Starting phenix.real_space_refine
on Mon May 12 15:32:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zmk_60250/05_2025/8zmk_60250.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zmk_60250/05_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_60250/05_2025/8zmk_60250.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zmk_60250/05_2025/8zmk_60250.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zmk_60250/05_2025/8zmk_60250.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zmk_60250/05_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-5687/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: 6.87, per 1000 atoms: 0.75
  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: 2.08
  Conformation dependent library (CDL) restraints added in 618.8 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: 3.08
  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: 2.63

  Time building geometry restraints manager: 2.46 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:             1.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.720
  Find NCS groups from input model:        0.150
  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:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.560
-------------------------------------------------------------------------------
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  : 0.783 
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: 0.2918
  time to fit residues: 69.7291
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  : 0.732 
-------------------------------------------------------------------------------
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 = 0.177980 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 = 73809.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4962 r_free = 0.4962 target = 0.164022 restraints weight = 49798.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4969 r_free = 0.4969 target = 0.164896 restraints weight = 39637.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.4640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6165
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 : 16.23
  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  : 0.696 
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: 0.8238 (mmtm) cc_final: 0.7317 (mmtm)
REVERT: A  133 MET cc_start: 0.4435 (mmp) cc_final: 0.3868 (mmm)
REVERT: A  161 LEU cc_start: 0.8425 (tt) cc_final: 0.8110 (tt)
REVERT: A  265 MET cc_start: 0.8260 (mmm) cc_final: 0.7846 (mmm)
REVERT: A  269 GLU cc_start: 0.9129 (tt0) cc_final: 0.8897 (tp30)
REVERT: A  273 ASN cc_start: 0.9357 (m-40) cc_final: 0.9051 (m-40)
REVERT: B   33 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8939 (pm20)
REVERT: B   51 LEU cc_start: 0.9584 (tt) cc_final: 0.9195 (tt)
REVERT: B  228 ASP cc_start: 0.8117 (m-30) cc_final: 0.7873 (m-30)
REVERT: B  229 ASP cc_start: 0.8214 (m-30) cc_final: 0.8010 (m-30)
REVERT: B  254 MET cc_start: 0.5610 (mmp) cc_final: 0.5180 (mmp)
  outliers start: 16
  outliers final: 9
  residues processed: 135
  average time/residue: 0.2599
  time to fit residues: 46.1107
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  : 0.720 
-------------------------------------------------------------------------------
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   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:   10.0000
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 3 optimal weight:    9.9990
   chunk 8 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0270
   chunk 67 optimal weight:    9.9990
   chunk 31 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.1442

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
A 165 GLN
** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4997 r_free = 0.4997 target = 0.174522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5028 r_free = 0.5028 target = 0.159139 restraints weight = 74801.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4934 r_free = 0.4934 target = 0.160437 restraints weight = 51111.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4942 r_free = 0.4942 target = 0.161221 restraints weight = 41031.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.4595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6306
moved from start:          0.3882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9738  Z= 0.135
  Angle     :  0.597  11.348  13953  Z= 0.294
  Chirality :  0.034   0.287   1674
  Planarity :  0.004   0.037   1157
  Dihedral  : 21.354 104.845   3372
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 15.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.89 %
    Favored  : 82.52 %
  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: -1.16 (0.32), residues: 694
  helix:  0.25 (0.28), residues: 388
  sheet: -1.59 (0.81), residues: 42
  loop : -2.15 (0.33), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 128 
 HIS   0.006   0.001   HIS B 242 
 PHE   0.020   0.002   PHE A 204 
 TYR   0.022   0.002   TYR B  64 
 ARG   0.010   0.001   ARG A 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04633 (  392)
  hydrogen bonds       : angle       4.18877 ( 1002)
  covalent geometry    : bond        0.00295 ( 9738)
  covalent geometry    : angle       0.59689 (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
  119 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.796 
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  115 LYS cc_start: 0.9596 (OUTLIER) cc_final: 0.9388 (tmtt)
REVERT: A  133 MET cc_start: 0.4658 (mmt) cc_final: 0.3913 (mmm)
REVERT: A  214 MET cc_start: 0.9188 (tpp) cc_final: 0.8820 (tpp)
REVERT: A  265 MET cc_start: 0.8523 (mmm) cc_final: 0.8015 (mmm)
REVERT: A  269 GLU cc_start: 0.9154 (tt0) cc_final: 0.8819 (tm-30)
REVERT: B   33 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8886 (pm20)
REVERT: B   85 VAL cc_start: 0.8758 (m) cc_final: 0.8255 (p)
REVERT: B  113 ASP cc_start: 0.9094 (p0) cc_final: 0.8607 (p0)
REVERT: B  228 ASP cc_start: 0.8170 (m-30) cc_final: 0.7886 (m-30)
REVERT: B  229 ASP cc_start: 0.8277 (m-30) cc_final: 0.8027 (m-30)
REVERT: B  254 MET cc_start: 0.5594 (mmp) cc_final: 0.5017 (mmp)
  outliers start: 16
  outliers final: 9
  residues processed: 118
  average time/residue: 0.2571
  time to fit residues: 40.0694
Evaluate side-chains
  97 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain B residue   33 GLU
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:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 64 optimal weight:    0.6980
   chunk 3 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0270
   chunk 25 optimal weight:    0.0870
   chunk 12 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
A 220 ASN
** B  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5007 r_free = 0.5007 target = 0.175298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5043 r_free = 0.5043 target = 0.160134 restraints weight = 73962.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4955 r_free = 0.4955 target = 0.161400 restraints weight = 50373.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4961 r_free = 0.4961 target = 0.162286 restraints weight = 40484.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.4609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6285
moved from start:          0.4247

