Starting phenix.real_space_refine
on Tue Mar  3 16:07:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7shs_25135/03_2026/7shs_25135.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7shs_25135/03_2026/7shs_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7shs_25135/03_2026/7shs_25135.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7shs_25135/03_2026/7shs_25135.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7shs_25135/03_2026/7shs_25135.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7shs_25135/03_2026/7shs_25135.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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:
    B, C
  Time building chain proxies: 1.49, per 1000 atoms: 0.22
  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: 0.58
  Conformation dependent library (CDL) restraints added in 381.3 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: 0.18
  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: 0.90

  Time building geometry restraints manager: 0.83 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             1.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.480
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.960
-------------------------------------------------------------------------------
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= 0.140
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (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
 ARG   0.002   0.000   ARG B  55 
 TYR   0.026   0.001   TYR A 156 
 PHE   0.014   0.001   PHE C 276 
 TRP   0.039   0.002   TRP C 223 
 HIS   0.001   0.000   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 7104)
  covalent geometry    : angle       0.73960 ( 9660)
  hydrogen bonds       : bond        0.13864 (  447)
  hydrogen bonds       : angle       5.22174 ( 1323)

*********************** 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  : 0.275 
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: 0.8267 (pmm) cc_final: 0.7982 (ppp)
REVERT: A  126 ASP cc_start: 0.8657 (t0) cc_final: 0.8268 (t0)
REVERT: A  158 GLU cc_start: 0.8677 (tp30) cc_final: 0.8258 (tm-30)
REVERT: A  250 CYS cc_start: 0.8771 (m) cc_final: 0.8271 (m)
REVERT: B   34 TRP cc_start: 0.6186 (m-10) cc_final: 0.5751 (m100)
REVERT: B  182 TYR cc_start: 0.6720 (t80) cc_final: 0.6196 (t80)
REVERT: B  240 ILE cc_start: 0.7110 (pt) cc_final: 0.6807 (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: 0.6600 (t80)
REVERT: C   70 GLU cc_start: 0.8353 (pm20) cc_final: 0.7875 (pm20)
REVERT: C   72 ASN cc_start: 0.8194 (m-40) cc_final: 0.7821 (m-40)
REVERT: C  130 GLN cc_start: 0.8803 (mm110) cc_final: 0.8105 (mm110)
REVERT: C  246 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7802 (mm-30)
REVERT: C  251 VAL cc_start: 0.9084 (m) cc_final: 0.8872 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.1032
  time to fit residues: 29.7215
Evaluate side-chains
  122 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.1980
   chunk 33 optimal weight:    0.0070
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    0.0670
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.3936

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

Flipped N/Q/H residues before XYZ refinement:
A 201 GLN
B  71 GLN
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 201 GLN
B 281 GLN
C  33 HIS
C 201 GLN
C 249 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.083528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.074816 restraints weight = 28861.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.076849 restraints weight = 16702.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.078294 restraints weight = 11156.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.079311 restraints weight = 7996.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.079890 restraints weight = 6065.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7232
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7104  Z= 0.104
  Angle     :  0.524   6.759   9660  Z= 0.266
  Chirality :  0.037   0.138   1005
  Planarity :  0.004   0.051   1206
  Dihedral  :  3.662  13.944    942
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  2.85 %
    Favored  : 96.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.29), residues: 843
  helix:  1.67 (0.20), residues: 615
  sheet:  None (None), residues: 0
  loop :  0.44 (0.43), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 136 
 TYR   0.015   0.001   TYR C  85 
 PHE   0.023   0.001   PHE B 173 
 TRP   0.019   0.001   TRP C 230 
 HIS   0.005   0.001   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 7104)
  covalent geometry    : angle       0.52446 ( 9660)
  hydrogen bonds       : bond        0.03538 (  447)
  hydrogen bonds       : angle       3.52287 ( 1323)

