Starting phenix.real_space_refine
on Wed Mar 12 00:15:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7shs_25135/03_2025/7shs_25135.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7shs_25135/03_2025/7shs_25135.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7shs_25135/03_2025/7shs_25135.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7shs_25135/03_2025/7shs_25135.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7shs_25135/03_2025/7shs_25135.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7shs_25135/03_2025/7shs_25135.cif"
  }
  resolution = 4.1
  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=   0.001 sd=   0.038
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      48      5.16       5
     C    4545      2.51       5
     N    1092      2.21       5
     O    1188      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6873
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2291
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2291
          Classifications: {'peptide': 283}
          Link IDs: {'PTRANS': 8, 'TRANS': 274}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 4.12, per 1000 atoms: 0.60
  Number of scatterers: 6873
  At special positions: 0
  Unit cell: (90.96, 81.864, 84.138, 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      48     16.00
     O    1188      8.00
     N    1092      7.00
     C    4545      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.71
  Conformation dependent library (CDL) restraints added in 916.4 milliseconds
  

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1560

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 0 sheets defined
      76.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 20
    Processing helix  chain 'A' and resid 26 through 53
    Processing helix  chain 'A' and resid 63 through 68
      removed outlier: 3.615A  pdb=" N   TYR A  67 " --> pdb=" O   PHE A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 71
      No H-bonds generated for 'chain 'A' and resid 69 through 71'
    Processing helix  chain 'A' and resid 72 through 95
      removed outlier: 3.807A  pdb=" N   GLY A  87 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 5.209A  pdb=" N   LYS A  88 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 117
      removed outlier: 3.574A  pdb=" N   MET A 117 " --> pdb=" O   ALA A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 131
      removed outlier: 3.843A  pdb=" N   LEU A 131 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 159
      removed outlier: 3.743A  pdb=" N   CYS A 139 " --> pdb=" O   TYR A 135 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   SER A 140 " --> pdb=" O   ARG A 136 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLU A 158 " --> pdb=" O   GLU A 154 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY A 159 " --> pdb=" O   PHE A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 163
    Processing helix  chain 'A' and resid 164 through 199
      removed outlier: 3.920A  pdb=" N   TYR A 168 " --> pdb=" O   ARG A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 222
    Processing helix  chain 'A' and resid 224 through 233
      removed outlier: 3.845A  pdb=" N   LEU A 228 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 269
      removed outlier: 3.587A  pdb=" N   ALA A 248 " --> pdb=" O   TRP A 244 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   CYS A 259 " --> pdb=" O   VAL A 255 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   TYR A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 283
    Processing helix  chain 'B' and resid 15 through 20
    Processing helix  chain 'B' and resid 26 through 53
    Processing helix  chain 'B' and resid 63 through 68
      removed outlier: 3.615A  pdb=" N   TYR B  67 " --> pdb=" O   PHE B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 71
      No H-bonds generated for 'chain 'B' and resid 69 through 71'
    Processing helix  chain 'B' and resid 72 through 95
      removed outlier: 3.807A  pdb=" N   GLY B  87 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
      removed outlier: 5.209A  pdb=" N   LYS B  88 " --> pdb=" O   SER B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 117
      removed outlier: 3.574A  pdb=" N   MET B 117 " --> pdb=" O   ALA B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 131
      removed outlier: 3.844A  pdb=" N   LEU B 131 " --> pdb=" O   LEU B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 159
      removed outlier: 3.744A  pdb=" N   CYS B 139 " --> pdb=" O   TYR B 135 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   SER B 140 " --> pdb=" O   ARG B 136 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLU B 158 " --> pdb=" O   GLU B 154 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY B 159 " --> pdb=" O   PHE B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 163
    Processing helix  chain 'B' and resid 164 through 199
      removed outlier: 3.920A  pdb=" N   TYR B 168 " --> pdb=" O   ARG B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 222
    Processing helix  chain 'B' and resid 224 through 233
      removed outlier: 3.846A  pdb=" N   LEU B 228 " --> pdb=" O   ILE B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 269
      removed outlier: 3.587A  pdb=" N   ALA B 248 " --> pdb=" O   TRP B 244 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   CYS B 259 " --> pdb=" O   VAL B 255 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   TYR B 260 " --> pdb=" O   ALA B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 283
    Processing helix  chain 'C' and resid 15 through 20
    Processing helix  chain 'C' and resid 26 through 53
    Processing helix  chain 'C' and resid 63 through 68
      removed outlier: 3.615A  pdb=" N   TYR C  67 " --> pdb=" O   PHE C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 71
      No H-bonds generated for 'chain 'C' and resid 69 through 71'
    Processing helix  chain 'C' and resid 72 through 95
      removed outlier: 3.808A  pdb=" N   GLY C  87 " --> pdb=" O   LEU C  83 " (cutoff:3.500A)
      removed outlier: 5.210A  pdb=" N   LYS C  88 " --> pdb=" O   SER C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 117
      removed outlier: 3.573A  pdb=" N   MET C 117 " --> pdb=" O   ALA C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 131
      removed outlier: 3.844A  pdb=" N   LEU C 131 " --> pdb=" O   LEU C 127 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 135 through 159
      removed outlier: 3.744A  pdb=" N   CYS C 139 " --> pdb=" O   TYR C 135 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   SER C 140 " --> pdb=" O   ARG C 136 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLU C 158 " --> pdb=" O   GLU C 154 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY C 159 " --> pdb=" O   PHE C 155 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 160 through 163
    Processing helix  chain 'C' and resid 164 through 199
      removed outlier: 3.920A  pdb=" N   TYR C 168 " --> pdb=" O   ARG C 164 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 205 through 222
    Processing helix  chain 'C' and resid 224 through 233
      removed outlier: 3.845A  pdb=" N   LEU C 228 " --> pdb=" O   ILE C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 269
      removed outlier: 3.588A  pdb=" N   ALA C 248 " --> pdb=" O   TRP C 244 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   CYS C 259 " --> pdb=" O   VAL C 255 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   TYR C 260 " --> pdb=" O   ALA C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 283

    447 hydrogen bonds defined for protein.
