Starting phenix.real_space_refine
on Wed Apr 30 02:07:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zmk_60250/04_2025/8zmk_60250.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zmk_60250/04_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_60250/04_2025/8zmk_60250.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zmk_60250/04_2025/8zmk_60250.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zmk_60250/04_2025/8zmk_60250.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zmk_60250/04_2025/8zmk_60250.cif"
  }
  resolution = 3.85
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 7.38, per 1000 atoms: 0.80
  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: 2.38
  Conformation dependent library (CDL) restraints added in 741.3 milliseconds
  

  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: 3.63
  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: 2.80

  Time building geometry restraints manager: 2.84 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:             2.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.550
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.390
-------------------------------------------------------------------------------
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 : 6.89
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (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
 TRP   0.002   0.000   TRP B 128 
 HIS   0.001   0.000   HIS B 358 
 PHE   0.004   0.001   PHE A 203 
 TYR   0.003   0.001   TYR B 226 
 ARG   0.001   0.000   ARG A 371 

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

*********************** 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  : 0.995 
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: 0.2998
  time to fit residues: 71.8004
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  : 0.720 
-------------------------------------------------------------------------------
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 70 optimal weight:   10.0000
   chunk 63 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 21 optimal weight:    9.9990
   chunk 42 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 49 optimal weight:    7.9990
   chunk 76 optimal weight:    9.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.5022 r_free = 0.5022 target = 0.177979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5056 r_free = 0.5056 target = 0.162625 restraints weight = 73809.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4961 r_free = 0.4961 target = 0.164047 restraints weight = 49799.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4969 r_free = 0.4969 target = 0.164921 restraints weight = 39544.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.4641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6163
moved from start:          0.3036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9738  Z= 0.145
  Angle     :  0.629   9.827  13953  Z= 0.310
  Chirality :  0.035   0.326   1674
  Planarity :  0.004   0.040   1157
  Dihedral  : 21.303 105.833   3372
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 16.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.24 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.31), residues: 694
  helix:  0.04 (0.27), residues: 384
  sheet: -1.20 (0.94), residues: 32
  loop : -2.50 (0.30), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 302 
 HIS   0.020   0.003   HIS B 242 
 PHE   0.030   0.003   PHE B 359 
 TYR   0.022   0.003   TYR A 123 
 ARG   0.008   0.001   ARG A  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04792 (  392)
  hydrogen bonds       : angle       4.11145 ( 1002)
  covalent geometry    : bond        0.00327 ( 9738)
  covalent geometry    : angle       0.62873 (13953)

*********************** 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
  138 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 LYS cc_start: 0.8239 (mmtm) cc_final: 0.7318 (mmtm)
REVERT: A  133 MET cc_start: 0.4433 (mmp) cc_final: 0.3867 (mmm)
REVERT: A  161 LEU cc_start: 0.8426 (tt) cc_final: 0.8111 (tt)
REVERT: A  265 MET cc_start: 0.8259 (mmm) cc_final: 0.7844 (mmm)
REVERT: A  269 GLU cc_start: 0.9129 (tt0) cc_final: 0.8897 (tp30)
REVERT: A  273 ASN cc_start: 0.9356 (m-40) cc_final: 0.9052 (m-40)
REVERT: B   33 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.8939 (pm20)
REVERT: B   51 LEU cc_start: 0.9580 (tt) cc_final: 0.9191 (tt)
REVERT: B  228 ASP cc_start: 0.8115 (m-30) cc_final: 0.7872 (m-30)
REVERT: B  229 ASP cc_start: 0.8215 (m-30) cc_final: 0.8010 (m-30)
REVERT: B  254 MET cc_start: 0.5609 (mmp) cc_final: 0.5177 (mmp)
  outliers start: 16
  outliers final: 9
  residues processed: 135
  average time/residue: 0.2924
  time to fit residues: 51.8902
Evaluate side-chains
  114 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
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   67 PHE
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  194 TYR
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 6 optimal weight:    9.9990
   chunk 71 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 57 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 8 optimal weight:   20.0000
   chunk 59 optimal weight:    0.0170
   chunk 67 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   overall best weight:    2.6024