*********************** 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
  166 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 164
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8411 (pmm) cc_final: 0.7899 (ppp)
REVERT: A   75 LEU cc_start: 0.9072 (tp) cc_final: 0.8865 (tp)
REVERT: A  126 ASP cc_start: 0.9028 (t0) cc_final: 0.8673 (t0)
REVERT: A  131 LEU cc_start: 0.9387 (tp) cc_final: 0.9124 (tp)
REVERT: A  177 TRP cc_start: 0.8071 (m100) cc_final: 0.7846 (m100)
REVERT: A  250 CYS cc_start: 0.8595 (m) cc_final: 0.8264 (m)
REVERT: B   34 TRP cc_start: 0.6271 (m-10) cc_final: 0.5915 (m100)
REVERT: B   40 LEU cc_start: 0.9093 (mp) cc_final: 0.8795 (tp)
REVERT: B   82 MET cc_start: 0.8428 (ttp) cc_final: 0.7865 (ttp)
REVERT: B  110 ASN cc_start: 0.8798 (p0) cc_final: 0.7905 (p0)
REVERT: B  117 MET cc_start: 0.8803 (mmp) cc_final: 0.8465 (mmp)
REVERT: B  210 HIS cc_start: 0.7211 (m90) cc_final: 0.6958 (m-70)
REVERT: B  246 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7441 (pp20)
REVERT: B  260 TYR cc_start: 0.7392 (t80) cc_final: 0.6928 (t80)
REVERT: C   72 ASN cc_start: 0.8377 (m-40) cc_final: 0.8104 (m-40)
REVERT: C   78 ASN cc_start: 0.8320 (m110) cc_final: 0.7900 (m-40)
REVERT: C   82 MET cc_start: 0.8399 (tmm) cc_final: 0.8108 (ttp)
REVERT: C   88 LYS cc_start: 0.8360 (mtmm) cc_final: 0.7859 (ptpp)
REVERT: C   94 LEU cc_start: 0.7724 (mt) cc_final: 0.7076 (mp)
REVERT: C  130 GLN cc_start: 0.8744 (mm110) cc_final: 0.7933 (mm110)
REVERT: C  230 TRP cc_start: 0.8083 (t60) cc_final: 0.7539 (t60)
  outliers start: 2
  outliers final: 1
  residues processed: 166
  average time/residue: 0.0609
  time to fit residues: 14.3827
Evaluate side-chains
  117 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 60 optimal weight:    9.9990
   chunk 77 optimal weight:    4.9990
   chunk 6 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 18 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 20 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9980
   overall best weight:    1.7382

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

Flipped N/Q/H residues before XYZ refinement:
C  33 HIS
C  71 GLN
C 249 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.076760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.068134 restraints weight = 31801.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.070042 restraints weight = 19689.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.071482 restraints weight = 13390.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.072398 restraints weight = 9848.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.073069 restraints weight = 7657.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.3937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7104  Z= 0.124
  Angle     :  0.538   7.200   9660  Z= 0.278
  Chirality :  0.038   0.144   1005
  Planarity :  0.004   0.051   1206
  Dihedral  :  3.761  16.505    942
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.24 (0.29), residues: 843
  helix:  1.78 (0.21), residues: 621
  sheet:  None (None), residues: 0
  loop :  0.85 (0.46), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  55 
 TYR   0.014   0.002   TYR C 193 
 PHE   0.019   0.002   PHE B 173 
 TRP   0.019   0.001   TRP C 223 
 HIS   0.004   0.001   HIS C  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 7104)
  covalent geometry    : angle       0.53784 ( 9660)
  hydrogen bonds       : bond        0.03540 (  447)
  hydrogen bonds       : angle       3.39333 ( 1323)

*********************** 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
  144 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8509 (pmm) cc_final: 0.8021 (ppp)
REVERT: A  126 ASP cc_start: 0.9026 (t0) cc_final: 0.8673 (t0)
REVERT: A  131 LEU cc_start: 0.9398 (tp) cc_final: 0.9091 (tp)
REVERT: B   34 TRP cc_start: 0.6423 (m-10) cc_final: 0.5949 (m100)
REVERT: B   40 LEU cc_start: 0.9232 (mp) cc_final: 0.8894 (tp)
REVERT: B   82 MET cc_start: 0.8378 (ttp) cc_final: 0.7942 (ttp)
REVERT: B  110 ASN cc_start: 0.8806 (p0) cc_final: 0.7960 (p0)
REVERT: B  117 MET cc_start: 0.8776 (mmp) cc_final: 0.8412 (mmm)
REVERT: B  123 LEU cc_start: 0.9210 (mt) cc_final: 0.8929 (tt)
REVERT: B  210 HIS cc_start: 0.7237 (m90) cc_final: 0.6874 (m170)
REVERT: B  246 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7554 (pp20)
REVERT: B  260 TYR cc_start: 0.7368 (t80) cc_final: 0.7130 (t80)
REVERT: C   72 ASN cc_start: 0.8500 (m-40) cc_final: 0.8052 (m-40)
REVERT: C   88 LYS cc_start: 0.8526 (mtmm) cc_final: 0.8218 (mtmm)
REVERT: C   94 LEU cc_start: 0.7659 (mt) cc_final: 0.7157 (mt)
REVERT: C  117 MET cc_start: 0.8624 (mmp) cc_final: 0.7622 (tpp)
REVERT: C  127 LEU cc_start: 0.8707 (pp) cc_final: 0.8398 (pp)
REVERT: C  130 GLN cc_start: 0.8800 (mm110) cc_final: 0.8060 (mm110)
REVERT: C  171 TYR cc_start: 0.7400 (t80) cc_final: 0.7017 (t80)
REVERT: C  175 CYS cc_start: 0.8768 (m) cc_final: 0.8299 (p)
REVERT: C  223 TRP cc_start: 0.7972 (m-90) cc_final: 0.6989 (m-90)
REVERT: C  246 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8039 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.0637
  time to fit residues: 13.4581
Evaluate side-chains
  111 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 37 optimal weight:   10.0000
   chunk 2 optimal weight:    4.9990
   chunk 78 optimal weight:    0.8980
   chunk 52 optimal weight:    8.9990
   chunk 26 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 76 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0470
   overall best weight:    0.7478

