Starting phenix.real_space_refine
on Thu Feb 13 17:54:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6d7l_7823/02_2025/6d7l_7823.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6d7l_7823/02_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_7823/02_2025/6d7l_7823.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6d7l_7823/02_2025/6d7l_7823.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6d7l_7823/02_2025/6d7l_7823.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6d7l_7823/02_2025/6d7l_7823.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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:
    C, B, D
  Time building chain proxies: 4.26, per 1000 atoms: 0.46
  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: 2.12
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.92
  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: 2.22

  Time building geometry restraints manager: 2.48 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  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:             1.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     20.740
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.220
-------------------------------------------------------------------------------
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= 0.265
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 HIS   0.005   0.002   HIS A 124 
 PHE   0.010   0.002   PHE A 193 
 TYR   0.014   0.002   TYR C 218 
 ARG   0.008   0.001   ARG B 785 

*********************** 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  : 1.086 
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: A   65 LEU cc_start: 0.7402 (mt) cc_final: 0.6838 (mp)
REVERT: A   72 TYR cc_start: 0.6654 (m-80) cc_final: 0.5605 (m-80)
REVERT: A  245 LEU cc_start: 0.9360 (mt) cc_final: 0.9144 (mt)
REVERT: A  265 GLN cc_start: 0.9335 (mt0) cc_final: 0.9003 (mt0)
REVERT: A  793 ASP cc_start: 0.8786 (m-30) cc_final: 0.8451 (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: 0.6463 (mp)
REVERT: B   72 TYR cc_start: 0.6631 (m-80) cc_final: 0.6130 (m-80)
REVERT: B  245 LEU cc_start: 0.9361 (mt) cc_final: 0.9142 (mt)
REVERT: B  265 GLN cc_start: 0.9336 (mt0) cc_final: 0.8992 (mt0)
REVERT: B  793 ASP cc_start: 0.8783 (m-30) cc_final: 0.8457 (t0)
REVERT: C   65 LEU cc_start: 0.7303 (mt) cc_final: 0.6465 (mp)
REVERT: C   72 TYR cc_start: 0.6668 (m-80) cc_final: 0.6067 (m-80)
REVERT: C  245 LEU cc_start: 0.9382 (mt) cc_final: 0.9163 (mt)
REVERT: C  265 GLN cc_start: 0.9345 (mt0) cc_final: 0.9014 (mt0)
REVERT: C  793 ASP cc_start: 0.8782 (m-30) cc_final: 0.8428 (t0)
REVERT: D   65 LEU cc_start: 0.7403 (mt) cc_final: 0.6835 (mp)
REVERT: D   72 TYR cc_start: 0.6656 (m-80) cc_final: 0.6088 (m-80)
REVERT: D  245 LEU cc_start: 0.9362 (mt) cc_final: 0.9143 (mt)
REVERT: D  265 GLN cc_start: 0.9337 (mt0) cc_final: 0.9004 (mt0)
REVERT: D  793 ASP cc_start: 0.8780 (m-30) cc_final: 0.8455 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 416
  average time/residue: 0.2822
  time to fit residues: 149.1315
Evaluate side-chains
  226 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 1.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.1980
   chunk 84 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0060
   chunk 87 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 101 optimal weight:    0.0770
   overall best weight:    0.3954

-------------------------------------------------------------------------------
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  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 124 HIS
D 177 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.103400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.091179 restraints weight = 33727.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.092802 restraints weight = 24487.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.093957 restraints weight = 19019.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.4390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9288  Z= 0.216
  Angle     :  0.750   6.462  12480  Z= 0.384
  Chirality :  0.043   0.128   1420
  Planarity :  0.004   0.046   1612
  Dihedral  :  5.669  19.694   1248
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 14.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  :  9.74 %
    Favored  : 87.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.09 (0.22), residues: 1128
  helix: -0.02 (0.17), residues: 784
  sheet:  None (None), residues: 0
  loop : -4.76 (0.20), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS D 169 
 PHE   0.006   0.001   PHE A  43 
 TYR   0.013   0.001   TYR C 192 
 ARG   0.006   0.001   ARG A 116 