    1323 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.75

  Time building geometry restraints manager: 2.04 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2076
        1.35 -     1.46: 2092
        1.46 -     1.58: 2864
        1.58 -     1.70: 0
        1.70 -     1.81: 72
  Bond restraints: 7104
  Sorted by residual:
  bond pdb=" CB  MET C  82 "
       pdb=" CG  MET C  82 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.93e-01
  bond pdb=" CB  MET A  82 "
       pdb=" CG  MET A  82 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 9.90e-01
  bond pdb=" CB  MET B  82 "
       pdb=" CG  MET B  82 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.49e-01
  bond pdb=" C   CYS B 120 "
       pdb=" N   PRO B 121 "
    ideal  model  delta    sigma   weight residual
    1.335  1.347 -0.012 1.36e-02 5.41e+03 7.28e-01
  bond pdb=" CB  MET C 186 "
       pdb=" CG  MET C 186 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 7.21e-01
  ... (remaining 7099 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 9402
        1.82 -     3.65: 201
        3.65 -     5.47: 24
        5.47 -     7.30: 12
        7.30 -     9.12: 21
  Bond angle restraints: 9660
  Sorted by residual:
  angle pdb=" CB  MET B  82 "
        pdb=" CG  MET B  82 "
        pdb=" SD  MET B  82 "
      ideal   model   delta    sigma   weight residual
     112.70  121.82   -9.12 3.00e+00 1.11e-01 9.25e+00
  angle pdb=" CB  MET A  82 "
        pdb=" CG  MET A  82 "
        pdb=" SD  MET A  82 "
      ideal   model   delta    sigma   weight residual
     112.70  121.80   -9.10 3.00e+00 1.11e-01 9.21e+00
  angle pdb=" CB  MET C  82 "
        pdb=" CG  MET C  82 "
        pdb=" SD  MET C  82 "
      ideal   model   delta    sigma   weight residual
     112.70  121.79   -9.09 3.00e+00 1.11e-01 9.17e+00
  angle pdb=" CB  MET B  16 "
        pdb=" CG  MET B  16 "
        pdb=" SD  MET B  16 "
      ideal   model   delta    sigma   weight residual
     112.70  120.62   -7.92 3.00e+00 1.11e-01 6.97e+00
  angle pdb=" CB  MET A  16 "
        pdb=" CG  MET A  16 "
        pdb=" SD  MET A  16 "
      ideal   model   delta    sigma   weight residual
     112.70  120.62   -7.92 3.00e+00 1.11e-01 6.96e+00
  ... (remaining 9655 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 3602
       17.70 -    35.40: 301
       35.40 -    53.11: 36
       53.11 -    70.81: 6
       70.81 -    88.51: 12
  Dihedral angle restraints: 3957
    sinusoidal: 1491
      harmonic: 2466
  Sorted by residual:
  dihedral pdb=" CA  ASP B 272 "
           pdb=" C   ASP B 272 "
           pdb=" N   GLU B 273 "
           pdb=" CA  GLU B 273 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.06  -15.94     0      5.00e+00 4.00e-02 1.02e+01
  dihedral pdb=" CA  ASP C 272 "
           pdb=" C   ASP C 272 "
           pdb=" N   GLU C 273 "
           pdb=" CA  GLU C 273 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.09  -15.91     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CA  ASP A 272 "
           pdb=" C   ASP A 272 "
           pdb=" N   GLU A 273 "
           pdb=" CA  GLU A 273 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.10  -15.90     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 3954 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 624
       0.029 -    0.058: 212
       0.058 -    0.087: 129
       0.087 -    0.116: 31
       0.116 -    0.145: 9
  Chirality restraints: 1005
  Sorted by residual:
  chirality pdb=" CA  ASP A 253 "
            pdb=" N   ASP A 253 "
            pdb=" C   ASP A 253 "
            pdb=" CB  ASP A 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.15 2.00e-01 2.50e+01 5.29e-01
  chirality pdb=" CA  ASP B 253 "
            pdb=" N   ASP B 253 "
            pdb=" C   ASP B 253 "
            pdb=" CB  ASP B 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.21e-01
  chirality pdb=" CA  ASP C 253 "
            pdb=" N   ASP C 253 "
            pdb=" C   ASP C 253 "
            pdb=" CB  ASP C 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.14e-01
  ... (remaining 1002 not shown)

  Planarity restraints: 1206
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 223 "    0.014 2.00e-02 2.50e+03   1.49e-02 5.51e+00
        pdb=" CG  TRP C 223 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 223 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 223 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 223 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 223 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 223 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 223 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 223 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 223 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 223 "    0.014 2.00e-02 2.50e+03   1.48e-02 5.50e+00
        pdb=" CG  TRP B 223 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 223 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 223 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 223 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 223 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 223 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 223 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 223 "    0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 223 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 223 "   -0.014 2.00e-02 2.50e+03   1.47e-02 5.39e+00