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

Flipped N/Q/H residues before XYZ refinement:
B  71 GLN
B  72 ASN
C  71 GLN
** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 210 HIS
C 249 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.077924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.069331 restraints weight = 31850.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.071233 restraints weight = 19093.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.072579 restraints weight = 12915.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.073506 restraints weight = 9508.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.074203 restraints weight = 7434.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7331
moved from start:          0.4235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7104  Z= 0.097
  Angle     :  0.510   6.761   9660  Z= 0.257
  Chirality :  0.037   0.139   1005
  Planarity :  0.004   0.049   1206
  Dihedral  :  3.629  14.400    942
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.33 (0.29), residues: 843
  helix:  1.83 (0.21), residues: 621
  sheet:  None (None), residues: 0
  loop :  0.93 (0.46), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  55 
 TYR   0.014   0.001   TYR A 156 
 PHE   0.017   0.001   PHE B 173 
 TRP   0.020   0.001   TRP B 230 
 HIS   0.006   0.001   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 7104)
  covalent geometry    : angle       0.50974 ( 9660)
  hydrogen bonds       : bond        0.03149 (  447)
  hydrogen bonds       : angle       3.22146 ( 1323)

*********************** 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
  143 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8527 (pmm) cc_final: 0.8000 (ppp)
REVERT: A  126 ASP cc_start: 0.8969 (t0) cc_final: 0.8625 (t0)
REVERT: A  131 LEU cc_start: 0.9396 (tp) cc_final: 0.9059 (tp)
REVERT: B   10 MET cc_start: 0.8179 (mtp) cc_final: 0.7956 (mtp)
REVERT: B   34 TRP cc_start: 0.6313 (m-10) cc_final: 0.5838 (m100)
REVERT: B   40 LEU cc_start: 0.9173 (mp) cc_final: 0.8878 (tp)
REVERT: B   82 MET cc_start: 0.8455 (ttp) cc_final: 0.8010 (ttp)
REVERT: B  110 ASN cc_start: 0.8776 (p0) cc_final: 0.7605 (t0)
REVERT: B  117 MET cc_start: 0.8716 (mmp) cc_final: 0.8337 (mmm)
REVERT: B  123 LEU cc_start: 0.9254 (mt) cc_final: 0.9036 (mt)
REVERT: B  210 HIS cc_start: 0.6838 (m90) cc_final: 0.6485 (m170)
REVERT: B  246 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7666 (pp20)
REVERT: C   67 TYR cc_start: 0.7738 (m-80) cc_final: 0.7329 (m-80)
REVERT: C   72 ASN cc_start: 0.8490 (m-40) cc_final: 0.7868 (m-40)
REVERT: C   82 MET cc_start: 0.8789 (ttm) cc_final: 0.8098 (mtm)
REVERT: C   88 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8157 (mtmm)
REVERT: C   94 LEU cc_start: 0.7592 (mt) cc_final: 0.6963 (mt)
REVERT: C  117 MET cc_start: 0.8525 (mmp) cc_final: 0.7589 (tpp)
REVERT: C  127 LEU cc_start: 0.8669 (pp) cc_final: 0.8402 (pp)
REVERT: C  130 GLN cc_start: 0.8752 (mm110) cc_final: 0.7974 (mm110)
REVERT: C  230 TRP cc_start: 0.8520 (t60) cc_final: 0.8171 (t60)
REVERT: C  246 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8065 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.0629
  time to fit residues: 13.0346
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  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 33 optimal weight:    0.0980
   chunk 58 optimal weight:    6.9990
   chunk 36 optimal weight:    0.0770
   chunk 76 optimal weight:    9.9990
   chunk 53 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 50 optimal weight:    0.6980
   chunk 25 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9990
   chunk 68 optimal weight:    6.9990
   chunk 79 optimal weight:    9.9990
   overall best weight:    0.5540

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

Flipped N/Q/H residues before XYZ refinement:
C  71 GLN
** C 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 210 HIS
C 249 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.078528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.069625 restraints weight = 31977.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.071588 restraints weight = 19151.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.073042 restraints weight = 12879.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.074041 restraints weight = 9400.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.074701 restraints weight = 7229.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.4383

