Starting phenix.real_space_refine
on Sat Aug 23 02:10:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zmk_60250/08_2025/8zmk_60250.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zmk_60250/08_2025/8zmk_60250.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zmk_60250/08_2025/8zmk_60250.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zmk_60250/08_2025/8zmk_60250.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zmk_60250/08_2025/8zmk_60250.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zmk_60250/08_2025/8zmk_60250.cif"
  }
  resolution = 3.85
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
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: 5
    Type Number    sf(0)   Gaussians
     P     168      5.49       5
     S      40      5.16       5
     C    5178      2.51       5
     N    1593      2.21       5
     O    2225      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9204
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 2805
          Classifications: {'peptide': 349}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 333}
    Chain: "C"
      Number of atoms: 3594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 3594
          Classifications: {'RNA': 169}
          Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 8, 'rna3p_pur': 78, 'rna3p_pyr': 74}
          Link IDs: {'rna2p': 17, 'rna3p': 151}
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.13, per 1000 atoms: 0.34
  Number of scatterers: 9204
  At special positions: 0
  Unit cell: (91.84, 110.7, 141.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     P     168     15.00
     O    2225      8.00
     N    1593      7.00
     C    5178      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Conformation dependent library (CDL) restraints added in 257.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1320

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 4 sheets defined
      58.7% alpha, 4.9% beta
      55 base pairs and 67 stacking pairs defined.
    Time for finding SS restraints: 1.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 42
      removed outlier: 4.033A  pdb=" N   GLY A  42 " --> pdb=" O   VAL A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 58
    Processing helix  chain 'A' and resid 78 through 92
    Processing helix  chain 'A' and resid 101 through 107
    Processing helix  chain 'A' and resid 109 through 112
    Processing helix  chain 'A' and resid 113 through 131
      removed outlier: 3.730A  pdb=" N   ILE A 117 " --> pdb=" O   ASP A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 152
      removed outlier: 3.604A  pdb=" N   ALA A 151 " --> pdb=" O   LYS A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 166
    Processing helix  chain 'A' and resid 168 through 175
    Processing helix  chain 'A' and resid 189 through 205
      Proline residue:  A 195  - end of helix
      removed outlier: 4.155A  pdb=" N   ILE A 202 " --> pdb=" O   GLN A 198 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   PHE A 203 " --> pdb=" O   CYS A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 215
      No H-bonds generated for 'chain 'A' and resid 213 through 215'
    Processing helix  chain 'A' and resid 216 through 231
    Processing helix  chain 'A' and resid 268 through 277
    Processing helix  chain 'A' and resid 289 through 298
      removed outlier: 4.338A  pdb=" N   GLU A 293 " --> pdb=" O   ASN A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 304
      removed outlier: 3.505A  pdb=" N   PHE A 303 " --> pdb=" O   ILE A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 331
    Processing helix  chain 'A' and resid 336 through 362
      Proline residue:  A 342  - end of helix
      Proline residue:  A 354  - end of helix
    Processing helix  chain 'A' and resid 362 through 373
      removed outlier: 3.742A  pdb=" N   LYS A 366 " --> pdb=" O   ASP A 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 42
      removed outlier: 4.034A  pdb=" N   GLY B  42 " --> pdb=" O   VAL B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 58
    Processing helix  chain 'B' and resid 78 through 92
    Processing helix  chain 'B' and resid 101 through 107
    Processing helix  chain 'B' and resid 109 through 112
    Processing helix  chain 'B' and resid 113 through 131
      removed outlier: 3.730A  pdb=" N   ILE B 117 " --> pdb=" O   ASP B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 152
      removed outlier: 3.605A  pdb=" N   ALA B 151 " --> pdb=" O   LYS B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 166
    Processing helix  chain 'B' and resid 168 through 175
    Processing helix  chain 'B' and resid 189 through 205
      Proline residue:  B 195  - end of helix
      removed outlier: 4.155A  pdb=" N   ILE B 202 " --> pdb=" O   GLN B 198 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   PHE B 203 " --> pdb=" O   CYS B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 215
      No H-bonds generated for 'chain 'B' and resid 213 through 215'
    Processing helix  chain 'B' and resid 216 through 231
    Processing helix  chain 'B' and resid 268 through 277
    Processing helix  chain 'B' and resid 289 through 298
      removed outlier: 4.338A  pdb=" N   GLU B 293 " --> pdb=" O   ASN B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 304
      removed outlier: 3.504A  pdb=" N   PHE B 303 " --> pdb=" O   ILE B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 331
    Processing helix  chain 'B' and resid 336 through 362
      Proline residue:  B 342  - end of helix
      Proline residue:  B 354  - end of helix
    Processing helix  chain 'B' and resid 362 through 373
      removed outlier: 3.743A  pdb=" N   LYS B 366 " --> pdb=" O   ASP B 362 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 66
      removed outlier: 3.928A  pdb=" N   ASP A  65 " --> pdb=" O   LYS A  96 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   TRP A  98 " --> pdb=" O   ASP A  65 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 306 through 308
      removed outlier: 3.565A  pdb=" N   LYS A 318 " --> pdb=" O   VAL A 308 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 62 through 66
      removed outlier: 3.927A  pdb=" N   ASP B  65 " --> pdb=" O   LYS B  96 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   TRP B  98 " --> pdb=" O   ASP B  65 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 306 through 308
      removed outlier: 3.564A  pdb=" N   LYS B 318 " --> pdb=" O   VAL B 308 " (cutoff:3.500A)

    254 hydrogen bonds defined for protein.
    750 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      138 hydrogen bonds
      252 hydrogen bond angles
      0 basepair planarities
      55 basepair parallelities
      67 stacking parallelities
  Total time for adding SS restraints: 1.60