        pdb=" CG  TRP A 223 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 223 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 223 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 223 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 223 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 223 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 223 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 223 "   -0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 223 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1203 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 2536
        2.86 -     3.37: 7146
        3.37 -     3.88: 11704
        3.88 -     4.39: 12583
        4.39 -     4.90: 21034
  Nonbonded interactions: 55003
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A  69 "
            pdb=" N   ARG B 136 "
     model   vdw
     2.349 3.120
  nonbonded pdb=" O   ASP A 242 "
            pdb=" OG1 THR A 245 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" O   ASP C 242 "
            pdb=" OG1 THR C 245 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" O   ASP B 242 "
            pdb=" OG1 THR B 245 "
     model   vdw
     2.355 3.040
  nonbonded pdb=" OE1 GLN C 192 "
            pdb=" NH2 ARG C 195 "
     model   vdw
     2.388 3.120
  ... (remaining 54998 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.740
  Find NCS groups from input model:        0.120
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7104  Z= 0.174
  Angle     :  0.740   9.123   9660  Z= 0.370
  Chirality :  0.040   0.145   1005
  Planarity :  0.005   0.050   1206
  Dihedral  : 13.648  88.509   2397
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.27), residues: 843
  helix:  0.85 (0.20), residues: 615
  sheet:  None (None), residues: 0
  loop : -0.26 (0.40), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP C 223 
 HIS   0.001   0.000   HIS C 210 
 PHE   0.014   0.001   PHE C 276 
 TYR   0.026   0.001   TYR A 156 
 ARG   0.002   0.000   ARG B  55 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.707 
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   10 MET cc_start: 0.8266 (pmm) cc_final: 0.7989 (ppp)
REVERT: A  126 ASP cc_start: 0.8657 (t0) cc_final: 0.8269 (t0)
REVERT: A  158 GLU cc_start: 0.8676 (tp30) cc_final: 0.8259 (tm-30)
REVERT: A  177 TRP cc_start: 0.8306 (m100) cc_final: 0.8093 (m100)
REVERT: A  250 CYS cc_start: 0.8771 (m) cc_final: 0.8270 (m)
REVERT: B   34 TRP cc_start: 0.6187 (m-10) cc_final: 0.5752 (m100)
REVERT: B  182 TYR cc_start: 0.6720 (t80) cc_final: 0.6194 (t80)
REVERT: B  240 ILE cc_start: 0.7110 (pt) cc_final: 0.6806 (tp)
REVERT: B  246 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7445 (pp20)
REVERT: B  254 ILE cc_start: 0.8982 (mm) cc_final: 0.8611 (mm)
REVERT: B  260 TYR cc_start: 0.7404 (t80) cc_final: 0.7027 (t80)
REVERT: C   70 GLU cc_start: 0.8353 (pm20) cc_final: 0.7873 (pm20)
REVERT: C   72 ASN cc_start: 0.8193 (m-40) cc_final: 0.7823 (m-40)
REVERT: C  130 GLN cc_start: 0.8802 (mm110) cc_final: 0.8102 (mm110)
REVERT: C  246 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7804 (mm-30)
REVERT: C  251 VAL cc_start: 0.9084 (m) cc_final: 0.8870 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.2386
  time to fit residues: 68.3582
Evaluate side-chains
  125 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    7.9990
   chunk 63 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 25 optimal weight:    8.9990
   chunk 40 optimal weight:    0.0020
   chunk 49 optimal weight:    3.9990
   chunk 76 optimal weight:    9.9990
   overall best weight:    2.5996

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

Flipped N/Q/H residues before XYZ refinement:
** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 201 GLN
B   9 GLN
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 281 GLN
C 249 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.075803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.067598 restraints weight = 30269.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.069433 restraints weight = 18525.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.070781 restraints weight = 12535.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.3698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7104  Z= 0.212
  Angle     :  0.577   6.791   9660  Z= 0.307
  Chirality :  0.040   0.139   1005
  Planarity :  0.005   0.049   1206
  Dihedral  :  3.982  18.617    942
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  5.13 %
    Favored  : 94.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.29), residues: 843
  helix:  1.72 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop :  0.65 (0.44), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP C 230 
 HIS   0.004   0.001   HIS C 249 
 PHE   0.021   0.002   PHE B 226 
 TYR   0.018   0.002   TYR C 193 
 ARG   0.004   0.001   ARG C 164 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8532 (pmm) cc_final: 0.8092 (ppp)
REVERT: A  126 ASP cc_start: 0.9024 (t0) cc_final: 0.8733 (t0)
REVERT: A  131 LEU cc_start: 0.9380 (tp) cc_final: 0.9106 (tp)
REVERT: A  250 CYS cc_start: 0.8520 (m) cc_final: 0.8299 (m)
REVERT: B   34 TRP cc_start: 0.6318 (m-10) cc_final: 0.5783 (m100)
REVERT: B   40 LEU cc_start: 0.9104 (mp) cc_final: 0.8505 (tp)