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= 0.098
  Angle     :  0.507   7.126   9660  Z= 0.255
  Chirality :  0.037   0.138   1005
  Planarity :  0.003   0.042   1206
  Dihedral  :  3.551  14.704    942
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.27 (0.29), residues: 843
  helix:  1.71 (0.21), residues: 633
  sheet:  None (None), residues: 0
  loop :  1.13 (0.48), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  55 
 TYR   0.020   0.001   TYR C  46 
 PHE   0.016   0.001   PHE B 173 
 TRP   0.021   0.001   TRP A 223 
 HIS   0.006   0.001   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 7104)
  covalent geometry    : angle       0.50748 ( 9660)
  hydrogen bonds       : bond        0.03104 (  447)
  hydrogen bonds       : angle       3.19120 ( 1323)

*********************** 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
  138 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8549 (pmm) cc_final: 0.8015 (ppp)
REVERT: A   55 ARG cc_start: 0.6091 (mmt180) cc_final: 0.5459 (mmp80)
REVERT: A  126 ASP cc_start: 0.9006 (t0) cc_final: 0.8648 (t0)
REVERT: A  131 LEU cc_start: 0.9406 (tp) cc_final: 0.9053 (tp)
REVERT: A  257 LYS cc_start: 0.8979 (mptt) cc_final: 0.8719 (mmtm)
REVERT: B   34 TRP cc_start: 0.6214 (m-10) cc_final: 0.5750 (m100)
REVERT: B   40 LEU cc_start: 0.9192 (mp) cc_final: 0.8859 (tp)
REVERT: B   82 MET cc_start: 0.8518 (ttp) cc_final: 0.8075 (ttp)
REVERT: B  110 ASN cc_start: 0.8743 (p0) cc_final: 0.7697 (t0)
REVERT: B  117 MET cc_start: 0.8720 (mmp) cc_final: 0.8291 (mmm)
REVERT: B  210 HIS cc_start: 0.6930 (m90) cc_final: 0.6564 (m170)
REVERT: B  246 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7703 (pp20)
REVERT: C   40 LEU cc_start: 0.8414 (pp) cc_final: 0.7763 (pp)
REVERT: C   67 TYR cc_start: 0.7687 (m-80) cc_final: 0.7316 (m-80)
REVERT: C   72 ASN cc_start: 0.8367 (m-40) cc_final: 0.7777 (m-40)
REVERT: C   82 MET cc_start: 0.8875 (ttm) cc_final: 0.8140 (mtm)
REVERT: C   88 LYS cc_start: 0.8475 (mtmm) cc_final: 0.8152 (mtmm)
REVERT: C   94 LEU cc_start: 0.7523 (mt) cc_final: 0.6991 (mt)
REVERT: C  108 PHE cc_start: 0.7406 (t80) cc_final: 0.6917 (t80)
REVERT: C  117 MET cc_start: 0.8591 (mmp) cc_final: 0.7623 (tpp)
REVERT: C  127 LEU cc_start: 0.8669 (pp) cc_final: 0.8391 (pp)
REVERT: C  130 GLN cc_start: 0.8696 (mm110) cc_final: 0.7944 (mm110)
REVERT: C  148 MET cc_start: 0.8727 (ttp) cc_final: 0.8411 (ttt)
REVERT: C  171 TYR cc_start: 0.7555 (t80) cc_final: 0.6962 (t80)
REVERT: C  230 TRP cc_start: 0.8540 (t60) cc_final: 0.7116 (t60)
REVERT: C  246 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8052 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 138
  average time/residue: 0.0701
  time to fit residues: 13.6576
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  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 27 optimal weight:    0.3980
   chunk 49 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 65 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 51 optimal weight:    9.9990
   chunk 78 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 22 optimal weight:    8.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
B   9 GLN
B 201 GLN
C  71 GLN
** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 249 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.075064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.066657 restraints weight = 32635.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.068509 restraints weight = 19248.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.069817 restraints weight = 12904.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.070742 restraints weight = 9416.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.071353 restraints weight = 7287.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.5060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7104  Z= 0.133
  Angle     :  0.550   8.053   9660  Z= 0.286
  Chirality :  0.039   0.141   1005
  Planarity :  0.004   0.043   1206
  Dihedral  :  3.766  14.882    942
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  2.28 %
    Favored  : 97.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.41 (0.29), residues: 843
  helix:  2.01 (0.21), residues: 588
  sheet:  None (None), residues: 0
  loop :  0.78 (0.44), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 132 
 TYR   0.024   0.002   TYR C  46 
 PHE   0.014   0.001   PHE B 173 
 TRP   0.017   0.002   TRP C  34 
 HIS   0.004   0.001   HIS C 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7104)
  covalent geometry    : angle       0.55040 ( 9660)
  hydrogen bonds       : bond        0.03662 (  447)
  hydrogen bonds       : angle       3.39057 ( 1323)