*********************** 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
  272 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 239
  time to evaluate  : 1.257 
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: A  174 GLU cc_start: 0.6955 (tp30) cc_final: 0.6518 (tp30)
REVERT: A  245 LEU cc_start: 0.9299 (mt) cc_final: 0.9097 (mt)
REVERT: A  793 ASP cc_start: 0.8722 (m-30) cc_final: 0.8476 (t0)
REVERT: A  794 LYS cc_start: 0.8898 (tptp) cc_final: 0.8532 (tppp)
REVERT: A  795 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8267 (mm-30)
REVERT: A  817 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8170 (mt-10)
REVERT: B  174 GLU cc_start: 0.6905 (tp30) cc_final: 0.6498 (tp30)
REVERT: B  245 LEU cc_start: 0.9282 (mt) cc_final: 0.9078 (mt)
REVERT: B  793 ASP cc_start: 0.8708 (m-30) cc_final: 0.8471 (t0)
REVERT: B  794 LYS cc_start: 0.8880 (tptp) cc_final: 0.8534 (tppp)
REVERT: B  795 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8214 (mm-30)
REVERT: C  174 GLU cc_start: 0.6902 (tp30) cc_final: 0.6483 (tp30)
REVERT: C  265 GLN cc_start: 0.9131 (mt0) cc_final: 0.8911 (mt0)
REVERT: C  793 ASP cc_start: 0.8724 (m-30) cc_final: 0.8487 (t0)
REVERT: C  794 LYS cc_start: 0.8893 (tptp) cc_final: 0.8531 (tppp)
REVERT: C  795 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8261 (mm-30)
REVERT: D  174 GLU cc_start: 0.6950 (tp30) cc_final: 0.6582 (tp30)
REVERT: D  245 LEU cc_start: 0.9290 (mt) cc_final: 0.9090 (mt)
REVERT: D  793 ASP cc_start: 0.8733 (m-30) cc_final: 0.8487 (t0)
REVERT: D  794 LYS cc_start: 0.8894 (tptp) cc_final: 0.8543 (tppp)
REVERT: D  795 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8246 (mm-30)
  outliers start: 33
  outliers final: 12
  residues processed: 265
  average time/residue: 0.2380
  time to fit residues: 84.5162
Evaluate side-chains
  175 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 163
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
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   79 GLN
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 58 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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  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 = 0.3868 r_free = 0.3868 target = 0.102270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.090598 restraints weight = 33109.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.092310 restraints weight = 23002.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.093554 restraints weight = 17286.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.5500

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= 0.251
  Angle     :  0.828  14.240  12480  Z= 0.406
  Chirality :  0.045   0.248   1420
  Planarity :  0.005   0.062   1612
  Dihedral  :  5.452  19.601   1248
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 17.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.11 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 12.89 %
    Favored  : 84.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.24), residues: 1128
  helix:  0.61 (0.18), residues: 784
  sheet:  None (None), residues: 0
  loop : -4.71 (0.19), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D 169 
 PHE   0.005   0.001   PHE D 193 
 TYR   0.017   0.001   TYR A  49 
 ARG   0.008   0.001   ARG B 815 