REVERT: B   82 MET cc_start: 0.8460 (ttp) cc_final: 0.8013 (ttp)
REVERT: B  110 ASN cc_start: 0.8797 (p0) cc_final: 0.7949 (p0)
REVERT: B  117 MET cc_start: 0.8801 (mmp) cc_final: 0.8389 (mmm)
REVERT: B  210 HIS cc_start: 0.7362 (m90) cc_final: 0.7064 (m90)
REVERT: B  246 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7524 (pp20)
REVERT: B  257 LYS cc_start: 0.8200 (mptt) cc_final: 0.7900 (mmmm)
REVERT: B  260 TYR cc_start: 0.7525 (t80) cc_final: 0.6938 (t80)
REVERT: C   71 GLN cc_start: 0.8212 (tm-30) cc_final: 0.7914 (tm-30)
REVERT: C   72 ASN cc_start: 0.8523 (m-40) cc_final: 0.8015 (m-40)
REVERT: C   88 LYS cc_start: 0.8649 (mtmm) cc_final: 0.8236 (mtmm)
REVERT: C   94 LEU cc_start: 0.7849 (mt) cc_final: 0.7190 (mt)
REVERT: C  130 GLN cc_start: 0.8801 (mm110) cc_final: 0.8067 (mm110)
REVERT: C  131 LEU cc_start: 0.9211 (tp) cc_final: 0.8945 (tp)
REVERT: C  171 TYR cc_start: 0.7629 (t80) cc_final: 0.7212 (t80)
REVERT: C  175 CYS cc_start: 0.8790 (m) cc_final: 0.8215 (p)
REVERT: C  246 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8103 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1508
  time to fit residues: 32.9252
Evaluate side-chains
  109 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 67 optimal weight:    7.9990
   chunk 17 optimal weight:    5.9990
   chunk 70 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 43 optimal weight:    8.9990
   chunk 68 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   9 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.075026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.067163 restraints weight = 33112.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.069036 restraints weight = 19492.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.070330 restraints weight = 13024.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.4620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7104  Z= 0.201
  Angle     :  0.562   6.550   9660  Z= 0.295
  Chirality :  0.040   0.140   1005
  Planarity :  0.004   0.053   1206
  Dihedral  :  3.970  18.523    942
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.56 %
    Favored  : 97.29 %
  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:  2.08 (0.30), residues: 843
  helix:  1.79 (0.21), residues: 606
  sheet:  None (None), residues: 0
  loop :  0.46 (0.46), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 177 
 HIS   0.005   0.001   HIS C 249 
 PHE   0.016   0.002   PHE B 226 
 TYR   0.018   0.002   TYR C  46 
 ARG   0.003   0.001   ARG C 136 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8603 (pmm) cc_final: 0.8150 (ppp)
REVERT: A  126 ASP cc_start: 0.9055 (t0) cc_final: 0.8749 (t0)
REVERT: A  131 LEU cc_start: 0.9426 (tp) cc_final: 0.9117 (tp)
REVERT: B   10 MET cc_start: 0.8623 (mtm) cc_final: 0.8202 (mmt)
REVERT: B   34 TRP cc_start: 0.6159 (m-10) cc_final: 0.5800 (m100)
REVERT: B   40 LEU cc_start: 0.9162 (mp) cc_final: 0.8818 (tp)
REVERT: B   82 MET cc_start: 0.8547 (ttp) cc_final: 0.8067 (ttm)
REVERT: B  108 PHE cc_start: 0.7860 (t80) cc_final: 0.7431 (t80)
REVERT: B  110 ASN cc_start: 0.8680 (p0) cc_final: 0.7669 (t0)
REVERT: B  117 MET cc_start: 0.8886 (mmp) cc_final: 0.8427 (mmm)
REVERT: B  123 LEU cc_start: 0.9338 (mt) cc_final: 0.8944 (tt)
REVERT: B  210 HIS cc_start: 0.7436 (m90) cc_final: 0.7036 (m170)
REVERT: B  257 LYS cc_start: 0.8277 (mptt) cc_final: 0.7964 (mmmm)
REVERT: B  260 TYR cc_start: 0.7600 (t80) cc_final: 0.7187 (t80)
REVERT: C   82 MET cc_start: 0.8540 (ttp) cc_final: 0.8185 (ttp)
REVERT: C   88 LYS cc_start: 0.8671 (mtmm) cc_final: 0.8299 (mtmm)
REVERT: C   94 LEU cc_start: 0.7765 (mt) cc_final: 0.7099 (mt)
REVERT: C  108 PHE cc_start: 0.7798 (t80) cc_final: 0.7448 (t80)
REVERT: C  117 MET cc_start: 0.8684 (mmp) cc_final: 0.7744 (tpp)
REVERT: C  127 LEU cc_start: 0.8810 (pp) cc_final: 0.8558 (pp)
REVERT: C  130 GLN cc_start: 0.8714 (mm110) cc_final: 0.7968 (mm110)
REVERT: C  148 MET cc_start: 0.8802 (ttp) cc_final: 0.8253 (ttp)
REVERT: C  171 TYR cc_start: 0.8017 (t80) cc_final: 0.7100 (t80)
REVERT: C  175 CYS cc_start: 0.8827 (m) cc_final: 0.8562 (p)
REVERT: C  230 TRP cc_start: 0.8702 (t60) cc_final: 0.7316 (t60)
REVERT: C  260 TYR cc_start: 0.7604 (t80) cc_final: 0.7394 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1454
  time to fit residues: 30.2829
Evaluate side-chains
  108 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 23 optimal weight:    8.9990
   chunk 4 optimal weight:    9.9990
   chunk 78 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 80 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 10 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
B   9 GLN
** C  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 192 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.072419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.064178 restraints weight = 32608.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.065962 restraints weight = 19602.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.067295 restraints weight = 13269.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.5276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7104  Z= 0.196
  Angle     :  0.553   7.197   9660  Z= 0.292
  Chirality :  0.040   0.136   1005
  Planarity :  0.004   0.045   1206
  Dihedral  :  4.032  19.173    942
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.42 %