*********************** 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
  137 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8577 (pmm) cc_final: 0.8097 (ppp)
REVERT: A   55 ARG cc_start: 0.6129 (mmt180) cc_final: 0.5329 (mmp80)
REVERT: A  126 ASP cc_start: 0.9001 (t0) cc_final: 0.8724 (t0)
REVERT: A  131 LEU cc_start: 0.9392 (tp) cc_final: 0.9022 (tp)
REVERT: B   10 MET cc_start: 0.8189 (mtp) cc_final: 0.7964 (mmp)
REVERT: B   34 TRP cc_start: 0.6361 (m-10) cc_final: 0.5837 (m100)
REVERT: B   40 LEU cc_start: 0.9218 (mp) cc_final: 0.8830 (tp)
REVERT: B   82 MET cc_start: 0.8533 (ttp) cc_final: 0.8090 (ttm)
REVERT: B  108 PHE cc_start: 0.8059 (t80) cc_final: 0.7699 (t80)
REVERT: B  110 ASN cc_start: 0.8549 (p0) cc_final: 0.7677 (t0)
REVERT: B  117 MET cc_start: 0.8793 (mmp) cc_final: 0.8247 (mmm)
REVERT: B  123 LEU cc_start: 0.9269 (mt) cc_final: 0.9060 (mt)
REVERT: B  210 HIS cc_start: 0.7302 (m90) cc_final: 0.6899 (m170)
REVERT: C   40 LEU cc_start: 0.8412 (pp) cc_final: 0.7720 (pp)
REVERT: C   82 MET cc_start: 0.8864 (ttm) cc_final: 0.8074 (mtm)
REVERT: C   88 LYS cc_start: 0.8483 (mtmm) cc_final: 0.8189 (mtmm)
REVERT: C  108 PHE cc_start: 0.7595 (t80) cc_final: 0.6914 (t80)
REVERT: C  118 LEU cc_start: 0.8734 (mt) cc_final: 0.8524 (pp)
REVERT: C  127 LEU cc_start: 0.8811 (pp) cc_final: 0.8544 (pp)
REVERT: C  130 GLN cc_start: 0.8814 (mm110) cc_final: 0.8100 (mm110)
REVERT: C  131 LEU cc_start: 0.9236 (tp) cc_final: 0.8980 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0609
  time to fit residues: 11.9960
Evaluate side-chains
  100 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 81 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 62 optimal weight:    8.9990
   overall best weight:    1.9986

-------------------------------------------------------------------------------
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 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  71 GLN
C 110 ASN
C 249 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.075217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.067008 restraints weight = 33983.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.068898 restraints weight = 20322.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.070220 restraints weight = 13592.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.071141 restraints weight = 9892.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.071774 restraints weight = 7606.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.5416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7104  Z= 0.132
  Angle     :  0.563   8.198   9660  Z= 0.294
  Chirality :  0.040   0.137   1005
  Planarity :  0.004   0.048   1206
  Dihedral  :  3.833  15.416    942
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.57 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.42 (0.29), residues: 843
  helix:  1.91 (0.21), residues: 594
  sheet:  None (None), residues: 0
  loop :  1.05 (0.45), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 132 
 TYR   0.022   0.001   TYR C  46 
 PHE   0.013   0.001   PHE B 217 
 TRP   0.017   0.001   TRP C  34 
 HIS   0.006   0.001   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 7104)
  covalent geometry    : angle       0.56338 ( 9660)
  hydrogen bonds       : bond        0.03614 (  447)
  hydrogen bonds       : angle       3.51111 ( 1323)