-------------------------------------------------------------------------------
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
** B 167 ASN ** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4727 r_free = 0.4727 target = 0.143636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.116196 restraints weight = 50425.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.118485 restraints weight = 37996.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.119974 restraints weight = 31914.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.4312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7093
moved from start:          0.5163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9738  Z= 0.224
  Angle     :  0.723  13.176  13953  Z= 0.366
  Chirality :  0.038   0.336   1674
  Planarity :  0.005   0.054   1157
  Dihedral  : 21.966 102.631   3372
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 24.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.35 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 14.08 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.31), residues: 694
  helix: -0.25 (0.27), residues: 388
  sheet: -2.00 (0.77), residues: 46
  loop : -2.22 (0.32), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 128 
 HIS   0.006   0.002   HIS A  74 
 PHE   0.025   0.003   PHE B 264 
 TYR   0.025   0.003   TYR B  64 
 ARG   0.006   0.001   ARG A 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07776 (  392)
  hydrogen bonds       : angle       4.67138 ( 1002)
  covalent geometry    : bond        0.00448 ( 9738)
  covalent geometry    : angle       0.72332 (13953)

*********************** 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
  127 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.727 
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  113 ASP cc_start: 0.8995 (t0) cc_final: 0.8766 (t0)
REVERT: A  133 MET cc_start: 0.6341 (mmt) cc_final: 0.5477 (mmm)
REVERT: A  214 MET cc_start: 0.9305 (tpp) cc_final: 0.8319 (mmp)
REVERT: A  265 MET cc_start: 0.9089 (mmm) cc_final: 0.8599 (mmm)
REVERT: A  269 GLU cc_start: 0.9418 (tt0) cc_final: 0.9168 (tm-30)
REVERT: A  294 TYR cc_start: 0.8873 (m-10) cc_final: 0.8582 (m-80)
REVERT: A  346 LYS cc_start: 0.9354 (tppt) cc_final: 0.9050 (tptp)
REVERT: B   33 GLU cc_start: 0.9524 (OUTLIER) cc_final: 0.9191 (pm20)
REVERT: B  113 ASP cc_start: 0.9473 (p0) cc_final: 0.9169 (p0)
REVERT: B  209 ILE cc_start: 0.8858 (mm) cc_final: 0.8343 (mm)
REVERT: B  228 ASP cc_start: 0.8641 (m-30) cc_final: 0.8266 (m-30)
REVERT: B  229 ASP cc_start: 0.8532 (m-30) cc_final: 0.8263 (m-30)
REVERT: B  254 MET cc_start: 0.6458 (mmp) cc_final: 0.5680 (mmp)
  outliers start: 23
  outliers final: 14
  residues processed: 122
  average time/residue: 0.2533
  time to fit residues: 40.9357
Evaluate side-chains
  102 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
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  188 THR
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain B residue   33 GLU
Chi-restraints excluded: chain B residue   35 PHE
Chi-restraints excluded: chain B residue   67 PHE
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  242 HIS
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  340 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 49 optimal weight:    5.9990
   chunk 64 optimal weight:    8.9990
   chunk 3 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0370
   chunk 12 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.7458

-------------------------------------------------------------------------------
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 167 ASN ** 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 = 0.4938 r_free = 0.4938 target = 0.167811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5109 r_free = 0.5109 target = 0.150788 restraints weight = 72668.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4860 r_free = 0.4860 target = 0.153362 restraints weight = 63059.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4893 r_free = 0.4893 target = 0.154512 restraints weight = 41038.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.4513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6587
moved from start:          0.5246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9738  Z= 0.118
  Angle     :  0.604  12.219  13953  Z= 0.292
  Chirality :  0.033   0.212   1674
  Planarity :  0.004   0.032   1157
  Dihedral  : 21.769 103.551   3368
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 18.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 15.86 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.32), residues: 694
  helix:  0.07 (0.28), residues: 390
  sheet: -1.84 (0.80), residues: 46
  loop : -2.05 (0.34), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  98 
 HIS   0.007   0.001   HIS B 242 
 PHE   0.012   0.002   PHE B  35 
 TYR   0.019   0.002   TYR A 123 
 ARG   0.004   0.001   ARG B  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04433 (  392)
  hydrogen bonds       : angle       4.42052 ( 1002)
  covalent geometry    : bond        0.00260 ( 9738)
  covalent geometry    : angle       0.60422 (13953)