    Favored  : 96.44 %
  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:  2.04 (0.30), residues: 843
  helix:  1.76 (0.21), residues: 606
  sheet:  None (None), residues: 0
  loop :  0.45 (0.46), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 177 
 HIS   0.006   0.001   HIS C 249 
 PHE   0.016   0.002   PHE B 226 
 TYR   0.018   0.002   TYR C  46 
 ARG   0.003   0.000   ARG B 164 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8568 (pmm) cc_final: 0.8148 (ppp)
REVERT: A   55 ARG cc_start: 0.6087 (mmt180) cc_final: 0.5429 (mmp80)
REVERT: A  126 ASP cc_start: 0.9058 (t0) cc_final: 0.8763 (t0)
REVERT: A  131 LEU cc_start: 0.9426 (tp) cc_final: 0.9058 (tp)
REVERT: A  176 PHE cc_start: 0.8574 (t80) cc_final: 0.8291 (t80)
REVERT: B    9 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7100 (pp30)
REVERT: B   10 MET cc_start: 0.8192 (mtm) cc_final: 0.7754 (mmt)
REVERT: B   82 MET cc_start: 0.8612 (ttp) cc_final: 0.8377 (ttp)
REVERT: B  108 PHE cc_start: 0.8074 (t80) cc_final: 0.7629 (t80)
REVERT: B  110 ASN cc_start: 0.8482 (p0) cc_final: 0.7740 (t0)
REVERT: B  117 MET cc_start: 0.8768 (mmp) cc_final: 0.8325 (mmm)
REVERT: B  210 HIS cc_start: 0.7620 (m90) cc_final: 0.7281 (m170)
REVERT: B  257 LYS cc_start: 0.8229 (mptt) cc_final: 0.7972 (mmmm)
REVERT: B  260 TYR cc_start: 0.7359 (t80) cc_final: 0.7062 (t80)
REVERT: C   82 MET cc_start: 0.8508 (ttp) cc_final: 0.8247 (ttp)
REVERT: C   88 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8053 (mtmm)
REVERT: C   94 LEU cc_start: 0.7687 (mt) cc_final: 0.6975 (mt)
REVERT: C  108 PHE cc_start: 0.7478 (t80) cc_final: 0.7227 (t80)
REVERT: C  130 GLN cc_start: 0.8631 (mm110) cc_final: 0.7988 (mm110)
REVERT: C  148 MET cc_start: 0.8846 (ttp) cc_final: 0.8594 (ttm)
REVERT: C  171 TYR cc_start: 0.8352 (t80) cc_final: 0.7831 (t80)
REVERT: C  175 CYS cc_start: 0.8807 (m) cc_final: 0.8583 (p)
REVERT: C  176 PHE cc_start: 0.8645 (t80) cc_final: 0.8436 (t80)
REVERT: C  246 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8132 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1521
  time to fit residues: 30.5081
Evaluate side-chains
  112 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 72 optimal weight:    7.9990
   chunk 6 optimal weight:    3.9990
   chunk 22 optimal weight:    0.4980
   chunk 52 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 34 optimal weight:    9.9990
   chunk 49 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9980
   chunk 20 optimal weight:   10.0000
   overall best weight:    1.8986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.072167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.063886 restraints weight = 32044.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.065783 restraints weight = 19233.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.067104 restraints weight = 12894.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.5481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7104  Z= 0.159
  Angle     :  0.532   7.412   9660  Z= 0.278
  Chirality :  0.039   0.139   1005
  Planarity :  0.003   0.042   1206
  Dihedral  :  3.855  17.601    942
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  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:  2.19 (0.30), residues: 843
  helix:  1.82 (0.21), residues: 609
  sheet:  None (None), residues: 0
  loop :  0.64 (0.47), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 223 
 HIS   0.007   0.001   HIS C 210 
 PHE   0.012   0.001   PHE C 276 
 TYR   0.016   0.001   TYR A 156 
 ARG   0.002   0.000   ARG A  55 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8547 (pmm) cc_final: 0.8155 (ppp)
REVERT: A  126 ASP cc_start: 0.8999 (t0) cc_final: 0.8675 (t0)
REVERT: A  131 LEU cc_start: 0.9422 (tp) cc_final: 0.9082 (tp)
REVERT: A  176 PHE cc_start: 0.8617 (t80) cc_final: 0.8407 (t80)
REVERT: B   40 LEU cc_start: 0.9032 (mp) cc_final: 0.8823 (mp)
REVERT: B   82 MET cc_start: 0.8511 (ttp) cc_final: 0.8175 (ttp)
REVERT: B  108 PHE cc_start: 0.8133 (t80) cc_final: 0.7611 (t80)
REVERT: B  110 ASN cc_start: 0.8336 (p0) cc_final: 0.7724 (t0)
REVERT: B  117 MET cc_start: 0.8733 (mmp) cc_final: 0.8344 (mmm)
REVERT: B  210 HIS cc_start: 0.7641 (m90) cc_final: 0.7360 (m170)
REVERT: B  260 TYR cc_start: 0.7336 (t80) cc_final: 0.7030 (t80)
REVERT: C   16 MET cc_start: 0.8442 (mmp) cc_final: 0.7719 (tpp)
REVERT: C   82 MET cc_start: 0.8491 (ttp) cc_final: 0.8164 (ttp)
REVERT: C   88 LYS cc_start: 0.8550 (mtmm) cc_final: 0.8173 (mtmm)
REVERT: C   94 LEU cc_start: 0.7660 (mt) cc_final: 0.6923 (mt)
REVERT: C  108 PHE cc_start: 0.7348 (t80) cc_final: 0.7054 (t80)
REVERT: C  117 MET cc_start: 0.8535 (mmp) cc_final: 0.6477 (tmm)
REVERT: C  125 TYR cc_start: 0.8028 (t80) cc_final: 0.7689 (t80)
REVERT: C  130 GLN cc_start: 0.8653 (mm110) cc_final: 0.8004 (mm110)
REVERT: C  171 TYR cc_start: 0.8455 (t80) cc_final: 0.8031 (t80)
REVERT: C  175 CYS cc_start: 0.8960 (m) cc_final: 0.8534 (p)
REVERT: C  176 PHE cc_start: 0.8704 (t80) cc_final: 0.8373 (t80)
REVERT: C  246 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8117 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1494
  time to fit residues: 27.9509
Evaluate side-chains
  106 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 50 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 31 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0980