*********************** 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
  132 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8557 (pmm) cc_final: 0.8166 (ppp)
REVERT: A  126 ASP cc_start: 0.8936 (t0) cc_final: 0.8627 (t0)
REVERT: A  131 LEU cc_start: 0.9378 (tp) cc_final: 0.9024 (tp)
REVERT: B   34 TRP cc_start: 0.6076 (m-10) cc_final: 0.5700 (m100)
REVERT: B   40 LEU cc_start: 0.9209 (mp) cc_final: 0.8322 (tp)
REVERT: B   82 MET cc_start: 0.8545 (ttp) cc_final: 0.8090 (ttm)
REVERT: B  108 PHE cc_start: 0.8057 (t80) cc_final: 0.7629 (t80)
REVERT: B  110 ASN cc_start: 0.8410 (p0) cc_final: 0.7855 (t0)
REVERT: B  117 MET cc_start: 0.8703 (mmp) cc_final: 0.8247 (mmm)
REVERT: B  123 LEU cc_start: 0.9236 (mt) cc_final: 0.9035 (mt)
REVERT: B  210 HIS cc_start: 0.7321 (m90) cc_final: 0.7011 (m170)
REVERT: B  260 TYR cc_start: 0.7615 (t80) cc_final: 0.7359 (t80)
REVERT: C   40 LEU cc_start: 0.8438 (pp) cc_final: 0.7720 (pp)
REVERT: C   82 MET cc_start: 0.8809 (ttm) cc_final: 0.8059 (mtm)
REVERT: C   88 LYS cc_start: 0.8500 (mtmm) cc_final: 0.8227 (mtmm)
REVERT: C  108 PHE cc_start: 0.7515 (t80) cc_final: 0.7245 (t80)
REVERT: C  117 MET cc_start: 0.8498 (mmp) cc_final: 0.7518 (tpp)
REVERT: C  130 GLN cc_start: 0.8718 (mm110) cc_final: 0.8073 (mm110)
REVERT: C  246 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8060 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 131
  average time/residue: 0.0642
  time to fit residues: 12.1359
Evaluate side-chains
  100 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 67 optimal weight:    4.9990
   chunk 54 optimal weight:    7.9990
   chunk 68 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 41 optimal weight:    8.9990
   chunk 55 optimal weight:    2.9990
   chunk 52 optimal weight:    7.9990
   chunk 31 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  71 GLN
C 249 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.076723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.068815 restraints weight = 31576.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.070775 restraints weight = 18146.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.072058 restraints weight = 11858.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.072890 restraints weight = 8405.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.073474 restraints weight = 6374.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.5523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7104  Z= 0.119
  Angle     :  0.593   9.675   9660  Z= 0.301
  Chirality :  0.040   0.155   1005
  Planarity :  0.004   0.053   1206
  Dihedral  :  3.846  16.566    942
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.71 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.19 (0.30), residues: 843
  helix:  1.68 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  1.09 (0.46), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 235 
 TYR   0.022   0.001   TYR A 156 
 PHE   0.014   0.001   PHE B 173 
 TRP   0.014   0.001   TRP C  34 
 HIS   0.007   0.001   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 7104)
  covalent geometry    : angle       0.59343 ( 9660)
  hydrogen bonds       : bond        0.03562 (  447)
  hydrogen bonds       : angle       3.47306 ( 1323)

*********************** 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
  133 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8563 (pmm) cc_final: 0.8126 (ppp)
REVERT: A  126 ASP cc_start: 0.8930 (t0) cc_final: 0.8669 (t0)
REVERT: A  131 LEU cc_start: 0.9383 (tp) cc_final: 0.9034 (tp)
REVERT: A  176 PHE cc_start: 0.8234 (t80) cc_final: 0.7955 (t80)
REVERT: A  257 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8638 (mmtm)
REVERT: B   34 TRP cc_start: 0.5982 (m-10) cc_final: 0.5589 (m100)
REVERT: B  108 PHE cc_start: 0.8136 (t80) cc_final: 0.7725 (t80)
REVERT: B  110 ASN cc_start: 0.8340 (p0) cc_final: 0.7862 (t0)
REVERT: B  117 MET cc_start: 0.8708 (mmp) cc_final: 0.8282 (mmm)
REVERT: B  123 LEU cc_start: 0.9221 (mt) cc_final: 0.8797 (mt)
REVERT: B  210 HIS cc_start: 0.7257 (m90) cc_final: 0.6987 (m170)
REVERT: B  257 LYS cc_start: 0.8157 (mptt) cc_final: 0.7665 (mmtm)
REVERT: C   40 LEU cc_start: 0.8369 (pp) cc_final: 0.7615 (pp)
REVERT: C   82 MET cc_start: 0.8739 (ttm) cc_final: 0.7998 (mtm)
REVERT: C   88 LYS cc_start: 0.8434 (mtmm) cc_final: 0.8093 (mtmm)
REVERT: C  108 PHE cc_start: 0.7442 (t80) cc_final: 0.6848 (t80)
REVERT: C  117 MET cc_start: 0.8399 (mmp) cc_final: 0.6527 (tmm)
REVERT: C  123 LEU cc_start: 0.9301 (tt) cc_final: 0.8995 (tt)
REVERT: C  127 LEU cc_start: 0.9131 (tt) cc_final: 0.8681 (mt)
REVERT: C  130 GLN cc_start: 0.8723 (mm110) cc_final: 0.8046 (mm110)
REVERT: C  148 MET cc_start: 0.8778 (ttp) cc_final: 0.8190 (ttp)
REVERT: C  246 GLU cc_start: 0.8509 (mm-30) cc_final: 0.8106 (mm-30)
REVERT: C  251 VAL cc_start: 0.9090 (m) cc_final: 0.8775 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0597
  time to fit residues: 11.4729
Evaluate side-chains
  103 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
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 69 optimal weight:    8.9990
   chunk 21 optimal weight:    4.9990
   chunk 78 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 25 optimal weight:    8.9990
   chunk 9 optimal weight:    0.0570
   chunk 40 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 82 optimal weight:    6.9990
   overall best weight:    0.9500