*********************** 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
  125 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  133 MET cc_start: 0.5424 (mmt) cc_final: 0.4219 (mmt)
REVERT: A  165 GLN cc_start: 0.8934 (mm110) cc_final: 0.8730 (mm110)
REVERT: A  166 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.8626 (ttmm)
REVERT: A  179 MET cc_start: 0.5309 (tpp) cc_final: 0.4737 (tpt)
REVERT: A  265 MET cc_start: 0.8640 (mmm) cc_final: 0.8265 (mmm)
REVERT: A  273 ASN cc_start: 0.9426 (m-40) cc_final: 0.8985 (m-40)
REVERT: A  346 LYS cc_start: 0.9343 (tppt) cc_final: 0.8975 (tptp)
REVERT: B   33 GLU cc_start: 0.9425 (OUTLIER) cc_final: 0.9011 (pm20)
REVERT: B  110 MET cc_start: 0.6971 (ptp) cc_final: 0.5714 (pmm)
REVERT: B  214 MET cc_start: 0.6842 (pmm) cc_final: 0.6070 (mmm)
REVERT: B  228 ASP cc_start: 0.8523 (m-30) cc_final: 0.8242 (m-30)
REVERT: B  229 ASP cc_start: 0.8445 (m-30) cc_final: 0.8185 (m-30)
REVERT: B  254 MET cc_start: 0.6275 (OUTLIER) cc_final: 0.5620 (mmp)
REVERT: B  325 GLU cc_start: 0.7551 (pt0) cc_final: 0.7018 (pm20)
  outliers start: 21
  outliers final: 12
  residues processed: 121
  average time/residue: 0.2613
  time to fit residues: 41.7944
Evaluate side-chains
  103 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 LYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain B residue   33 GLU
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue   95 VAL
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  242 HIS
Chi-restraints excluded: chain B residue  254 MET
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 57 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 24 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0570
   chunk 58 optimal weight:    0.6980
   chunk 48 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 54 optimal weight:    5.9990
   overall best weight:    0.6300

-------------------------------------------------------------------------------
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**
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 ASN ** 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 = 0.4943 r_free = 0.4943 target = 0.168372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4986 r_free = 0.4986 target = 0.152381 restraints weight = 72740.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4895 r_free = 0.4895 target = 0.154170 restraints weight = 57290.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4886 r_free = 0.4886 target = 0.154820 restraints weight = 43045.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.4514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6521
moved from start:          0.5407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9738  Z= 0.111
  Angle     :  0.593  11.048  13953  Z= 0.286
  Chirality :  0.033   0.315   1674
  Planarity :  0.004   0.035   1157
  Dihedral  : 21.609 102.858   3367
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 17.48 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.32), residues: 694
  helix:  0.30 (0.28), residues: 392
  sheet: -1.60 (0.86), residues: 42
  loop : -1.83 (0.35), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  98 
 HIS   0.010   0.002   HIS B  74 
 PHE   0.038   0.002   PHE B 359 
 TYR   0.019   0.002   TYR A 123 
 ARG   0.009   0.000   ARG B  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04375 (  392)
  hydrogen bonds       : angle       4.33543 ( 1002)
  covalent geometry    : bond        0.00243 ( 9738)
  covalent geometry    : angle       0.59328 (13953)

