ILE cc_start: 0.9354 (mm) cc_final: 0.8926 (tt)
REVERT: A  174 GLU cc_start: 0.7204 (tp30) cc_final: 0.6887 (tp30)
REVERT: A  793 ASP cc_start: 0.8727 (m-30) cc_final: 0.8482 (t0)
REVERT: A  794 LYS cc_start: 0.8860 (tptp) cc_final: 0.8629 (tptm)
REVERT: A  795 GLU cc_start: 0.8303 (mp0) cc_final: 0.7938 (mp0)
REVERT: B  165 ILE cc_start: 0.9358 (mm) cc_final: 0.8934 (tt)
REVERT: B  174 GLU cc_start: 0.7207 (tp30) cc_final: 0.6884 (tp30)
REVERT: B  793 ASP cc_start: 0.8691 (m-30) cc_final: 0.8428 (t0)
REVERT: B  794 LYS cc_start: 0.8804 (tptp) cc_final: 0.8441 (tppp)
REVERT: B  795 GLU cc_start: 0.8399 (mp0) cc_final: 0.8013 (mp0)
REVERT: C  165 ILE cc_start: 0.9348 (mm) cc_final: 0.8927 (tt)
REVERT: C  174 GLU cc_start: 0.7202 (tp30) cc_final: 0.6878 (tp30)
REVERT: C  793 ASP cc_start: 0.8678 (m-30) cc_final: 0.8402 (t0)
REVERT: C  794 LYS cc_start: 0.8807 (tptp) cc_final: 0.8416 (tppp)
REVERT: C  795 GLU cc_start: 0.8393 (mp0) cc_final: 0.8021 (mp0)
REVERT: D  165 ILE cc_start: 0.9347 (mm) cc_final: 0.8931 (tt)
REVERT: D  174 GLU cc_start: 0.7213 (tp30) cc_final: 0.6900 (tp30)
REVERT: D  793 ASP cc_start: 0.8708 (m-30) cc_final: 0.8458 (t0)
REVERT: D  794 LYS cc_start: 0.8813 (tptp) cc_final: 0.8415 (tppp)
REVERT: D  795 GLU cc_start: 0.8431 (mp0) cc_final: 0.8015 (mp0)
  outliers start: 18
  outliers final: 16
  residues processed: 183
  average time/residue: 0.0782
  time to fit residues: 21.4261
Evaluate side-chains
  173 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 157
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue   88 GLU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain D residue   88 GLU
Chi-restraints excluded: chain D residue   91 GLU
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  116 ARG
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  788 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0770
   chunk 15 optimal weight:    0.0770
   chunk 21 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0070
   chunk 31 optimal weight:    1.9990
   chunk 13 optimal weight:    0.1980
   chunk 30 optimal weight:    6.9990
   overall best weight:    0.2314

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  84 ASN
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 ASN
D  75 GLN
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.102716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.090509 restraints weight = 33745.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.092446 restraints weight = 23112.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.093880 restraints weight = 17139.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.094936 restraints weight = 13399.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.095685 restraints weight = 10990.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.6810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9288  Z= 0.145
  Angle     :  0.874  14.676  12480  Z= 0.428
  Chirality :  0.046   0.294   1420
  Planarity :  0.004   0.032   1612
  Dihedral  :  4.789  23.610   1248
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 21.46 %
    Favored  : 76.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -0.23 (0.25), residues: 1128
  helix:  1.59 (0.19), residues: 760
  sheet:  None (None), residues: 0
  loop : -4.20 (0.22), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 188 
 TYR   0.014   0.001   TYR C  72 
 PHE   0.013   0.001   PHE A 269 
 HIS   0.003   0.001   HIS C 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9288)
  covalent geometry    : angle       0.87398 (12480)
  hydrogen bonds       : bond        0.03220 (  509)
  hydrogen bonds       : angle       4.18849 ( 1503)