  Time building geometry restraints manager: 1.34 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2208
        1.34 -     1.45: 2687
        1.45 -     1.57: 4447
        1.57 -     1.69: 336
        1.69 -     1.81: 60
  Bond restraints: 9738
  Sorted by residual:
  bond pdb=" CB  PRO B  61 "
       pdb=" CG  PRO B  61 "
    ideal  model  delta    sigma   weight residual
    1.492  1.529 -0.037 5.00e-02 4.00e+02 5.56e-01
  bond pdb=" CB  PRO A  61 "
       pdb=" CG  PRO A  61 "
    ideal  model  delta    sigma   weight residual
    1.492  1.529 -0.037 5.00e-02 4.00e+02 5.41e-01
  bond pdb=" C   TRP B 157 "
       pdb=" N   PRO B 158 "
    ideal  model  delta    sigma   weight residual
    1.335  1.344 -0.009 1.28e-02 6.10e+03 5.25e-01
  bond pdb=" N   LYS A 206 "
       pdb=" CA  LYS A 206 "
    ideal  model  delta    sigma   weight residual
    1.460  1.470 -0.011 1.54e-02 4.22e+03 4.85e-01
  bond pdb=" CB  PRO A  31 "
       pdb=" CG  PRO A  31 "
    ideal  model  delta    sigma   weight residual
    1.492  1.527 -0.035 5.00e-02 4.00e+02 4.78e-01
  ... (remaining 9733 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.99: 13515
        0.99 -     1.99: 336
        1.99 -     2.98: 70
        2.98 -     3.98: 16
        3.98 -     4.97: 16
  Bond angle restraints: 13953
  Sorted by residual:
  angle pdb=" N   TYR A 323 "
        pdb=" CA  TYR A 323 "
        pdb=" C   TYR A 323 "
      ideal   model   delta    sigma   weight residual
     114.75  111.41    3.34 1.26e+00 6.30e-01 7.02e+00
  angle pdb=" N   TYR B 323 "
        pdb=" CA  TYR B 323 "
        pdb=" C   TYR B 323 "
      ideal   model   delta    sigma   weight residual
     114.75  111.48    3.27 1.26e+00 6.30e-01 6.73e+00
  angle pdb=" C3'   U C  90 "
        pdb=" O3'   U C  90 "
        pdb=" P     G C  91 "
      ideal   model   delta    sigma   weight residual
     120.20  123.65   -3.45 1.50e+00 4.44e-01 5.28e+00
  angle pdb=" CA  TYR A 323 "
        pdb=" C   TYR A 323 "
        pdb=" N   GLU A 324 "
      ideal   model   delta    sigma   weight residual
     119.80  117.27    2.53 1.34e+00 5.57e-01 3.58e+00
  angle pdb=" CA  TYR B 323 "
        pdb=" C   TYR B 323 "
        pdb=" N   GLU B 324 "
      ideal   model   delta    sigma   weight residual
     119.80  117.28    2.52 1.34e+00 5.57e-01 3.54e+00
  ... (remaining 13948 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.06: 5438
       21.06 -    42.12: 382
       42.12 -    63.18: 229
       63.18 -    84.25: 98
       84.25 -   105.31: 7
  Dihedral angle restraints: 6154
    sinusoidal: 4116
      harmonic: 2038
  Sorted by residual:
  dihedral pdb=" O4'   C C  68 "
           pdb=" C1'   C C  68 "
           pdb=" N1    C C  68 "
           pdb=" C2    C C  68 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -60.54  -99.46     1      1.50e+01 4.44e-03 4.97e+01
  dihedral pdb=" O4'   A C  72 "
           pdb=" C1'   A C  72 "
           pdb=" N9    A C  72 "
           pdb=" C4    A C  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -159.32   53.32     1      1.70e+01 3.46e-03 1.34e+01
  dihedral pdb=" O4'   G C  95 "
           pdb=" C1'   G C  95 "
           pdb=" N9    G C  95 "
           pdb=" C4    G C  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -154.18   48.18     1      1.70e+01 3.46e-03 1.11e+01
  ... (remaining 6151 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 1325
       0.027 -    0.053: 228
       0.053 -    0.080: 70
       0.080 -    0.107: 44
       0.107 -    0.134: 7
  Chirality restraints: 1674
  Sorted by residual:
  chirality pdb=" CA  ILE A  46 "
            pdb=" N   ILE A  46 "
            pdb=" C   ILE A  46 "
            pdb=" CB  ILE A  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.46e-01
  chirality pdb=" CA  ILE B  46 "
            pdb=" N   ILE B  46 "
            pdb=" C   ILE B  46 "
            pdb=" CB  ILE B  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.42e-01
  chirality pdb=" CA  ILE B  97 "
            pdb=" N   ILE B  97 "
            pdb=" C   ILE B  97 "
            pdb=" CB  ILE B  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.17e-01
  ... (remaining 1671 not shown)