*********************** 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
  118 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.765 
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  133 MET cc_start: 0.5056 (mmt) cc_final: 0.3857 (mmt)
REVERT: A  165 GLN cc_start: 0.8917 (mm110) cc_final: 0.8683 (mm110)
REVERT: A  166 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8543 (ttmm)
REVERT: A  179 MET cc_start: 0.5434 (tpp) cc_final: 0.5102 (tpt)
REVERT: A  265 MET cc_start: 0.8567 (mmm) cc_final: 0.8060 (mmm)
REVERT: A  346 LYS cc_start: 0.9316 (tppt) cc_final: 0.8954 (tptp)
REVERT: B   33 GLU cc_start: 0.9363 (OUTLIER) cc_final: 0.8927 (pm20)
REVERT: B   77 GLN cc_start: 0.9095 (pt0) cc_final: 0.8497 (mm-40)
REVERT: B   80 MET cc_start: 0.8501 (tpp) cc_final: 0.7785 (mtp)
REVERT: B   86 ASN cc_start: 0.9092 (m110) cc_final: 0.8768 (p0)
REVERT: B  110 MET cc_start: 0.6256 (ptp) cc_final: 0.4611 (pmm)
REVERT: B  179 MET cc_start: 0.6682 (ttt) cc_final: 0.4542 (tpp)
REVERT: B  214 MET cc_start: 0.6841 (pmm) cc_final: 0.6226 (mmm)
REVERT: B  228 ASP cc_start: 0.8498 (m-30) cc_final: 0.8215 (m-30)
REVERT: B  229 ASP cc_start: 0.8502 (m-30) cc_final: 0.8260 (m-30)
REVERT: B  254 MET cc_start: 0.5827 (OUTLIER) cc_final: 0.5126 (mmp)
  outliers start: 20
  outliers final: 13
  residues processed: 116
  average time/residue: 0.2625
  time to fit residues: 40.4625
Evaluate side-chains
  102 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 LYS
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   33 GLU
Chi-restraints excluded: chain B residue   58 LYS
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  222 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 37 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 60 optimal weight:    4.9990
   chunk 21 optimal weight:    0.3980
   chunk 83 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 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 = 0.4754 r_free = 0.4754 target = 0.146184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.117760 restraints weight = 47861.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.120329 restraints weight = 36662.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.121409 restraints weight = 30686.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.4343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.5864

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= 0.128
  Angle     :  0.609   9.102  13953  Z= 0.302
  Chirality :  0.034   0.304   1674
  Planarity :  0.004   0.039   1157
  Dihedral  : 21.665 102.023   3363
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 18.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 17.80 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.33), residues: 694
  helix:  0.33 (0.28), residues: 394
  sheet: -1.70 (0.87), residues: 42
  loop : -1.65 (0.35), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  98 
 HIS   0.004   0.001   HIS B 242 
 PHE   0.041   0.002   PHE B 359 
 TYR   0.019   0.001   TYR A 123 
 ARG   0.004   0.000   ARG B  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04979 (  392)
  hydrogen bonds       : angle       4.38794 ( 1002)
  covalent geometry    : bond        0.00279 ( 9738)
  covalent geometry    : angle       0.60861 (13953)

*********************** 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
  119 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.776 
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  133 MET cc_start: 0.6390 (mmt) cc_final: 0.5138 (mmt)
REVERT: A  166 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.8609 (ttmt)
REVERT: A  243 MET cc_start: 0.8970 (pmm) cc_final: 0.8495 (mpp)
REVERT: A  265 MET cc_start: 0.8878 (mmm) cc_final: 0.8414 (mmm)
REVERT: A  346 LYS cc_start: 0.9322 (tppt) cc_final: 0.8951 (tptp)
REVERT: B   33 GLU cc_start: 0.9461 (OUTLIER) cc_final: 0.9039 (pm20)
REVERT: B   49 ASP cc_start: 0.9274 (t0) cc_final: 0.8776 (p0)
REVERT: B   50 GLU cc_start: 0.9139 (pt0) cc_final: 0.8855 (pt0)
REVERT: B  110 MET cc_start: 0.6821 (ptp) cc_final: 0.5144 (pmm)
REVERT: B  161 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9131 (tp)
REVERT: B  214 MET cc_start: 0.6980 (pmm) cc_final: 0.6375 (mmm)
REVERT: B  228 ASP cc_start: 0.8608 (m-30) cc_final: 0.8225 (m-30)
REVERT: B  229 ASP cc_start: 0.8617 (m-30) cc_final: 0.8350 (m-30)
REVERT: B  254 MET cc_start: 0.6274 (OUTLIER) cc_final: 0.5450 (mmp)
REVERT: B  325 GLU cc_start: 0.7534 (pt0) cc_final: 0.6924 (pm20)
  outliers start: 24
  outliers final: 16
  residues processed: 116
  average time/residue: 0.2468
  time to fit residues: 38.4408
Evaluate side-chains
  105 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 85
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 LYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  203 PHE
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   33 GLU
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  222 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0060
   chunk 15 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 6 optimal weight:    7.9990
   chunk 69 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 75 optimal weight:   10.0000
   chunk 25 optimal weight:    0.7980
   chunk 78 optimal weight:    4.9990
   overall best weight:    0.6796