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

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

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2256 Ramachandran restraints generated.
    1128 Oldfield, 0 Emsley, 1128 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 176
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 ILE cc_start: 0.9348 (mm) cc_final: 0.8949 (tt)
REVERT: A  174 GLU cc_start: 0.7261 (tp30) cc_final: 0.6891 (tp30)
REVERT: B  165 ILE cc_start: 0.9353 (mm) cc_final: 0.8953 (tt)
REVERT: B  174 GLU cc_start: 0.7300 (tp30) cc_final: 0.6924 (tp30)
REVERT: B  791 GLN cc_start: 0.9014 (mt0) cc_final: 0.8429 (mt0)
REVERT: B  793 ASP cc_start: 0.8609 (m-30) cc_final: 0.8339 (t0)
REVERT: B  794 LYS cc_start: 0.8825 (tptp) cc_final: 0.8366 (tppp)
REVERT: B  795 GLU cc_start: 0.8411 (mp0) cc_final: 0.7950 (mp0)
REVERT: C  165 ILE cc_start: 0.9344 (mm) cc_final: 0.8884 (tt)
REVERT: C  174 GLU cc_start: 0.7280 (tp30) cc_final: 0.6904 (tp30)
REVERT: C  793 ASP cc_start: 0.8614 (m-30) cc_final: 0.8337 (t0)
REVERT: C  794 LYS cc_start: 0.8832 (tptp) cc_final: 0.8376 (tppp)
REVERT: C  795 GLU cc_start: 0.8407 (mp0) cc_final: 0.7986 (mp0)
REVERT: D  165 ILE cc_start: 0.9341 (mm) cc_final: 0.8951 (tt)
REVERT: D  174 GLU cc_start: 0.7307 (tp30) cc_final: 0.7017 (tp30)
REVERT: D  791 GLN cc_start: 0.9050 (mt0) cc_final: 0.8481 (mt0)
REVERT: D  793 ASP cc_start: 0.8635 (m-30) cc_final: 0.8356 (t0)
REVERT: D  794 LYS cc_start: 0.8834 (tptp) cc_final: 0.8353 (tppp)
REVERT: D  795 GLU cc_start: 0.8475 (mp0) cc_final: 0.8012 (mp0)
  outliers start: 22
  outliers final: 16
  residues processed: 192
  average time/residue: 0.0772
  time to fit residues: 22.2766
Evaluate side-chains
  178 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 162
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain B residue   84 ASN
Chi-restraints excluded: chain B residue   87 LEU
Chi-restraints excluded: chain B residue   88 GLU
Chi-restraints excluded: chain C residue   84 ASN
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain D residue   84 ASN
Chi-restraints excluded: chain D residue   88 GLU
Chi-restraints excluded: chain D residue   91 GLU
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  221 LEU
Chi-restraints excluded: chain D residue  788 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 66 optimal weight:    0.4980
   chunk 49 optimal weight:    3.9990
   chunk 32 optimal weight:    5.9990
   chunk 108 optimal weight:    1.9990
   chunk 14 optimal weight:    9.9990
   chunk 104 optimal weight:    3.9990
   chunk 100 optimal weight:    0.0270
   overall best weight:    0.9042

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

Flipped N/Q/H residues before XYZ refinement:
A  75 GLN
** A  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 800 ASN
** B  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  84 ASN
B 800 ASN
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 ASN
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 800 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.102597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.090426 restraints weight = 33249.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.092344 restraints weight = 22694.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.093720 restraints weight = 16778.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.094710 restraints weight = 13173.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.095475 restraints weight = 10855.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.6875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.403   9288  Z= 0.458
  Angle     :  1.440  59.195  12480  Z= 0.879
  Chirality :  0.073   1.349   1420
  Planarity :  0.007   0.229   1612
  Dihedral  :  4.928  28.745   1248
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 17.57
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.60 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 22.34 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    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 are not related in a simple way.
  whole: -0.30 (0.25), residues: 1128
  helix:  1.53 (0.19), residues: 760
  sheet:  None (None), residues: 0
  loop : -4.23 (0.22), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 188 
 TYR   0.014   0.001   TYR D 192 
 PHE   0.012   0.001   PHE A 269 
 HIS   0.003   0.001   HIS C 169 

Details of bonding type rmsd
  covalent geometry    : bond        0.00907 ( 9288)
  covalent geometry    : angle       1.44008 (12480)
  hydrogen bonds       : bond        0.03266 (  509)
  hydrogen bonds       : angle       4.20738 ( 1503)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1454.22 seconds
wall clock time: 26 minutes 1.21 seconds (1561.21 seconds total)