*********************** 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
  201 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 179
  time to evaluate  : 1.187 
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: 0.6969 (tp30) cc_final: 0.6541 (tp30)
REVERT: A  264 MET cc_start: 0.8533 (mmm) cc_final: 0.8190 (mmm)
REVERT: A  793 ASP cc_start: 0.8711 (m-30) cc_final: 0.8368 (t0)
REVERT: B  174 GLU cc_start: 0.6936 (tp30) cc_final: 0.6528 (tp30)
REVERT: B  264 MET cc_start: 0.8539 (mmm) cc_final: 0.8188 (mmm)
REVERT: B  793 ASP cc_start: 0.8694 (m-30) cc_final: 0.8353 (t0)
REVERT: C  174 GLU cc_start: 0.6935 (tp30) cc_final: 0.6517 (tp30)
REVERT: C  264 MET cc_start: 0.8453 (mmm) cc_final: 0.8115 (mmm)
REVERT: C  793 ASP cc_start: 0.8710 (m-30) cc_final: 0.8358 (t0)
REVERT: D  174 GLU cc_start: 0.6927 (tp30) cc_final: 0.6602 (tp30)
REVERT: D  178 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7832 (ptm)
REVERT: D  264 MET cc_start: 0.8493 (mmm) cc_final: 0.8163 (mmm)
REVERT: D  793 ASP cc_start: 0.8727 (m-30) cc_final: 0.8376 (t0)
  outliers start: 22
  outliers final: 9
  residues processed: 195
  average time/residue: 0.1780
  time to fit residues: 50.2954
Evaluate side-chains
  162 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 152
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
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   79 GLN
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 109 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 107 optimal weight:    8.9990
   chunk 58 optimal weight:    0.8980
   chunk 92 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 79 optimal weight:    8.9990
   chunk 85 optimal weight:    0.1980
   chunk 111 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0870
   overall best weight:    0.8362

-------------------------------------------------------------------------------
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  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  66 ASN
C  75 GLN
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.101511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.089782 restraints weight = 33378.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.091514 restraints weight = 23207.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.092733 restraints weight = 17439.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7504
moved from start:          0.5812

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= 0.211
  Angle     :  0.759  11.361  12480  Z= 0.384
  Chirality :  0.043   0.212   1420
  Planarity :  0.005   0.066   1612
  Dihedral  :  5.260  19.307   1248
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 12.89 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.25), residues: 1128
  helix:  0.90 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop : -4.56 (0.21), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 169 
 PHE   0.005   0.001   PHE B 193 
 TYR   0.010   0.001   TYR A  49 
 ARG   0.004   0.001   ARG A 815 

*********************** 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
  199 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 172
  time to evaluate  : 1.137 
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: 0.7024 (tp30) cc_final: 0.6504 (tp30)
REVERT: A  793 ASP cc_start: 0.8724 (m-30) cc_final: 0.8438 (t0)
REVERT: B  174 GLU cc_start: 0.6996 (tp30) cc_final: 0.6478 (tp30)
REVERT: B  264 MET cc_start: 0.8454 (mmm) cc_final: 0.8241 (mmm)
REVERT: B  793 ASP cc_start: 0.8689 (m-30) cc_final: 0.8427 (t0)
REVERT: C  174 GLU cc_start: 0.7056 (tp30) cc_final: 0.6566 (tp30)
REVERT: C  793 ASP cc_start: 0.8692 (m-30) cc_final: 0.8425 (t0)
REVERT: D  174 GLU cc_start: 0.6985 (tp30) cc_final: 0.6528 (tp30)
REVERT: D  793 ASP cc_start: 0.8736 (m-30) cc_final: 0.8434 (t0)
  outliers start: 27
  outliers final: 13
  residues processed: 196
  average time/residue: 0.1806
  time to fit residues: 51.2575
Evaluate side-chains
  168 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 155
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
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  788 LEU
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  788 LEU
Chi-restraints excluded: chain C residue   89 VAL
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   92 LEU
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 77 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   chunk 44 optimal weight:    0.1980
   chunk 67 optimal weight:    0.9980
   chunk 102 optimal weight:    0.7980
   chunk 90 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0870
   chunk 17 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0170
   chunk 96 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.4196

-------------------------------------------------------------------------------
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  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  75 GLN
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.103518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.091853 restraints weight = 32562.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.093593 restraints weight = 22602.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.094854 restraints weight = 16923.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start:          0.6056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9288  Z= 0.192
  Angle     :  0.748  12.181  12480  Z= 0.374
  Chirality :  0.044   0.300   1420
  Planarity :  0.004   0.038   1612
  Dihedral  :  5.071  18.531   1248
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 15.26 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.25), residues: 1128
  helix:  1.07 (0.19), residues: 784
  sheet:  None (None), residues: 0
  loop : -4.38 (0.22), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 169 
 PHE   0.007   0.001   PHE C 193 
 TYR   0.016   0.001   TYR B  72 
 ARG   0.004   0.000   ARG A 815 