-------------------------------------------------------------------------------
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**
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 273 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4772 r_free = 0.4772 target = 0.147418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.119648 restraints weight = 49221.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.122113 restraints weight = 37489.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.123279 restraints weight = 30865.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.4368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.6014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9738  Z= 0.112
  Angle     :  0.602   8.364  13953  Z= 0.297
  Chirality :  0.033   0.251   1674
  Planarity :  0.004   0.038   1157
  Dihedral  : 21.601 102.210   3363
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 16.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 18.12 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.32), residues: 694
  helix:  0.26 (0.28), residues: 398
  sheet: -1.57 (0.87), residues: 42
  loop : -1.68 (0.35), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  98 
 HIS   0.004   0.001   HIS B  74 
 PHE   0.012   0.001   PHE B  35 
 TYR   0.020   0.002   TYR A 123 
 ARG   0.006   0.000   ARG B  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04480 (  392)
  hydrogen bonds       : angle       4.35685 ( 1002)
  covalent geometry    : bond        0.00241 ( 9738)
  covalent geometry    : angle       0.60183 (13953)

*********************** 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
  108 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.969 
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: A  133 MET cc_start: 0.6155 (mmt) cc_final: 0.4847 (mmt)
REVERT: A  166 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.8625 (ttmm)
REVERT: A  243 MET cc_start: 0.8946 (pmm) cc_final: 0.8693 (tpp)
REVERT: A  265 MET cc_start: 0.8691 (mmm) cc_final: 0.8234 (mmp)
REVERT: A  294 TYR cc_start: 0.8737 (m-10) cc_final: 0.8406 (m-80)
REVERT: A  346 LYS cc_start: 0.9278 (tppt) cc_final: 0.8914 (tptp)
REVERT: B   33 GLU cc_start: 0.9413 (OUTLIER) cc_final: 0.9050 (pm20)
REVERT: B   80 MET cc_start: 0.8465 (tpp) cc_final: 0.7975 (mtp)
REVERT: B  110 MET cc_start: 0.6614 (ptp) cc_final: 0.5017 (pmm)
REVERT: B  161 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9120 (tp)
REVERT: B  179 MET cc_start: 0.7091 (ttt) cc_final: 0.6441 (tpp)
REVERT: B  214 MET cc_start: 0.7039 (pmm) cc_final: 0.6444 (mmm)
REVERT: B  228 ASP cc_start: 0.8601 (m-30) cc_final: 0.8226 (m-30)
REVERT: B  229 ASP cc_start: 0.8610 (m-30) cc_final: 0.8335 (m-30)
REVERT: B  254 MET cc_start: 0.6249 (OUTLIER) cc_final: 0.5433 (mmp)
REVERT: B  325 GLU cc_start: 0.7495 (pt0) cc_final: 0.6989 (pm20)
  outliers start: 20
  outliers final: 13
  residues processed: 103
  average time/residue: 0.2454
  time to fit residues: 33.8879
Evaluate side-chains
  102 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 LYS
Chi-restraints excluded: chain A residue  214 MET
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain B residue   33 GLU
Chi-restraints excluded: chain B residue   35 PHE
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue   85 VAL
Chi-restraints excluded: chain B residue  161 LEU
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  340 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 43 optimal weight:    0.1980
   chunk 20 optimal weight:    4.9990
   chunk 71 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0970
   chunk 65 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.5778