   chunk 10 optimal weight:    6.9990
   chunk 73 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.076579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.068741 restraints weight = 31176.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.070619 restraints weight = 17867.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.071945 restraints weight = 11847.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.5562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7104  Z= 0.137
  Angle     :  0.513   8.404   9660  Z= 0.259
  Chirality :  0.038   0.134   1005
  Planarity :  0.003   0.049   1206
  Dihedral  :  3.632  16.066    942
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  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:  2.47 (0.30), residues: 843
  helix:  1.92 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop :  1.08 (0.47), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 223 
 HIS   0.006   0.001   HIS C 210 
 PHE   0.013   0.001   PHE C 173 
 TYR   0.020   0.001   TYR A 156 
 ARG   0.002   0.000   ARG C 164 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8553 (pmm) cc_final: 0.8152 (ppp)
REVERT: A  126 ASP cc_start: 0.8943 (t0) cc_final: 0.8686 (t0)
REVERT: A  131 LEU cc_start: 0.9432 (tp) cc_final: 0.9063 (tp)
REVERT: B   40 LEU cc_start: 0.9034 (mp) cc_final: 0.8793 (tp)
REVERT: B   82 MET cc_start: 0.8423 (ttp) cc_final: 0.8107 (ttp)
REVERT: B  108 PHE cc_start: 0.8196 (t80) cc_final: 0.7574 (t80)
REVERT: B  110 ASN cc_start: 0.8320 (p0) cc_final: 0.7725 (t0)
REVERT: B  117 MET cc_start: 0.8682 (mmp) cc_final: 0.8349 (mmm)
REVERT: B  127 LEU cc_start: 0.8737 (tt) cc_final: 0.8472 (tp)
REVERT: B  210 HIS cc_start: 0.7387 (m90) cc_final: 0.7143 (m170)
REVERT: B  260 TYR cc_start: 0.7261 (t80) cc_final: 0.6777 (t80)
REVERT: C   82 MET cc_start: 0.8406 (ttp) cc_final: 0.7986 (ttp)
REVERT: C   88 LYS cc_start: 0.8540 (mtmm) cc_final: 0.8174 (mtmm)
REVERT: C   94 LEU cc_start: 0.7489 (mt) cc_final: 0.7096 (mt)
REVERT: C  117 MET cc_start: 0.8492 (mmp) cc_final: 0.7329 (tpp)
REVERT: C  123 LEU cc_start: 0.9191 (tt) cc_final: 0.8784 (tt)
REVERT: C  125 TYR cc_start: 0.8051 (t80) cc_final: 0.7687 (t80)
REVERT: C  127 LEU cc_start: 0.9179 (tt) cc_final: 0.8739 (mt)
REVERT: C  130 GLN cc_start: 0.8639 (mm110) cc_final: 0.7967 (mm110)
REVERT: C  148 MET cc_start: 0.8831 (ttp) cc_final: 0.8419 (ttp)
REVERT: C  171 TYR cc_start: 0.8438 (t80) cc_final: 0.7848 (t80)
REVERT: C  175 CYS cc_start: 0.8961 (m) cc_final: 0.8676 (p)
REVERT: C  246 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8090 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1519
  time to fit residues: 30.1909
Evaluate side-chains
  110 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 52 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0970
   chunk 54 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 50 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.4182

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.074706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.066794 restraints weight = 31409.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.068621 restraints weight = 18707.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.069893 restraints weight = 12565.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.5786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7104  Z= 0.144
  Angle     :  0.525   8.001   9660  Z= 0.269
  Chirality :  0.038   0.141   1005
  Planarity :  0.003   0.049   1206
  Dihedral  :  3.647  15.422    942
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  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:  2.31 (0.30), residues: 843
  helix:  1.74 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop :  1.15 (0.50), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 223 
 HIS   0.006   0.001   HIS C 210 
 PHE   0.011   0.001   PHE C 173 
 TYR   0.019   0.001   TYR A 156 
 ARG   0.002   0.000   ARG A  55 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8541 (pmm) cc_final: 0.8144 (ppp)
REVERT: A  126 ASP cc_start: 0.8997 (t0) cc_final: 0.8692 (t0)
REVERT: A  131 LEU cc_start: 0.9427 (tp) cc_final: 0.9051 (tp)
REVERT: A  257 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8667 (mmtm)
REVERT: B    9 GLN cc_start: 0.7787 (pp30) cc_final: 0.7381 (pp30)
REVERT: B  108 PHE cc_start: 0.8280 (t80) cc_final: 0.7643 (t80)
REVERT: B  110 ASN cc_start: 0.8282 (p0) cc_final: 0.7775 (t0)
REVERT: B  117 MET cc_start: 0.8695 (mmp) cc_final: 0.8334 (mmm)
REVERT: B  210 HIS cc_start: 0.7495 (m90) cc_final: 0.7273 (m170)
REVERT: B  260 TYR cc_start: 0.7143 (t80) cc_final: 0.6921 (t80)
REVERT: C   69 GLU cc_start: 0.8432 (pm20) cc_final: 0.7864 (mm-30)
REVERT: C   82 MET cc_start: 0.8422 (ttp) cc_final: 0.7996 (ttp)
REVERT: C   94 LEU cc_start: 0.7526 (mt) cc_final: 0.6983 (mt)
REVERT: C  117 MET cc_start: 0.8433 (mmp) cc_final: 0.7285 (tpp)
REVERT: C  123 LEU cc_start: 0.9219 (tt) cc_final: 0.8812 (tt)
REVERT: C  127 LEU cc_start: 0.9172 (tt) cc_final: 0.8727 (mt)
REVERT: C  130 GLN cc_start: 0.8677 (mm110) cc_final: 0.7993 (mm110)
REVERT: C  171 TYR cc_start: 0.8449 (t80) cc_final: 0.7992 (t80)
REVERT: C  175 CYS cc_start: 0.8965 (m) cc_final: 0.8555 (p)
REVERT: C  176 PHE cc_start: 0.8621 (t80) cc_final: 0.8333 (t80)
REVERT: C  246 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8123 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1593