  Planarity restraints: 1157
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C C 112 "   -0.001 2.00e-02 2.50e+03   1.07e-02 2.59e+00
        pdb=" N1    C C 112 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    C C 112 "    0.027 2.00e-02 2.50e+03
        pdb=" O2    C C 112 "   -0.015 2.00e-02 2.50e+03
        pdb=" N3    C C 112 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    C C 112 "    0.004 2.00e-02 2.50e+03
        pdb=" N4    C C 112 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    C C 112 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    C C 112 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  97 "   -0.010 2.00e-02 2.50e+03   7.94e-03 1.89e+00
        pdb=" N9    G C  97 "    0.015 2.00e-02 2.50e+03
        pdb=" C8    G C  97 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    G C  97 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    G C  97 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    G C  97 "   -0.005 2.00e-02 2.50e+03
        pdb=" O6    G C  97 "    0.000 2.00e-02 2.50e+03
        pdb=" N1    G C  97 "   -0.000 2.00e-02 2.50e+03
        pdb=" C2    G C  97 "   -0.015 2.00e-02 2.50e+03
        pdb=" N2    G C  97 "    0.012 2.00e-02 2.50e+03
        pdb=" N3    G C  97 "   -0.000 2.00e-02 2.50e+03
        pdb=" C4    G C  97 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C C  98 "   -0.017 2.00e-02 2.50e+03   8.13e-03 1.49e+00
        pdb=" N1    C C  98 "    0.014 2.00e-02 2.50e+03
        pdb=" C2    C C  98 "    0.005 2.00e-02 2.50e+03
        pdb=" O2    C C  98 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    C C  98 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    C C  98 "    0.001 2.00e-02 2.50e+03
        pdb=" N4    C C  98 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5    C C  98 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    C C  98 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1154 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1173
        2.75 -     3.29: 8617
        3.29 -     3.83: 16460
        3.83 -     4.36: 19113
        4.36 -     4.90: 29367
  Nonbonded interactions: 74730
  Sorted by model distance:
  nonbonded pdb=" O2'   G C  73 "
            pdb=" O2'   U C 125 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" N4    C C   1 "
            pdb=" O6    G C   2 "
     model   vdw
     2.247 3.120
  nonbonded pdb=" O2    U C  43 "
            pdb=" O6    G C 122 "
     model   vdw
     2.258 2.432
  nonbonded pdb=" OD1 ASP B 101 "
            pdb=" OG  SER B 145 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OD1 ASP A 101 "
            pdb=" OG  SER A 145 "
     model   vdw
     2.272 3.040
  ... (remaining 74725 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             4.060
  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:             0.020
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.170
  Find NCS groups from input model:        0.080
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3513
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      :  0.002   0.037   9738  Z= 0.082
  Angle     :  0.421   4.969  13953  Z= 0.216
  Chirality :  0.028   0.134   1674
  Planarity :  0.003   0.027   1157
  Dihedral  : 18.722 105.308   4834
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.58 %
    Allowed  : 10.37 %
    Favored  : 89.05 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  :  3.56 %
    Favored  : 94.17 %
  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 aren not related in a simple way.
  whole: -2.54 (0.28), residues: 694
  helix: -0.84 (0.25), residues: 384
  sheet: -2.71 (0.66), residues: 46
  loop : -2.68 (0.31), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 371 
 TYR   0.003   0.001   TYR B 226 
 PHE   0.004   0.001   PHE A 203 
 TRP   0.002   0.000   TRP B 128 
 HIS   0.001   0.000   HIS B 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00162 ( 9738)
  covalent geometry    : angle       0.42084 (13953)
  hydrogen bonds       : bond        0.13572 (  392)
  hydrogen bonds       : angle       4.84441 ( 1002)

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 176
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 LEU cc_start: 0.7275 (tt) cc_final: 0.6686 (tt)
REVERT: A  317 ASN cc_start: 0.7327 (m-40) cc_final: 0.7098 (m-40)
REVERT: B   33 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.5897 (pm20)
REVERT: B  254 MET cc_start: 0.1854 (mmp) cc_final: 0.1424 (mmp)
REVERT: B  327 ILE cc_start: 0.6261 (mm) cc_final: 0.6004 (tp)
  outliers start: 14
  outliers final: 3
  residues processed: 188
  average time/residue: 0.1326
  time to fit residues: 31.9991
Evaluate side-chains
  110 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain B residue   33 GLU
Chi-restraints excluded: chain B residue   94 ARG
Chi-restraints excluded: chain B residue  147 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A  47 GLN
A 220 ASN
A 241 HIS
B 165 GLN
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5042 r_free = 0.5042 target = 0.180221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4997 r_free = 0.4997 target = 0.163233 restraints weight = 74021.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.5001 r_free = 0.5001 target = 0.165319 restraints weight = 51088.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.5007 r_free = 0.5007 target = 0.166829 restraints weight = 40185.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.5015 r_free = 0.5015 target = 0.167785 restraints weight = 33838.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.5020 r_free = 0.5020 target = 0.168458 restraints weight = 29965.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.4723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6381
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9738  Z= 0.130
  Angle     :  0.616   9.881  13953  Z= 0.302
  Chirality :  0.034   0.313   1674
  Planarity :  0.004   0.041   1157
  Dihedral  : 21.220 106.170   3372
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 15.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 14.40 %
    Favored  : 83.33 %
  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 aren not related in a simple way.
  whole: -1.49 (0.31), residues: 694
  helix:  0.07 (0.28), residues: 384
  sheet: -1.20 (0.93), residues: 32
  loop : -2.49 (0.30), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  94 
 TYR   0.023   0.002   TYR B 323 
 PHE   0.034   0.003   PHE B 359 
 TRP   0.009   0.001   TRP B  98 
 HIS   0.017   0.003   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9738)
  covalent geometry    : angle       0.61560 (13953)
  hydrogen bonds       : bond        0.04355 (  392)
  hydrogen bonds       : angle       4.05142 ( 1002)