-------------------------------------------------------------------------------
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**
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4787 r_free = 0.4787 target = 0.148738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.120857 restraints weight = 50083.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.123408 restraints weight = 38098.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.124660 restraints weight = 31608.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.4381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
moved from start:          0.6164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9738  Z= 0.105
  Angle     :  0.597  14.003  13953  Z= 0.291
  Chirality :  0.034   0.442   1674
  Planarity :  0.004   0.042   1157
  Dihedral  : 21.506 101.979   3363
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 15.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 18.61 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.32), residues: 694
  helix:  0.26 (0.28), residues: 404
  sheet: -1.33 (0.89), residues: 42
  loop : -1.45 (0.35), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  98 
 HIS   0.003   0.001   HIS A 358 
 PHE   0.016   0.001   PHE B  35 
 TYR   0.019   0.002   TYR A 123 
 ARG   0.007   0.000   ARG B  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04359 (  392)
  hydrogen bonds       : angle       4.31293 ( 1002)
  covalent geometry    : bond        0.00226 ( 9738)
  covalent geometry    : angle       0.59729 (13953)

*********************** 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
  113 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.722 
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  133 MET cc_start: 0.6197 (mmt) cc_final: 0.4998 (mmt)
REVERT: A  152 ARG cc_start: 0.7278 (mtm180) cc_final: 0.7020 (mtm180)
REVERT: A  166 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8527 (ttmm)
REVERT: A  179 MET cc_start: 0.3991 (tpp) cc_final: 0.3452 (tpp)
REVERT: A  197 MET cc_start: 0.4323 (tpt) cc_final: 0.4104 (tpp)
REVERT: A  243 MET cc_start: 0.8922 (pmm) cc_final: 0.8614 (tpp)
REVERT: A  251 GLN cc_start: 0.4524 (OUTLIER) cc_final: 0.2934 (pp30)
REVERT: A  254 MET cc_start: 0.6252 (mmm) cc_final: 0.3669 (mmm)
REVERT: A  265 MET cc_start: 0.8542 (mmm) cc_final: 0.8095 (mmt)
REVERT: A  346 LYS cc_start: 0.9289 (tppt) cc_final: 0.8918 (tptp)
REVERT: B   33 GLU cc_start: 0.9418 (OUTLIER) cc_final: 0.9083 (pm20)
REVERT: B   49 ASP cc_start: 0.9173 (t0) cc_final: 0.8671 (p0)
REVERT: B   58 LYS cc_start: 0.5150 (OUTLIER) cc_final: 0.4902 (pttp)
REVERT: B  110 MET cc_start: 0.6398 (ptp) cc_final: 0.4876 (pmm)
REVERT: B  179 MET cc_start: 0.7151 (ttt) cc_final: 0.6471 (tpp)
REVERT: B  214 MET cc_start: 0.7027 (pmm) cc_final: 0.6543 (mmm)
REVERT: B  228 ASP cc_start: 0.8592 (m-30) cc_final: 0.8222 (m-30)
REVERT: B  229 ASP cc_start: 0.8570 (m-30) cc_final: 0.8297 (m-30)
REVERT: B  254 MET cc_start: 0.5843 (OUTLIER) cc_final: 0.5035 (mmp)
REVERT: B  325 GLU cc_start: 0.7517 (pt0) cc_final: 0.7082 (pm20)
  outliers start: 19
  outliers final: 10
  residues processed: 111
  average time/residue: 0.2525
  time to fit residues: 37.3250
Evaluate side-chains
  103 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 LYS
Chi-restraints excluded: chain A residue  214 MET
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   33 GLU
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  222 LEU
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  340 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 11 optimal weight:    8.9990
   chunk 81 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 64 optimal weight:    0.0980
   chunk 37 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 73 optimal weight:    9.9990
   chunk 65 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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**
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 GLN
B 198 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4771 r_free = 0.4771 target = 0.147679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.122906 restraints weight = 48976.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.124160 restraints weight = 36115.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.124725 restraints weight = 33766.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.4384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6898
moved from start:          0.6312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9738  Z= 0.108
  Angle     :  0.606  16.902  13953  Z= 0.295
  Chirality :  0.034   0.470   1674
  Planarity :  0.004   0.052   1157
  Dihedral  : 21.503 101.739   3363
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 16.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 20.06 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.32), residues: 694
  helix:  0.30 (0.28), residues: 404
  sheet: -1.27 (0.90), residues: 42
  loop : -1.42 (0.35), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  98 
 HIS   0.011   0.002   HIS A 358 
 PHE   0.016   0.001   PHE B  35 
 TYR   0.020   0.001   TYR A 123 
 ARG   0.008   0.000   ARG B  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04525 (  392)
  hydrogen bonds       : angle       4.32295 ( 1002)
  covalent geometry    : bond        0.00234 ( 9738)
  covalent geometry    : angle       0.60561 (13953)