*********************** 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
  212 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 192
  time to evaluate  : 1.073 
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: A  174 GLU cc_start: 0.7044 (tp30) cc_final: 0.6726 (tp30)
REVERT: A  793 ASP cc_start: 0.8707 (m-30) cc_final: 0.8400 (t0)
REVERT: B  174 GLU cc_start: 0.7035 (tp30) cc_final: 0.6705 (tp30)
REVERT: B  793 ASP cc_start: 0.8677 (m-30) cc_final: 0.8391 (t0)
REVERT: B  810 ASP cc_start: 0.7916 (p0) cc_final: 0.7598 (m-30)
REVERT: C  165 ILE cc_start: 0.9259 (mm) cc_final: 0.8798 (tt)
REVERT: C  174 GLU cc_start: 0.7051 (tp30) cc_final: 0.6738 (tp30)
REVERT: C  793 ASP cc_start: 0.8703 (m-30) cc_final: 0.8502 (t0)
REVERT: D  174 GLU cc_start: 0.7070 (tp30) cc_final: 0.6472 (tp30)
REVERT: D  793 ASP cc_start: 0.8691 (m-30) cc_final: 0.8465 (t0)
REVERT: D  810 ASP cc_start: 0.8020 (p0) cc_final: 0.7606 (m-30)
  outliers start: 20
  outliers final: 12
  residues processed: 207
  average time/residue: 0.1790
  time to fit residues: 54.0069
Evaluate side-chains
  162 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 1.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  788 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  265 GLN
Chi-restraints excluded: chain C residue  788 LEU
Chi-restraints excluded: chain D residue   87 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 9 optimal weight:    0.4980
   chunk 93 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 69 optimal weight:    0.1980
   chunk 77 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  68 ASN ** 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 = 0.3875 r_free = 0.3875 target = 0.101878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.089197 restraints weight = 33897.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.090971 restraints weight = 23808.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.092256 restraints weight = 18111.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.6382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9288  Z= 0.201
  Angle     :  0.785  12.757  12480  Z= 0.394
  Chirality :  0.045   0.335   1420
  Planarity :  0.004   0.033   1612
  Dihedral  :  4.942  18.165   1248
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 16.83 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.25), residues: 1128
  helix:  1.31 (0.19), residues: 784
  sheet:  None (None), residues: 0
  loop : -4.41 (0.21), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 169 
 PHE   0.004   0.001   PHE C 193 
 TYR   0.012   0.001   TYR C  72 
 ARG   0.003   0.000   ARG A 815 

*********************** 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
  195 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 170
  time to evaluate  : 1.079 
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: A  174 GLU cc_start: 0.7134 (tp30) cc_final: 0.6798 (tp30)
REVERT: A  793 ASP cc_start: 0.8714 (m-30) cc_final: 0.8459 (t0)
REVERT: A  795 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7974 (mp0)
REVERT: B  174 GLU cc_start: 0.7123 (tp30) cc_final: 0.6807 (tp30)
REVERT: B  264 MET cc_start: 0.8415 (mmm) cc_final: 0.8203 (mmm)
REVERT: B  773 THR cc_start: 0.5820 (p) cc_final: 0.5544 (t)
REVERT: B  793 ASP cc_start: 0.8680 (m-30) cc_final: 0.8443 (t0)
REVERT: B  795 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7999 (mp0)
REVERT: C  165 ILE cc_start: 0.9303 (mm) cc_final: 0.8851 (tt)
REVERT: C  174 GLU cc_start: 0.7131 (tp30) cc_final: 0.6875 (tp30)
REVERT: C  773 THR cc_start: 0.5561 (p) cc_final: 0.5345 (t)
REVERT: C  793 ASP cc_start: 0.8694 (m-30) cc_final: 0.8458 (t0)
REVERT: C  795 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7957 (mp0)
REVERT: D  174 GLU cc_start: 0.7107 (tp30) cc_final: 0.6723 (tp30)
REVERT: D  773 THR cc_start: 0.5708 (p) cc_final: 0.5458 (t)
REVERT: D  793 ASP cc_start: 0.8731 (m-30) cc_final: 0.8476 (t0)
REVERT: D  810 ASP cc_start: 0.8035 (p0) cc_final: 0.7701 (m-30)
  outliers start: 25
  outliers final: 12
  residues processed: 188
  average time/residue: 0.1774
  time to fit residues: 48.6455
Evaluate side-chains
  162 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 150
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
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  788 LEU
Chi-restraints excluded: chain C residue   87 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   87 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0370
   chunk 3 optimal weight:    6.9990
   chunk 109 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    1.1464