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 MET cc_start: 0.4445 (ptm) cc_final: 0.4020 (tmm)
REVERT: A  133 MET cc_start: 0.6287 (mmp) cc_final: 0.5659 (mmm)
REVERT: A  203 PHE cc_start: 0.7640 (t80) cc_final: 0.7437 (m-80)
REVERT: A  265 MET cc_start: 0.8627 (mmm) cc_final: 0.8291 (mmm)
REVERT: A  280 TYR cc_start: 0.8206 (t80) cc_final: 0.7904 (t80)
REVERT: B   35 PHE cc_start: 0.9012 (t80) cc_final: 0.8730 (t80)
REVERT: B   64 TYR cc_start: 0.7393 (p90) cc_final: 0.7013 (p90)
REVERT: B   73 MET cc_start: 0.5160 (ptm) cc_final: 0.4867 (ptm)
REVERT: B  228 ASP cc_start: 0.8292 (m-30) cc_final: 0.8077 (m-30)
REVERT: B  254 MET cc_start: 0.7061 (mmp) cc_final: 0.6346 (mmp)
  outliers start: 14
  outliers final: 7
  residues processed: 131
  average time/residue: 0.1231
  time to fit residues: 21.2573
Evaluate side-chains
  103 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain B residue   94 ARG
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  147 LYS
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  340 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   chunk 79 optimal weight:    9.9990
   chunk 20 optimal weight:    8.9990
   chunk 78 optimal weight:    4.9990
   chunk 52 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   chunk 82 optimal weight:    9.9990
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 220 ASN
** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 198 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.134948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.107302 restraints weight = 49422.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.110194 restraints weight = 50339.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.111168 restraints weight = 33726.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.111883 restraints weight = 30301.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.112209 restraints weight = 28094.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.4223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.6276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   9738  Z= 0.309
  Angle     :  0.906  13.438  13953  Z= 0.455
  Chirality :  0.046   0.441   1674
  Planarity :  0.006   0.045   1157
  Dihedral  : 22.438 116.650   3369
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 36.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 13.92 %
    Favored  : 80.58 %
  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 aren not related in a simple way.
  whole: -2.46 (0.29), residues: 694
  helix: -0.89 (0.26), residues: 386
  sheet: -2.39 (0.74), residues: 46
  loop : -2.51 (0.31), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  72 
 TYR   0.021   0.003   TYR B 297 
 PHE   0.027   0.005   PHE B 264 
 TRP   0.018   0.003   TRP B 302 
 HIS   0.006   0.002   HIS A  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00630 ( 9738)
  covalent geometry    : angle       0.90628 (13953)
  hydrogen bonds       : bond        0.11881 (  392)
  hydrogen bonds       : angle       5.19915 ( 1002)

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 108
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.6133 (mmt) cc_final: 0.5366 (mmt)
REVERT: A  280 TYR cc_start: 0.8288 (t80) cc_final: 0.7902 (t80)
REVERT: A  346 LYS cc_start: 0.9387 (tppt) cc_final: 0.9084 (tptp)
REVERT: B   72 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6137 (ptt-90)
REVERT: B  110 MET cc_start: 0.8309 (ptt) cc_final: 0.7820 (ptp)
REVERT: B  113 ASP cc_start: 0.9401 (p0) cc_final: 0.9016 (p0)
REVERT: B  209 ILE cc_start: 0.8728 (mm) cc_final: 0.8510 (mm)
REVERT: B  233 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8696 (pptt)
REVERT: B  254 MET cc_start: 0.6236 (OUTLIER) cc_final: 0.5611 (mmp)
  outliers start: 34
  outliers final: 22
  residues processed: 133
  average time/residue: 0.1192
  time to fit residues: 21.2534
Evaluate side-chains
  115 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  256 LYS
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain B residue   35 PHE
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue   72 ARG
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  147 LYS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  208 ASP
Chi-restraints excluded: chain B residue  233 LYS
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  254 MET
Chi-restraints excluded: chain B residue  256 LYS
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  313 ASP
Chi-restraints excluded: chain B residue  340 LEU
Chi-restraints excluded: chain B residue  347 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 58 optimal weight:    4.9990
   chunk 74 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 72 optimal weight:   10.0000
   chunk 61 optimal weight:    0.0970
   chunk 39 optimal weight:    0.9990
   chunk 81 optimal weight:   10.0000
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4748 r_free = 0.4748 target = 0.144427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.115867 restraints weight = 49381.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.118597 restraints weight = 37242.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.120385 restraints weight = 30856.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.120938 restraints weight = 27048.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.120938 restraints weight = 25445.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.4358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7003
moved from start:          0.5975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9738  Z= 0.130
  Angle     :  0.640  14.151  13953  Z= 0.313
  Chirality :  0.036   0.408   1674
  Planarity :  0.004   0.034   1157
  Dihedral  : 22.020 104.072   3365
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 18.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 16.67 %
    Favored  : 79.77 %
  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 aren not related in a simple way.
  whole: -1.63 (0.31), residues: 694
  helix: -0.23 (0.27), residues: 388
  sheet: -2.27 (0.73), residues: 46
  loop : -2.08 (0.34), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  72 
 TYR   0.024   0.002   TYR A  64 
 PHE   0.017   0.002   PHE B  35 
 TRP   0.011   0.001   TRP B 102 
 HIS   0.006   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9738)
  covalent geometry    : angle       0.63989 (13953)
  hydrogen bonds       : bond        0.04700 (  392)
  hydrogen bonds       : angle       4.59317 ( 1002)