-------------------------------------------------------------------------------
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 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 = 0.3562 r_free = 0.3562 target = 0.077247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.069534 restraints weight = 31175.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.071417 restraints weight = 17664.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.072614 restraints weight = 11662.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.073462 restraints weight = 8349.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.073971 restraints weight = 6357.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.5684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7104  Z= 0.107
  Angle     :  0.579   9.069   9660  Z= 0.291
  Chirality :  0.039   0.158   1005
  Planarity :  0.004   0.051   1206
  Dihedral  :  3.737  16.577    942
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.27 (0.30), residues: 843
  helix:  1.76 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop :  1.03 (0.46), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 235 
 TYR   0.022   0.001   TYR A 156 
 PHE   0.014   0.001   PHE B 173 
 TRP   0.013   0.001   TRP C  34 
 HIS   0.007   0.001   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 7104)
  covalent geometry    : angle       0.57928 ( 9660)
  hydrogen bonds       : bond        0.03354 (  447)
  hydrogen bonds       : angle       3.37522 ( 1323)

*********************** 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
  129 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8567 (pmm) cc_final: 0.8130 (ppp)
REVERT: A  117 MET cc_start: 0.8254 (mmp) cc_final: 0.7582 (mmp)
REVERT: A  126 ASP cc_start: 0.8947 (t0) cc_final: 0.8615 (t0)
REVERT: A  131 LEU cc_start: 0.9413 (tp) cc_final: 0.9060 (tp)
REVERT: A  176 PHE cc_start: 0.8206 (t80) cc_final: 0.7938 (t80)
REVERT: A  257 LYS cc_start: 0.9126 (mmtt) cc_final: 0.8738 (mmtm)
REVERT: B   40 LEU cc_start: 0.9196 (mm) cc_final: 0.8719 (tp)
REVERT: B   60 ARG cc_start: 0.6686 (ptt-90) cc_final: 0.5760 (tpt-90)
REVERT: B   82 MET cc_start: 0.8446 (ttp) cc_final: 0.8133 (ttp)
REVERT: B  108 PHE cc_start: 0.8213 (t80) cc_final: 0.7809 (t80)
REVERT: B  110 ASN cc_start: 0.8273 (p0) cc_final: 0.7836 (t0)
REVERT: B  117 MET cc_start: 0.8703 (mmp) cc_final: 0.8281 (mmm)
REVERT: B  119 THR cc_start: 0.7090 (p) cc_final: 0.6858 (p)
REVERT: B  123 LEU cc_start: 0.9224 (mt) cc_final: 0.8789 (mt)
REVERT: B  210 HIS cc_start: 0.7181 (m90) cc_final: 0.6962 (m170)
REVERT: B  257 LYS cc_start: 0.8077 (mptt) cc_final: 0.7720 (mmtm)
REVERT: C   40 LEU cc_start: 0.8433 (pp) cc_final: 0.7711 (pp)
REVERT: C   71 GLN cc_start: 0.7996 (pp30) cc_final: 0.7727 (pp30)
REVERT: C   82 MET cc_start: 0.8701 (ttm) cc_final: 0.8072 (mtm)
REVERT: C   88 LYS cc_start: 0.8459 (mtmm) cc_final: 0.8051 (mtmm)
REVERT: C  117 MET cc_start: 0.8378 (mmp) cc_final: 0.7238 (tpp)
REVERT: C  123 LEU cc_start: 0.9293 (tt) cc_final: 0.8962 (tt)
REVERT: C  125 TYR cc_start: 0.7924 (t80) cc_final: 0.7565 (t80)
REVERT: C  127 LEU cc_start: 0.9128 (tt) cc_final: 0.8707 (mt)
REVERT: C  130 GLN cc_start: 0.8716 (mm110) cc_final: 0.8011 (mm110)
REVERT: C  131 LEU cc_start: 0.9161 (tp) cc_final: 0.8880 (tp)
REVERT: C  148 MET cc_start: 0.8645 (ttp) cc_final: 0.8349 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0697
  time to fit residues: 12.8550
Evaluate side-chains
  104 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 36 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 44 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 56 optimal weight:   20.0000
   chunk 59 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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 = 0.3542 r_free = 0.3542 target = 0.076458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.068700 restraints weight = 31398.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.070663 restraints weight = 18191.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.071927 restraints weight = 11779.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.072793 restraints weight = 8283.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.073314 restraints weight = 6227.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.5884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7104  Z= 0.120
  Angle     :  0.600   9.822   9660  Z= 0.301
  Chirality :  0.040   0.155   1005
  Planarity :  0.004   0.052   1206
  Dihedral  :  3.797  16.464    942
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.28 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.08 (0.29), residues: 843
  helix:  1.61 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop :  0.92 (0.46), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 235 
 TYR   0.021   0.001   TYR A 156 
 PHE   0.013   0.001   PHE B 219 
 TRP   0.029   0.002   TRP B 223 
 HIS   0.007   0.001   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7104)
  covalent geometry    : angle       0.60044 ( 9660)
  hydrogen bonds       : bond        0.03556 (  447)
  hydrogen bonds       : angle       3.44903 ( 1323)