-------------------------------------------------------------------------------
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  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  84 ASN ** 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 = 0.3835 r_free = 0.3835 target = 0.099895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.087738 restraints weight = 34483.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.089399 restraints weight = 24424.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.090592 restraints weight = 18737.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.6602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9288  Z= 0.236
  Angle     :  0.800  12.974  12480  Z= 0.408
  Chirality :  0.046   0.353   1420
  Planarity :  0.004   0.034   1612
  Dihedral  :  4.978  19.580   1248
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 14.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.40 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.22 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.26), residues: 1128
  helix:  1.26 (0.19), residues: 784
  sheet:  None (None), residues: 0
  loop : -4.43 (0.21), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D 124 
 PHE   0.008   0.001   PHE C 193 
 TYR   0.015   0.001   TYR A  72 
 ARG   0.002   0.001   ARG C 101 

*********************** 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
  184 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 157
  time to evaluate  : 1.055 
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: A  174 GLU cc_start: 0.7138 (tp30) cc_final: 0.6801 (tp30)
REVERT: A  793 ASP cc_start: 0.8724 (m-30) cc_final: 0.8448 (t0)
REVERT: B  174 GLU cc_start: 0.7154 (tp30) cc_final: 0.6835 (tp30)
REVERT: B  793 ASP cc_start: 0.8685 (m-30) cc_final: 0.8442 (t0)
REVERT: C  165 ILE cc_start: 0.9289 (mm) cc_final: 0.8875 (tt)
REVERT: C  174 GLU cc_start: 0.7250 (tp30) cc_final: 0.6869 (tp30)
REVERT: C  793 ASP cc_start: 0.8698 (m-30) cc_final: 0.8457 (t0)
REVERT: D  793 ASP cc_start: 0.8746 (m-30) cc_final: 0.8471 (t0)
REVERT: D  795 GLU cc_start: 0.8217 (mp0) cc_final: 0.7831 (mp0)
  outliers start: 27
  outliers final: 12
  residues processed: 180
  average time/residue: 0.1737
  time to fit residues: 46.2153
Evaluate side-chains
  159 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 147
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
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  221 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 C residue  245 LEU
Chi-restraints excluded: chain D residue   87 LEU
Chi-restraints excluded: chain D residue   88 GLU
Chi-restraints excluded: chain D residue   92 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 8 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 97 optimal weight:    0.0980
   chunk 17 optimal weight:    0.9980
   chunk 22 optimal weight:    7.9990
   chunk 16 optimal weight:    0.0040
   chunk 51 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    0.5992

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.101422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.089233 restraints weight = 35012.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.091019 restraints weight = 24348.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.092296 restraints weight = 18210.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.6723