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.6138 (mmt) cc_final: 0.4801 (mmt)
REVERT: A  152 ARG cc_start: 0.7326 (mtm180) cc_final: 0.7012 (mtm180)
REVERT: A  265 MET cc_start: 0.8579 (mmm) cc_final: 0.7979 (mmm)
REVERT: A  269 GLU cc_start: 0.9298 (tt0) cc_final: 0.8903 (tm-30)
REVERT: A  280 TYR cc_start: 0.8115 (t80) cc_final: 0.7879 (t80)
REVERT: A  346 LYS cc_start: 0.9288 (tppt) cc_final: 0.8905 (tptp)
REVERT: B   47 GLN cc_start: 0.7428 (tp-100) cc_final: 0.6758 (tp40)
REVERT: B   49 ASP cc_start: 0.9406 (t0) cc_final: 0.9010 (p0)
REVERT: B   50 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8670 (mt-10)
REVERT: B   94 ARG cc_start: 0.7550 (mmt90) cc_final: 0.7211 (mmt-90)
REVERT: B  177 GLN cc_start: 0.6783 (pm20) cc_final: 0.6154 (mp10)
REVERT: B  254 MET cc_start: 0.6068 (OUTLIER) cc_final: 0.5475 (mmp)
  outliers start: 22
  outliers final: 16
  residues processed: 120
  average time/residue: 0.1218
  time to fit residues: 19.5854
Evaluate side-chains
  111 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  256 LYS
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  254 MET
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  340 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 83 optimal weight:   10.0000
   chunk 43 optimal weight:    1.9990
   chunk 6 optimal weight:   10.0000
   chunk 76 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0050
   chunk 22 optimal weight:    5.9990
   chunk 44 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.9798

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

Flipped N/Q/H residues before XYZ refinement:
** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 198 GLN
** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4734 r_free = 0.4734 target = 0.143314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.114982 restraints weight = 49930.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.117508 restraints weight = 37921.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.119245 restraints weight = 31536.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.120029 restraints weight = 27916.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.121055 restraints weight = 25853.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.4350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6996
moved from start:          0.6220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9738  Z= 0.126
  Angle     :  0.627  12.949  13953  Z= 0.305
  Chirality :  0.035   0.375   1674
  Planarity :  0.004   0.033   1157
  Dihedral  : 21.844 102.401   3360
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 19.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 17.96 %
    Favored  : 78.32 %
  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 aren not related in a simple way.
  whole: -1.22 (0.32), residues: 694
  helix:  0.08 (0.27), residues: 388
  sheet: -2.09 (0.77), residues: 46
  loop : -1.86 (0.35), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 217 
 TYR   0.023   0.002   TYR B  64 
 PHE   0.024   0.002   PHE B 359 
 TRP   0.013   0.002   TRP A 102 
 HIS   0.006   0.001   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 9738)
  covalent geometry    : angle       0.62743 (13953)
  hydrogen bonds       : bond        0.04860 (  392)
  hydrogen bonds       : angle       4.67343 ( 1002)

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  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: A  129 LYS cc_start: 0.9209 (tttt) cc_final: 0.8893 (tppt)
REVERT: A  133 MET cc_start: 0.6269 (mmt) cc_final: 0.4003 (mmt)
REVERT: A  152 ARG cc_start: 0.7331 (mtm180) cc_final: 0.7052 (mtm180)
REVERT: A  243 MET cc_start: 0.8991 (pmm) cc_final: 0.8419 (mpp)
REVERT: A  265 MET cc_start: 0.8732 (mmm) cc_final: 0.8265 (mmt)
REVERT: A  269 GLU cc_start: 0.9323 (tt0) cc_final: 0.8925 (tm-30)
REVERT: A  280 TYR cc_start: 0.8208 (t80) cc_final: 0.7979 (t80)
REVERT: A  294 TYR cc_start: 0.8841 (m-10) cc_final: 0.8554 (m-80)
REVERT: A  346 LYS cc_start: 0.9330 (tppt) cc_final: 0.8941 (tptp)
REVERT: B   47 GLN cc_start: 0.7680 (tp-100) cc_final: 0.7429 (tp-100)
REVERT: B   49 ASP cc_start: 0.9410 (t0) cc_final: 0.8997 (p0)
REVERT: B   50 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8687 (mt-10)
REVERT: B   81 LYS cc_start: 0.9056 (tptt) cc_final: 0.8748 (mmmt)
REVERT: B  110 MET cc_start: 0.7410 (ptp) cc_final: 0.6061 (pmm)
REVERT: B  133 MET cc_start: 0.5321 (ptm) cc_final: 0.4547 (ptt)
REVERT: B  214 MET cc_start: 0.7123 (pmm) cc_final: 0.6414 (mmm)
REVERT: B  254 MET cc_start: 0.6031 (OUTLIER) cc_final: 0.5535 (mmp)
  outliers start: 23
  outliers final: 16
  residues processed: 116
  average time/residue: 0.1170
  time to fit residues: 18.0649
Evaluate side-chains
  104 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LYS
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  254 MET
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  340 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 72 optimal weight:    9.9990
   chunk 47 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 67 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   chunk 36 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0670
   chunk 39 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.6720

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

Flipped N/Q/H residues before XYZ refinement:
** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4751 r_free = 0.4751 target = 0.144231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.116433 restraints weight = 50612.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.119040 restraints weight = 38647.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.120840 restraints weight = 31977.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 14)----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.121371 restraints weight = 28094.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.122458 restraints weight = 26464.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.4377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6935
moved from start:          0.6318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9738  Z= 0.112
  Angle     :  0.617  15.878  13953  Z= 0.295
  Chirality :  0.035   0.426   1674
  Planarity :  0.004   0.040   1157
  Dihedral  : 21.704 102.326   3360
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 18.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 18.77 %
    Favored  : 77.67 %
  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 aren not related in a simple way.
  whole: -0.87 (0.33), residues: 694
  helix:  0.31 (0.28), residues: 390
  sheet: -1.90 (0.84), residues: 42
  loop : -1.63 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 217 
 TYR   0.018   0.002   TYR A 123 
 PHE   0.045   0.002   PHE B 359 
 TRP   0.040   0.002   TRP B 102 
 HIS   0.005   0.001   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 9738)
  covalent geometry    : angle       0.61713 (13953)
  hydrogen bonds       : bond        0.04462 (  392)
  hydrogen bonds       : angle       4.50488 ( 1002)