*********************** 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
  107 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.714 
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: 0.5918 (mmt) cc_final: 0.4632 (mmt)
REVERT: A  152 ARG cc_start: 0.7264 (mtm180) cc_final: 0.7017 (mtm180)
REVERT: A  162 ASP cc_start: 0.9382 (p0) cc_final: 0.9177 (p0)
REVERT: A  166 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8474 (ttmt)
REVERT: A  179 MET cc_start: 0.4591 (tpp) cc_final: 0.4140 (tpp)
REVERT: A  197 MET cc_start: 0.4381 (tpt) cc_final: 0.4130 (tpp)
REVERT: A  243 MET cc_start: 0.8881 (pmm) cc_final: 0.8541 (tpp)
REVERT: A  254 MET cc_start: 0.6120 (mmm) cc_final: 0.3725 (mmm)
REVERT: A  265 MET cc_start: 0.8493 (mmm) cc_final: 0.8116 (mmp)
REVERT: A  294 TYR cc_start: 0.8712 (m-10) cc_final: 0.8335 (m-80)
REVERT: A  346 LYS cc_start: 0.9286 (tppt) cc_final: 0.8926 (tptp)
REVERT: B   33 GLU cc_start: 0.9427 (OUTLIER) cc_final: 0.9085 (pm20)
REVERT: B   58 LYS cc_start: 0.5266 (OUTLIER) cc_final: 0.4784 (pttp)
REVERT: B   80 MET cc_start: 0.8393 (tpp) cc_final: 0.7951 (mtp)
REVERT: B  110 MET cc_start: 0.6285 (ptp) cc_final: 0.4796 (pmm)
REVERT: B  179 MET cc_start: 0.7048 (ttt) cc_final: 0.6342 (tpp)
REVERT: B  228 ASP cc_start: 0.8604 (m-30) cc_final: 0.8232 (m-30)
REVERT: B  229 ASP cc_start: 0.8589 (m-30) cc_final: 0.8311 (m-30)
REVERT: B  254 MET cc_start: 0.5850 (OUTLIER) cc_final: 0.5088 (mmp)
REVERT: B  325 GLU cc_start: 0.7457 (pt0) cc_final: 0.7008 (pm20)
  outliers start: 18
  outliers final: 10
  residues processed: 106
  average time/residue: 0.2574
  time to fit residues: 36.2115
Evaluate side-chains
  102 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LYS
Chi-restraints excluded: chain A residue  166 LYS
Chi-restraints excluded: chain A residue  188 THR
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   33 GLU
Chi-restraints excluded: chain B residue   58 LYS
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  340 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 18 optimal weight:    0.2980
   chunk 33 optimal weight:    8.9990
   chunk 8 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 63 optimal weight:    0.5980
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.7184

-------------------------------------------------------------------------------
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**
A 251 GLN
B 198 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.147328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.122434 restraints weight = 49160.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4470 r_free = 0.4470 target = 0.123431 restraints weight = 35698.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.124145 restraints weight = 33379.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.4374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6910
moved from start:          0.6506

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= 0.109
  Angle     :  0.626  17.921  13953  Z= 0.300
  Chirality :  0.034   0.444   1674
  Planarity :  0.004   0.046   1157
  Dihedral  : 21.493 101.550   3363
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 16.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 20.39 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.32), residues: 694
  helix:  0.32 (0.28), residues: 404
  sheet: -1.26 (0.90), residues: 42
  loop : -1.33 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 102 
 HIS   0.011   0.001   HIS A 358 
 PHE   0.018   0.001   PHE B  35 
 TYR   0.022   0.002   TYR A 297 
 ARG   0.008   0.001   ARG B  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04528 (  392)
  hydrogen bonds       : angle       4.30369 ( 1002)
  covalent geometry    : bond        0.00237 ( 9738)
  covalent geometry    : angle       0.62575 (13953)