  time to fit residues: 30.2802
Evaluate side-chains
  113 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 42 optimal weight:    9.9990
   chunk 20 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 75 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 33 optimal weight:   10.0000
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
B   9 GLN
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.073595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.065813 restraints weight = 31942.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.067662 restraints weight = 18566.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.068887 restraints weight = 12330.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.5973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7104  Z= 0.154
  Angle     :  0.537   8.414   9660  Z= 0.279
  Chirality :  0.039   0.152   1005
  Planarity :  0.004   0.050   1206
  Dihedral  :  3.687  15.117    942
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.85 %
    Favored  : 99.00 %
  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:  2.48 (0.30), residues: 843
  helix:  1.86 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  1.32 (0.48), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  34 
 HIS   0.007   0.001   HIS C 210 
 PHE   0.014   0.001   PHE A 276 
 TYR   0.021   0.001   TYR A 156 
 ARG   0.003   0.000   ARG C 277 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8520 (pmm) cc_final: 0.8125 (ppp)
REVERT: A  126 ASP cc_start: 0.8964 (t0) cc_final: 0.8668 (t0)
REVERT: A  131 LEU cc_start: 0.9427 (tp) cc_final: 0.9055 (tp)
REVERT: A  257 LYS cc_start: 0.9094 (mmtt) cc_final: 0.8699 (mmtm)
REVERT: B    9 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7608 (pp30)
REVERT: B   82 MET cc_start: 0.8513 (ttp) cc_final: 0.8109 (ttm)
REVERT: B  108 PHE cc_start: 0.8302 (t80) cc_final: 0.7786 (t80)
REVERT: B  110 ASN cc_start: 0.8247 (p0) cc_final: 0.7731 (t0)
REVERT: B  117 MET cc_start: 0.8697 (mmp) cc_final: 0.8275 (mmm)
REVERT: B  210 HIS cc_start: 0.7618 (m90) cc_final: 0.7391 (m170)
REVERT: B  260 TYR cc_start: 0.7208 (t80) cc_final: 0.6944 (t80)
REVERT: C   69 GLU cc_start: 0.8510 (pm20) cc_final: 0.7888 (mm-30)
REVERT: C   82 MET cc_start: 0.8431 (ttp) cc_final: 0.7985 (ttp)
REVERT: C   88 LYS cc_start: 0.8841 (mttt) cc_final: 0.8593 (mttp)
REVERT: C   94 LEU cc_start: 0.7520 (mt) cc_final: 0.7023 (mt)
REVERT: C  104 PHE cc_start: 0.9097 (t80) cc_final: 0.8870 (t80)
REVERT: C  117 MET cc_start: 0.8409 (mmp) cc_final: 0.7227 (tpp)
REVERT: C  123 LEU cc_start: 0.9215 (tt) cc_final: 0.8791 (tt)
REVERT: C  125 TYR cc_start: 0.7955 (t80) cc_final: 0.7628 (t80)
REVERT: C  127 LEU cc_start: 0.9200 (tt) cc_final: 0.8774 (mt)
REVERT: C  130 GLN cc_start: 0.8650 (mm110) cc_final: 0.8001 (mm110)
REVERT: C  171 TYR cc_start: 0.8489 (t80) cc_final: 0.8045 (t80)
REVERT: C  175 CYS cc_start: 0.8905 (m) cc_final: 0.8496 (p)
REVERT: C  176 PHE cc_start: 0.8737 (t80) cc_final: 0.8404 (t80)
REVERT: C  223 TRP cc_start: 0.8702 (m-90) cc_final: 0.8023 (m-90)
REVERT: C  246 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8185 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1507
  time to fit residues: 29.1396
Evaluate side-chains
  110 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 64 optimal weight:   10.0000
   chunk 78 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0270
   chunk 77 optimal weight:    6.9990
   chunk 31 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 50 optimal weight:    7.9990
   overall best weight:    0.7040

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

Flipped N/Q/H residues before XYZ refinement:
B 192 GLN
C 210 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.076288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.068362 restraints weight = 31431.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.070223 restraints weight = 18384.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.071509 restraints weight = 12265.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.5993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7104  Z= 0.127
  Angle     :  0.528   8.135   9660  Z= 0.267
  Chirality :  0.038   0.147   1005
  Planarity :  0.003   0.049   1206
  Dihedral  :  3.533  13.051    942
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  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:  2.34 (0.30), residues: 843
  helix:  1.80 (0.21), residues: 633
  sheet:  None (None), residues: 0
  loop :  1.04 (0.49), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 223 
 HIS   0.008   0.001   HIS C 210 
 PHE   0.013   0.001   PHE A 104 
 TYR   0.022   0.001   TYR A 156 
 ARG   0.003   0.000   ARG A  55 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 ASP cc_start: 0.8916 (t0) cc_final: 0.8609 (t0)
REVERT: A  131 LEU cc_start: 0.9434 (tp) cc_final: 0.9058 (tp)
REVERT: A  257 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8756 (mmtm)
REVERT: B   40 LEU cc_start: 0.9036 (tt) cc_final: 0.8495 (tt)
REVERT: B   82 MET cc_start: 0.8537 (ttp) cc_final: 0.8272 (ttm)
REVERT: B  108 PHE cc_start: 0.8446 (t80) cc_final: 0.7772 (t80)
REVERT: B  110 ASN cc_start: 0.8172 (p0) cc_final: 0.7751 (t0)
REVERT: B  117 MET cc_start: 0.8686 (mmp) cc_final: 0.8417 (mmm)
REVERT: B  127 LEU cc_start: 0.8689 (tt) cc_final: 0.8332 (tp)