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.6272 (mmt) cc_final: 0.5001 (mmt)
REVERT: A  152 ARG cc_start: 0.7317 (mtm180) cc_final: 0.6783 (mtm180)
REVERT: A  179 MET cc_start: 0.4888 (tpp) cc_final: 0.4466 (tpp)
REVERT: A  243 MET cc_start: 0.9001 (pmm) cc_final: 0.8500 (mpp)
REVERT: A  265 MET cc_start: 0.8663 (mmm) cc_final: 0.8292 (mmm)
REVERT: A  269 GLU cc_start: 0.9332 (tt0) cc_final: 0.8914 (tm-30)
REVERT: A  280 TYR cc_start: 0.8233 (t80) cc_final: 0.7973 (t80)
REVERT: A  346 LYS cc_start: 0.9320 (tppt) cc_final: 0.8926 (tptp)
REVERT: B   48 GLU cc_start: 0.8796 (pt0) cc_final: 0.8380 (pm20)
REVERT: B   49 ASP cc_start: 0.9368 (t0) cc_final: 0.8777 (p0)
REVERT: B   50 GLU cc_start: 0.9120 (mt-10) cc_final: 0.8666 (mt-10)
REVERT: B   53 ASN cc_start: 0.9411 (m110) cc_final: 0.9045 (p0)
REVERT: B   81 LYS cc_start: 0.8997 (tptt) cc_final: 0.8734 (mmmt)
REVERT: B   86 ASN cc_start: 0.9137 (m110) cc_final: 0.8891 (p0)
REVERT: B  110 MET cc_start: 0.7304 (ptp) cc_final: 0.5806 (pmm)
REVERT: B  133 MET cc_start: 0.5292 (ptm) cc_final: 0.4703 (ptt)
REVERT: B  179 MET cc_start: 0.7544 (ttt) cc_final: 0.6995 (tpp)
REVERT: B  214 MET cc_start: 0.7095 (pmm) cc_final: 0.6478 (mmm)
REVERT: B  254 MET cc_start: 0.5864 (mmp) cc_final: 0.5314 (mmp)
  outliers start: 22
  outliers final: 13
  residues processed: 118
  average time/residue: 0.1094
  time to fit residues: 17.5678
Evaluate side-chains
  107 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LYS
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  340 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 57 optimal weight:    0.9990
   chunk 45 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9980
   chunk 76 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4725 r_free = 0.4725 target = 0.142404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.114166 restraints weight = 49433.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.116426 restraints weight = 37570.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.117613 restraints weight = 31502.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.119225 restraints weight = 27996.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.119630 restraints weight = 25650.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.4334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7028
moved from start:          0.6683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9738  Z= 0.129
  Angle     :  0.642  15.551  13953  Z= 0.312
  Chirality :  0.036   0.453   1674
  Planarity :  0.004   0.039   1157
  Dihedral  : 21.738 101.460   3360
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 20.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 18.93 %
    Favored  : 78.16 %
  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 aren not related in a simple way.
  whole: -0.83 (0.33), residues: 694
  helix:  0.25 (0.28), residues: 390
  sheet: -1.94 (0.84), residues: 42
  loop : -1.44 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 217 
 TYR   0.019   0.001   TYR A 123 
 PHE   0.022   0.002   PHE B 103 
 TRP   0.058   0.002   TRP B 102 
 HIS   0.004   0.001   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9738)
  covalent geometry    : angle       0.64156 (13953)
  hydrogen bonds       : bond        0.05078 (  392)
  hydrogen bonds       : angle       4.58357 ( 1002)

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.6349 (mmt) cc_final: 0.5114 (mmt)
REVERT: A  166 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.8735 (ttmt)
REVERT: A  243 MET cc_start: 0.8987 (pmm) cc_final: 0.8591 (mpp)
REVERT: A  265 MET cc_start: 0.8700 (mmm) cc_final: 0.8400 (mmm)
REVERT: A  269 GLU cc_start: 0.9348 (tt0) cc_final: 0.8964 (tm-30)
REVERT: A  280 TYR cc_start: 0.8311 (t80) cc_final: 0.8049 (t80)
REVERT: A  294 TYR cc_start: 0.8836 (m-10) cc_final: 0.8477 (m-80)
REVERT: A  346 LYS cc_start: 0.9327 (tppt) cc_final: 0.8962 (tptp)
REVERT: B   49 ASP cc_start: 0.9421 (t0) cc_final: 0.8999 (p0)
REVERT: B   81 LYS cc_start: 0.9012 (tptt) cc_final: 0.8740 (mmmt)
REVERT: B   86 ASN cc_start: 0.9120 (m110) cc_final: 0.8848 (p0)
REVERT: B  133 MET cc_start: 0.5370 (ptm) cc_final: 0.4833 (ptt)
REVERT: B  162 ASP cc_start: 0.9316 (t0) cc_final: 0.8713 (t0)
REVERT: B  166 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.9052 (mmtm)
REVERT: B  177 GLN cc_start: 0.7676 (pm20) cc_final: 0.6854 (mm-40)
REVERT: B  254 MET cc_start: 0.4994 (OUTLIER) cc_final: 0.4588 (mmp)
  outliers start: 18
  outliers final: 13
  residues processed: 110
  average time/residue: 0.1198
  time to fit residues: 17.7173
Evaluate side-chains
  108 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LYS
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain A residue  166 LYS
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue  166 LYS
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  254 MET
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  340 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 56 optimal weight:    0.5980
   chunk 21 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 78 optimal weight:    4.9990
   chunk 4 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 44 optimal weight:    0.3980
   overall best weight:    2.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 165 GLN
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 198 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.129406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.100591 restraints weight = 49136.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.102712 restraints weight = 38024.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 14)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.103567 restraints weight = 32321.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 12)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.103568 restraints weight = 29487.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.103568 restraints weight = 29487.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.4106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.8519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   9738  Z= 0.244
  Angle     :  0.821  14.637  13953  Z= 0.410
  Chirality :  0.043   0.530   1674
  Planarity :  0.005   0.048   1157
  Dihedral  : 22.453 104.745   3360
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 38.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 18.77 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.53 (0.31), residues: 694
  helix: -0.36 (0.26), residues: 388
  sheet: -2.38 (0.96), residues: 30
  loop : -1.69 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 224 
 TYR   0.022   0.003   TYR A 123 
 PHE   0.025   0.003   PHE B 264 
 TRP   0.049   0.003   TRP B 102 
 HIS   0.009   0.002   HIS B  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 9738)
  covalent geometry    : angle       0.82144 (13953)
  hydrogen bonds       : bond        0.09260 (  392)
  hydrogen bonds       : angle       5.34969 ( 1002)