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= 0.211
  Angle     :  0.818  13.439  12480  Z= 0.410
  Chirality :  0.047   0.333   1420
  Planarity :  0.004   0.033   1612
  Dihedral  :  4.906  18.542   1248
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.69 %
    Favored  : 91.31 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 19.00 %
    Favored  : 79.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.25), residues: 1128
  helix:  1.26 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop : -4.45 (0.21), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 169 
 PHE   0.004   0.001   PHE C 193 
 TYR   0.015   0.001   TYR D  72 
 ARG   0.002   0.000   ARG D 116 

*********************** 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
  180 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 160
  time to evaluate  : 1.166 
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: A  174 GLU cc_start: 0.7146 (tp30) cc_final: 0.6501 (tp30)
REVERT: A  795 GLU cc_start: 0.8178 (mp0) cc_final: 0.7917 (mp0)
REVERT: B  174 GLU cc_start: 0.7144 (tp30) cc_final: 0.6493 (tp30)
REVERT: C  165 ILE cc_start: 0.9290 (mm) cc_final: 0.8880 (tt)
REVERT: C  174 GLU cc_start: 0.7202 (tp30) cc_final: 0.6494 (tp30)
REVERT: D  793 ASP cc_start: 0.8718 (m-30) cc_final: 0.8473 (t0)
REVERT: D  795 GLU cc_start: 0.8294 (mp0) cc_final: 0.7818 (mp0)
  outliers start: 20
  outliers final: 13
  residues processed: 178
  average time/residue: 0.1980
  time to fit residues: 50.8397
Evaluate side-chains
  160 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 147
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain B residue   84 ASN
Chi-restraints excluded: chain B residue   88 GLU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  161 ILE
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain D residue   87 LEU
Chi-restraints excluded: chain D residue   88 GLU
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 39 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9990
   chunk 37 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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  76 ASN ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.100509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.088492 restraints weight = 33869.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.090123 restraints weight = 24062.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.091319 restraints weight = 18377.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.6873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9288  Z= 0.232
  Angle     :  0.859  13.769  12480  Z= 0.429
  Chirality :  0.048   0.364   1420
  Planarity :  0.004   0.034   1612
  Dihedral  :  4.906  18.062   1248
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 19.78 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.26), residues: 1128
  helix:  1.24 (0.19), residues: 788
  sheet:  None (None), residues: 0
  loop : -4.47 (0.22), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS D  86 
 PHE   0.009   0.001   PHE C 193 
 TYR   0.019   0.001   TYR A  72 
 ARG   0.004   0.000   ARG C 188 

*********************** 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
  176 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 150
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 TYR cc_start: 0.6374 (m-10) cc_final: 0.4883 (m-10)
REVERT: A  174 GLU cc_start: 0.7090 (tp30) cc_final: 0.6764 (tp30)
REVERT: A  795 GLU cc_start: 0.8155 (mp0) cc_final: 0.7903 (mp0)
REVERT: B  174 GLU cc_start: 0.7069 (tp30) cc_final: 0.6771 (tp30)
REVERT: B  795 GLU cc_start: 0.8164 (mp0) cc_final: 0.7942 (mp0)
REVERT: C  165 ILE cc_start: 0.9308 (mm) cc_final: 0.8969 (tt)
REVERT: C  174 GLU cc_start: 0.7126 (tp30) cc_final: 0.6797 (tp30)
REVERT: C  795 GLU cc_start: 0.8124 (mp0) cc_final: 0.7889 (mp0)
REVERT: D  793 ASP cc_start: 0.8752 (m-30) cc_final: 0.8502 (t0)
REVERT: D  795 GLU cc_start: 0.8362 (mp0) cc_final: 0.7910 (mp0)
  outliers start: 26
  outliers final: 19
  residues processed: 173
  average time/residue: 0.1701
  time to fit residues: 42.9847
Evaluate side-chains
  163 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
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  245 LEU
Chi-restraints excluded: chain A residue  788 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  221 LEU
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain C residue   88 GLU
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain C residue  161 ILE
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain D residue   87 LEU
Chi-restraints excluded: chain D residue   88 GLU
Chi-restraints excluded: chain D residue   92 LEU
Chi-restraints excluded: chain D residue  245 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 102 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    0.5980
   chunk 91 optimal weight:    0.0970
   chunk 30 optimal weight:    2.9990
   chunk 92 optimal weight:    0.7980
   chunk 43 optimal weight:    0.4980
   chunk 98 optimal weight:    0.0060
   chunk 58 optimal weight:    4.9990
   overall best weight:    0.3794