********************** 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
  108 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.847 
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  133 MET cc_start: 0.5875 (mmt) cc_final: 0.4616 (mmt)
REVERT: A  152 ARG cc_start: 0.7275 (mtm180) cc_final: 0.7035 (mtm180)
REVERT: A  162 ASP cc_start: 0.9379 (p0) cc_final: 0.9173 (p0)
REVERT: A  166 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8492 (ttmt)
REVERT: A  179 MET cc_start: 0.4555 (tpp) cc_final: 0.4185 (tpp)
REVERT: A  197 MET cc_start: 0.4506 (tpt) cc_final: 0.4266 (tpp)
REVERT: A  243 MET cc_start: 0.8854 (pmm) cc_final: 0.8520 (tpp)
REVERT: A  251 GLN cc_start: 0.4464 (OUTLIER) cc_final: 0.3050 (pp30)
REVERT: A  254 MET cc_start: 0.6239 (mmm) cc_final: 0.3602 (mmm)
REVERT: A  265 MET cc_start: 0.8413 (mmm) cc_final: 0.7995 (mmt)
REVERT: A  294 TYR cc_start: 0.8778 (m-10) cc_final: 0.8383 (m-80)
REVERT: A  346 LYS cc_start: 0.9295 (tppt) cc_final: 0.8936 (tptp)
REVERT: B   33 GLU cc_start: 0.9423 (OUTLIER) cc_final: 0.9096 (pm20)
REVERT: B   80 MET cc_start: 0.8448 (tpp) cc_final: 0.7989 (mtp)
REVERT: B   86 ASN cc_start: 0.9021 (m110) cc_final: 0.8676 (p0)
REVERT: B  110 MET cc_start: 0.6246 (ptp) cc_final: 0.5459 (pmm)
REVERT: B  179 MET cc_start: 0.7094 (ttt) cc_final: 0.6375 (tpp)
REVERT: B  228 ASP cc_start: 0.8630 (m-30) cc_final: 0.8271 (m-30)
REVERT: B  229 ASP cc_start: 0.8572 (m-30) cc_final: 0.8283 (m-30)
REVERT: B  254 MET cc_start: 0.5707 (OUTLIER) cc_final: 0.5053 (mmp)
REVERT: B  325 GLU cc_start: 0.7389 (pt0) cc_final: 0.6914 (pm20)
  outliers start: 17
  outliers final: 12
  residues processed: 106
  average time/residue: 0.2579
  time to fit residues: 36.5585
Evaluate side-chains
  107 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LYS
Chi-restraints excluded: chain A residue  166 LYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  251 GLN
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   33 GLU
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  203 PHE
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  340 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 54 optimal weight:    9.9990
   chunk 19 optimal weight:    8.9990
   chunk 75 optimal weight:   10.0000
   chunk 42 optimal weight:    0.5980
   chunk 43 optimal weight:    0.4980
   chunk 33 optimal weight:    6.9990
   chunk 20 optimal weight:    9.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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**
A 251 GLN
B 198 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4773 r_free = 0.4773 target = 0.147597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.123315 restraints weight = 51097.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.123823 restraints weight = 39180.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.124448 restraints weight = 37840.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.4361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.6510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.163   9738  Z= 0.188
  Angle     :  0.911  59.167  13953  Z= 0.503
  Chirality :  0.041   0.940   1674
  Planarity :  0.005   0.044   1157
  Dihedral  : 21.498 101.540   3363
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 18.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 20.39 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.32), residues: 694
  helix:  0.30 (0.27), residues: 404
  sheet: -1.25 (0.90), residues: 42
  loop : -1.28 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 102 
 HIS   0.009   0.001   HIS A 358 
 PHE   0.033   0.002   PHE B 204 
 TYR   0.020   0.002   TYR A 297 
 ARG   0.009   0.000   ARG B  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04558 (  392)
  hydrogen bonds       : angle       4.30414 ( 1002)
  covalent geometry    : bond        0.00403 ( 9738)
  covalent geometry    : angle       0.91082 (13953)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 4078.99 seconds
wall clock time: 73 minutes 14.26 seconds (4394.26 seconds total)