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.9300 (tttt) cc_final: 0.9015 (tppt)
REVERT: A  133 MET cc_start: 0.6844 (mmt) cc_final: 0.4835 (mmt)
REVERT: A  179 MET cc_start: 0.5949 (tpp) cc_final: 0.5327 (tpp)
REVERT: A  242 HIS cc_start: 0.7024 (OUTLIER) cc_final: 0.6748 (p90)
REVERT: A  243 MET cc_start: 0.9062 (pmm) cc_final: 0.8443 (mpp)
REVERT: A  265 MET cc_start: 0.8847 (mmm) cc_final: 0.8583 (mmm)
REVERT: A  269 GLU cc_start: 0.9407 (tt0) cc_final: 0.9045 (tm-30)
REVERT: A  280 TYR cc_start: 0.8596 (t80) cc_final: 0.8273 (t80)
REVERT: A  346 LYS cc_start: 0.9408 (tppt) cc_final: 0.9067 (tptp)
REVERT: B   81 LYS cc_start: 0.9140 (tptt) cc_final: 0.8891 (mmmt)
REVERT: B   94 ARG cc_start: 0.8190 (mmm160) cc_final: 0.7744 (mmm160)
REVERT: B  110 MET cc_start: 0.7539 (ptp) cc_final: 0.6155 (pmm)
REVERT: B  133 MET cc_start: 0.6298 (ptm) cc_final: 0.5555 (ptt)
REVERT: B  179 MET cc_start: 0.8295 (ttt) cc_final: 0.6863 (tpp)
REVERT: B  214 MET cc_start: 0.7560 (pmm) cc_final: 0.6973 (mmt)
REVERT: B  254 MET cc_start: 0.6046 (OUTLIER) cc_final: 0.5672 (mmp)
  outliers start: 26
  outliers final: 20
  residues processed: 121
  average time/residue: 0.1098
  time to fit residues: 18.2301
Evaluate side-chains
  112 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LYS
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  242 HIS
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain B residue   35 PHE
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  254 MET
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  303 PHE
Chi-restraints excluded: chain B residue  306 PHE
Chi-restraints excluded: chain B residue  340 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 83 optimal weight:   10.0000
   chunk 17 optimal weight:    3.9990
   chunk 79 optimal weight:   10.0000
   chunk 12 optimal weight:    0.8980
   chunk 66 optimal weight:    0.4980
   chunk 53 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 GLN
** B  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.136799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.111302 restraints weight = 47773.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.112820 restraints weight = 44906.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.113147 restraints weight = 32419.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.113390 restraints weight = 28823.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.115106 restraints weight = 28054.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start:          0.8234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9738  Z= 0.146
  Angle     :  0.720  17.486  13953  Z= 0.354
  Chirality :  0.038   0.452   1674
  Planarity :  0.004   0.035   1157
  Dihedral  : 22.146 106.533   3360
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 22.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 21.20 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.19 (0.32), residues: 694
  helix: -0.08 (0.27), residues: 390
  sheet: -2.07 (1.02), residues: 30
  loop : -1.57 (0.37), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 217 
 TYR   0.021   0.002   TYR A 123 
 PHE   0.023   0.002   PHE B  35 
 TRP   0.045   0.003   TRP B 102 
 HIS   0.004   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 9738)
  covalent geometry    : angle       0.72001 (13953)
  hydrogen bonds       : bond        0.05596 (  392)
  hydrogen bonds       : angle       4.91115 ( 1002)