********************** 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
  131 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 MET cc_start: 0.8609 (pmm) cc_final: 0.8185 (ppp)
REVERT: A  126 ASP cc_start: 0.8926 (t0) cc_final: 0.8576 (t0)
REVERT: A  131 LEU cc_start: 0.9411 (tp) cc_final: 0.9051 (tp)
REVERT: A  176 PHE cc_start: 0.8187 (t80) cc_final: 0.7902 (t80)
REVERT: A  257 LYS cc_start: 0.9123 (mmtt) cc_final: 0.8758 (mmtm)
REVERT: B   60 ARG cc_start: 0.6725 (ptt-90) cc_final: 0.5741 (tpt-90)
REVERT: B  108 PHE cc_start: 0.8227 (t80) cc_final: 0.7819 (t80)
REVERT: B  110 ASN cc_start: 0.8245 (p0) cc_final: 0.7814 (t0)
REVERT: B  117 MET cc_start: 0.8750 (mmp) cc_final: 0.8292 (mmm)
REVERT: B  119 THR cc_start: 0.7110 (p) cc_final: 0.6873 (p)
REVERT: B  123 LEU cc_start: 0.9233 (mt) cc_final: 0.8801 (mt)
REVERT: B  257 LYS cc_start: 0.8105 (mptt) cc_final: 0.7648 (mmtm)
REVERT: C   40 LEU cc_start: 0.8445 (pp) cc_final: 0.7707 (pp)
REVERT: C   82 MET cc_start: 0.8647 (ttm) cc_final: 0.8053 (mtm)
REVERT: C   88 LYS cc_start: 0.8457 (mtmm) cc_final: 0.8080 (mtmm)
REVERT: C  108 PHE cc_start: 0.7548 (t80) cc_final: 0.7248 (t80)
REVERT: C  117 MET cc_start: 0.8382 (mmp) cc_final: 0.7236 (tpp)
REVERT: C  123 LEU cc_start: 0.9300 (tt) cc_final: 0.8973 (tt)
REVERT: C  125 TYR cc_start: 0.7936 (t80) cc_final: 0.7575 (t80)
REVERT: C  127 LEU cc_start: 0.9170 (tt) cc_final: 0.8744 (mt)
REVERT: C  130 GLN cc_start: 0.8713 (mm110) cc_final: 0.7995 (mm110)
REVERT: C  131 LEU cc_start: 0.9177 (tp) cc_final: 0.8885 (tp)
REVERT: C  148 MET cc_start: 0.8689 (ttp) cc_final: 0.8343 (tmm)
REVERT: C  246 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8135 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 130
  average time/residue: 0.0695
  time to fit residues: 12.9634
Evaluate side-chains
  105 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 78 optimal weight:    3.9990
   chunk 18 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 3 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   overall best weight:    1.4586

-------------------------------------------------------------------------------
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  78 ASN
B 210 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.076519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.068822 restraints weight = 31321.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.070726 restraints weight = 18169.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.071991 restraints weight = 11921.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.072781 restraints weight = 8493.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.073365 restraints weight = 6588.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
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   0.042   7104  Z= 0.115
  Angle     :  0.591   9.756   9660  Z= 0.296
  Chirality :  0.040   0.156   1005
  Planarity :  0.004   0.052   1206
  Dihedral  :  3.783  16.034    942
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.07 (0.29), residues: 843
  helix:  1.61 (0.21), residues: 636
  sheet:  None (None), residues: 0
  loop :  0.90 (0.46), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 235 
 TYR   0.022   0.001   TYR A 156 
 PHE   0.015   0.001   PHE A 173 
 TRP   0.029   0.002   TRP B 223 
 HIS   0.007   0.001   HIS C 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 7104)
  covalent geometry    : angle       0.59078 ( 9660)
  hydrogen bonds       : bond        0.03481 (  447)
  hydrogen bonds       : angle       3.43176 ( 1323)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1018.45 seconds
wall clock time: 18 minutes 21.93 seconds (1101.93 seconds total)