-------------------------------------------------------------------------------
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 800 ASN
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 ASN
C 800 ASN
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 = 0.3843 r_free = 0.3843 target = 0.101746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.089817 restraints weight = 34218.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.091543 restraints weight = 24122.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.092805 restraints weight = 18225.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.6994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9288  Z= 0.223
  Angle     :  0.879  14.257  12480  Z= 0.429
  Chirality :  0.049   0.338   1420
  Planarity :  0.004   0.033   1612
  Dihedral  :  4.860  30.520   1248
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.04 %
    Favored  : 90.96 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 20.47 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.25), residues: 1128
  helix:  1.31 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop : -4.51 (0.21), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 169 
 PHE   0.011   0.001   PHE C 269 
 TYR   0.024   0.001   TYR A  49 
 ARG   0.005   0.000   ARG C 188 

********************** 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
  185 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 163
  time to evaluate  : 0.913 
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  174 GLU cc_start: 0.7050 (tp30) cc_final: 0.6725 (tp30)
REVERT: A  795 GLU cc_start: 0.8174 (mp0) cc_final: 0.7895 (mp0)
REVERT: B  174 GLU cc_start: 0.7046 (tp30) cc_final: 0.6715 (tp30)
REVERT: B  795 GLU cc_start: 0.8144 (mp0) cc_final: 0.7908 (mp0)
REVERT: C  165 ILE cc_start: 0.9289 (mm) cc_final: 0.8951 (tt)
REVERT: C  174 GLU cc_start: 0.7090 (tp30) cc_final: 0.6682 (tp30)
REVERT: C  795 GLU cc_start: 0.8140 (mp0) cc_final: 0.7878 (mp0)
REVERT: D  793 ASP cc_start: 0.8688 (m-30) cc_final: 0.8461 (t0)
REVERT: D  795 GLU cc_start: 0.8390 (mp0) cc_final: 0.7900 (mp0)
  outliers start: 22
  outliers final: 16
  residues processed: 183
  average time/residue: 0.1888
  time to fit residues: 49.3719
Evaluate side-chains
  160 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 1.253 
-------------------------------------------------------------------------------
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  245 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain B residue   88 GLU
Chi-restraints excluded: chain B residue   92 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  245 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  161 ILE
Chi-restraints excluded: chain D residue   87 LEU
Chi-restraints excluded: chain D residue   88 GLU
Chi-restraints excluded: chain D residue  245 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 1 optimal weight:    0.7980
   chunk 23 optimal weight:    6.9990
   chunk 11 optimal weight:    0.9980
   chunk 102 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 98 optimal weight:    0.0770
   chunk 0 optimal weight:    3.9990
   chunk 111 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.7740

-------------------------------------------------------------------------------
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**
** C  76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 ASN
C 800 ASN
** 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 = 0.3833 r_free = 0.3833 target = 0.100869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.088760 restraints weight = 34817.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.090500 restraints weight = 24221.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.091790 restraints weight = 18158.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.7081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9288  Z= 0.233
  Angle     :  0.865  13.779  12480  Z= 0.426
  Chirality :  0.048   0.312   1420
  Planarity :  0.004   0.033   1612
  Dihedral  :  4.801  24.309   1248
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.75 %
    Favored  : 90.25 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 21.36 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.26), residues: 1128
  helix:  1.39 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop : -4.49 (0.22), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 124 
 PHE   0.017   0.001   PHE C 193 
 TYR   0.025   0.001   TYR A  49 
 ARG   0.011   0.001   ARG D 188 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2542.24 seconds
wall clock time: 46 minutes 49.19 seconds (2809.19 seconds total)