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 LYS cc_start: 0.9320 (tttt) cc_final: 0.8997 (tppt)
REVERT: A  133 MET cc_start: 0.6275 (mmt) cc_final: 0.4166 (mmt)
REVERT: A  152 ARG cc_start: 0.7382 (mtm180) cc_final: 0.7091 (mtm180)
REVERT: A  179 MET cc_start: 0.6183 (tpp) cc_final: 0.5604 (tpp)
REVERT: A  242 HIS cc_start: 0.7371 (OUTLIER) cc_final: 0.6724 (p90)
REVERT: A  243 MET cc_start: 0.9109 (pmm) cc_final: 0.8526 (mpp)
REVERT: A  251 GLN cc_start: 0.4711 (OUTLIER) cc_final: 0.3212 (pp30)
REVERT: A  269 GLU cc_start: 0.9324 (tt0) cc_final: 0.8912 (tm-30)
REVERT: A  280 TYR cc_start: 0.8460 (t80) cc_final: 0.8198 (t80)
REVERT: A  294 TYR cc_start: 0.8978 (m-10) cc_final: 0.8614 (m-80)
REVERT: A  346 LYS cc_start: 0.9352 (tppt) cc_final: 0.9021 (tptp)
REVERT: B   94 ARG cc_start: 0.8027 (mmm160) cc_final: 0.7681 (mmm160)
REVERT: B  110 MET cc_start: 0.6786 (ptp) cc_final: 0.5188 (pmm)
REVERT: B  133 MET cc_start: 0.5581 (ptm) cc_final: 0.4906 (ptt)
REVERT: B  179 MET cc_start: 0.8013 (ttt) cc_final: 0.6298 (tpp)
REVERT: B  228 ASP cc_start: 0.8878 (m-30) cc_final: 0.8506 (m-30)
REVERT: B  303 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8616 (t80)
  outliers start: 19
  outliers final: 13
  residues processed: 108
  average time/residue: 0.1220
  time to fit residues: 17.6507
Evaluate side-chains
  103 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LYS
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  242 HIS
Chi-restraints excluded: chain A residue  251 GLN
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  303 PHE
Chi-restraints excluded: chain B residue  340 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 12 optimal weight:    0.3980
   chunk 10 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   chunk 70 optimal weight:   10.0000
   chunk 55 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 GLN
** B  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.137487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.109064 restraints weight = 50152.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.111458 restraints weight = 38101.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.113127 restraints weight = 31868.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.113642 restraints weight = 28255.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.113642 restraints weight = 26680.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.4263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.8261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9738  Z= 0.144
  Angle     :  0.743  18.822  13953  Z= 0.361
  Chirality :  0.038   0.454   1674
  Planarity :  0.004   0.040   1157
  Dihedral  : 22.018 104.775   3360
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 23.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 22.49 %
    Favored  : 74.60 %
  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 aren not related in a simple way.
  whole: -1.19 (0.32), residues: 694
  helix: -0.12 (0.27), residues: 392
  sheet: -2.32 (0.83), residues: 42
  loop : -1.41 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 217 
 TYR   0.018   0.002   TYR A 297 
 PHE   0.022   0.002   PHE B  35 
 TRP   0.044   0.002   TRP B 102 
 HIS   0.007   0.001   HIS B  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 9738)
  covalent geometry    : angle       0.74315 (13953)
  hydrogen bonds       : bond        0.05567 (  392)
  hydrogen bonds       : angle       4.87422 ( 1002)

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7457 (mt)
REVERT: A  129 LYS cc_start: 0.9270 (tttt) cc_final: 0.8964 (tppt)
REVERT: A  133 MET cc_start: 0.6741 (mmt) cc_final: 0.4567 (mmt)
REVERT: A  152 ARG cc_start: 0.7409 (mtm180) cc_final: 0.7113 (mtm180)
REVERT: A  179 MET cc_start: 0.5855 (tpp) cc_final: 0.5272 (tpp)
REVERT: A  217 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6859 (mmt180)
REVERT: A  243 MET cc_start: 0.9116 (pmm) cc_final: 0.8797 (mpp)
REVERT: A  251 GLN cc_start: 0.4970 (OUTLIER) cc_final: 0.3590 (pp30)
REVERT: A  269 GLU cc_start: 0.9364 (tt0) cc_final: 0.8962 (tm-30)
REVERT: A  280 TYR cc_start: 0.8383 (t80) cc_final: 0.8094 (t80)
REVERT: A  346 LYS cc_start: 0.9331 (tppt) cc_final: 0.9005 (tptp)
REVERT: B   94 ARG cc_start: 0.7940 (mmm160) cc_final: 0.7588 (mmm160)
REVERT: B  110 MET cc_start: 0.6758 (ptp) cc_final: 0.5158 (pmm)
REVERT: B  133 MET cc_start: 0.5870 (ptm) cc_final: 0.5160 (ptt)
REVERT: B  228 ASP cc_start: 0.8750 (m-30) cc_final: 0.8345 (m-30)
  outliers start: 18
  outliers final: 14
  residues processed: 108
  average time/residue: 0.1314
  time to fit residues: 18.7234
Evaluate side-chains
  106 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LYS
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  123 TYR
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  251 GLN
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  303 PHE
Chi-restraints excluded: chain B residue  340 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 59 optimal weight:    0.2980
   chunk 44 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 83 optimal weight:    9.9990
   chunk 81 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 19 optimal weight:   20.0000
   chunk 49 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 51 optimal weight:    0.3980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 GLN
A 304 ASN
** B  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 248 GLN
B 358 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4719 r_free = 0.4719 target = 0.139517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.111803 restraints weight = 50175.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.114187 restraints weight = 38018.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.115916 restraints weight = 31718.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.117309 restraints weight = 27888.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.117853 restraints weight = 25166.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.4339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
moved from start:          0.8142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9738  Z= 0.127
  Angle     :  0.723  17.592  13953  Z= 0.348
  Chirality :  0.037   0.425   1674
  Planarity :  0.004   0.047   1157
  Dihedral  : 21.833 104.652   3360
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 19.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 22.98 %
    Favored  : 73.95 %
  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 aren not related in a simple way.
  whole: -1.09 (0.32), residues: 694
  helix: -0.03 (0.27), residues: 388
  sheet: -2.11 (0.85), residues: 46
  loop : -1.39 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 217 
 TYR   0.022   0.002   TYR A 297 
 PHE   0.024   0.002   PHE B  35 
 TRP   0.044   0.002   TRP B 102 
 HIS   0.004   0.001   HIS A 358 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9738)
  covalent geometry    : angle       0.72263 (13953)
  hydrogen bonds       : bond        0.05075 (  392)
  hydrogen bonds       : angle       4.69305 ( 1002)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2428.36 seconds
wall clock time: 42 minutes 37.24 seconds (2557.24 seconds total)