REVERT: B  260 TYR cc_start: 0.7202 (t80) cc_final: 0.6619 (t80)
REVERT: C   69 GLU cc_start: 0.8442 (pm20) cc_final: 0.7789 (mm-30)
REVERT: C   82 MET cc_start: 0.8476 (ttp) cc_final: 0.7997 (ttp)
REVERT: C   94 LEU cc_start: 0.7547 (mt) cc_final: 0.7303 (mm)
REVERT: C  117 MET cc_start: 0.8383 (mmp) cc_final: 0.7113 (tpp)
REVERT: C  125 TYR cc_start: 0.7938 (t80) cc_final: 0.7599 (t80)
REVERT: C  130 GLN cc_start: 0.8604 (mm110) cc_final: 0.7925 (mm110)
REVERT: C  171 TYR cc_start: 0.8463 (t80) cc_final: 0.8012 (t80)
REVERT: C  175 CYS cc_start: 0.8908 (m) cc_final: 0.8533 (p)
REVERT: C  176 PHE cc_start: 0.8661 (t80) cc_final: 0.8408 (t80)
REVERT: C  223 TRP cc_start: 0.8691 (m-90) cc_final: 0.7871 (m-90)
REVERT: C  246 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8253 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.1604
  time to fit residues: 30.8530
Evaluate side-chains
  110 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 39 optimal weight:    0.2980
   chunk 69 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 59 optimal weight:    0.6980
   chunk 12 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 210 HIS
C   3 HIS
C 210 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.077345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.069518 restraints weight = 32021.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.071343 restraints weight = 18882.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.072649 restraints weight = 12788.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.6124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   7104  Z= 0.136
  Angle     :  0.564  12.821   9660  Z= 0.287
  Chirality :  0.038   0.145   1005
  Planarity :  0.005   0.102   1206
  Dihedral  :  3.694  21.103    942
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  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:  2.31 (0.30), residues: 843
  helix:  1.79 (0.21), residues: 633
  sheet:  None (None), residues: 0
  loop :  0.98 (0.48), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 230 
 HIS   0.008   0.001   HIS C 210 
 PHE   0.015   0.001   PHE C  76 
 TYR   0.022   0.001   TYR A 156 
 ARG   0.013   0.000   ARG B  55 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8521 (pmm) cc_final: 0.8107 (ppp)
REVERT: A  126 ASP cc_start: 0.8926 (t0) cc_final: 0.8610 (t0)
REVERT: A  131 LEU cc_start: 0.9424 (tp) cc_final: 0.9041 (tp)
REVERT: A  257 LYS cc_start: 0.9055 (mmtt) cc_final: 0.8732 (mmtm)
REVERT: B   40 LEU cc_start: 0.8957 (tt) cc_final: 0.8483 (tt)
REVERT: B   82 MET cc_start: 0.8597 (ttp) cc_final: 0.8314 (ttm)
REVERT: B   86 PHE cc_start: 0.8808 (t80) cc_final: 0.8604 (t80)
REVERT: B  108 PHE cc_start: 0.8378 (t80) cc_final: 0.7665 (t80)
REVERT: B  110 ASN cc_start: 0.8201 (p0) cc_final: 0.7772 (t0)
REVERT: B  117 MET cc_start: 0.8660 (mmp) cc_final: 0.8243 (mmm)
REVERT: B  127 LEU cc_start: 0.8720 (tt) cc_final: 0.8378 (tp)
REVERT: B  260 TYR cc_start: 0.7156 (t80) cc_final: 0.6727 (t80)
REVERT: C   10 MET cc_start: 0.7164 (mmt) cc_final: 0.6844 (mmt)
REVERT: C   69 GLU cc_start: 0.8421 (pm20) cc_final: 0.7737 (mm-30)
REVERT: C   82 MET cc_start: 0.8443 (ttp) cc_final: 0.8016 (ttp)
REVERT: C   94 LEU cc_start: 0.7560 (mt) cc_final: 0.7129 (mt)
REVERT: C  125 TYR cc_start: 0.7930 (t80) cc_final: 0.7578 (t80)
REVERT: C  127 LEU cc_start: 0.9129 (tt) cc_final: 0.8875 (tt)
REVERT: C  130 GLN cc_start: 0.8599 (mm110) cc_final: 0.7928 (mm110)
REVERT: C  171 TYR cc_start: 0.8585 (t80) cc_final: 0.8148 (t80)
REVERT: C  175 CYS cc_start: 0.8895 (m) cc_final: 0.8512 (p)
REVERT: C  176 PHE cc_start: 0.8641 (t80) cc_final: 0.8391 (t80)
REVERT: C  246 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8273 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1662
  time to fit residues: 32.1895
Evaluate side-chains
  107 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 66 optimal weight:    8.9990
   chunk 39 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 71 optimal weight:    7.9990
   chunk 17 optimal weight:    6.9990
   chunk 64 optimal weight:    6.9990
   chunk 20 optimal weight:    8.9990
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** C  71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.070908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.063210 restraints weight = 32920.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.064922 restraints weight = 19303.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.066153 restraints weight = 13091.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.6632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7104  Z= 0.245
  Angle     :  0.638  12.870   9660  Z= 0.339
  Chirality :  0.042   0.152   1005
  Planarity :  0.004   0.050   1206
  Dihedral  :  4.108  18.435    942
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  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:  1.90 (0.29), residues: 843
  helix:  1.52 (0.20), residues: 630
  sheet:  None (None), residues: 0
  loop :  0.73 (0.49), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP C  34 
 HIS   0.008   0.002   HIS C 249 
 PHE   0.015   0.002   PHE B  80 
 TYR   0.025   0.002   TYR C  46 
 ARG   0.009   0.001   ARG B  55 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1863.95 seconds
wall clock time: 33 minutes 18.63 seconds (1998.63 seconds total)