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= 0.109
  Angle     :  0.579  10.992  13953  Z= 0.280
  Chirality :  0.033   0.318   1674
  Planarity :  0.004   0.045   1157
  Dihedral  : 21.300 104.280   3367
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 15.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 16.50 %
    Favored  : 81.07 %
  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: -1.23 (0.32), residues: 694
  helix:  0.15 (0.28), residues: 396
  sheet: -1.38 (0.85), residues: 42
  loop : -2.22 (0.33), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  98 
 HIS   0.007   0.001   HIS B 242 
 PHE   0.014   0.002   PHE B  35 
 TYR   0.018   0.002   TYR A 123 
 ARG   0.005   0.000   ARG A 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04086 (  392)
  hydrogen bonds       : angle       4.17131 ( 1002)
  covalent geometry    : bond        0.00238 ( 9738)
  covalent geometry    : angle       0.57871 (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
  114 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.700 
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: 0.4693 (mmt) cc_final: 0.3556 (mmt)
REVERT: A  214 MET cc_start: 0.9210 (tpp) cc_final: 0.8885 (tpp)
REVERT: A  243 MET cc_start: 0.8773 (pmm) cc_final: 0.8467 (tpp)
REVERT: A  265 MET cc_start: 0.8351 (mmm) cc_final: 0.7858 (mmm)
REVERT: A  273 ASN cc_start: 0.9358 (m-40) cc_final: 0.9073 (m-40)
REVERT: A  294 TYR cc_start: 0.8463 (m-10) cc_final: 0.8151 (m-80)
REVERT: B   33 GLU cc_start: 0.9256 (OUTLIER) cc_final: 0.8936 (pm20)
REVERT: B  179 MET cc_start: 0.6042 (ttt) cc_final: 0.3988 (tpt)
REVERT: B  214 MET cc_start: 0.6684 (pmm) cc_final: 0.5915 (mmm)
REVERT: B  228 ASP cc_start: 0.8210 (m-30) cc_final: 0.7961 (m-30)
REVERT: B  229 ASP cc_start: 0.8236 (m-30) cc_final: 0.7984 (m-30)
REVERT: B  254 MET cc_start: 0.5035 (mmp) cc_final: 0.4242 (mmp)
  outliers start: 15
  outliers final: 10
  residues processed: 113
  average time/residue: 0.2466
  time to fit residues: 37.1745
Evaluate side-chains
  101 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain B residue   33 GLU
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  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:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0770
   chunk 58 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
A 211 GLN
A 251 GLN
** B  77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4990 r_free = 0.4990 target = 0.173463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4970 r_free = 0.4970 target = 0.157136 restraints weight = 74287.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4957 r_free = 0.4957 target = 0.158893 restraints weight = 50608.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4963 r_free = 0.4963 target = 0.160100 restraints weight = 39437.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.4580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6338
moved from start:          0.4643

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= 0.109
  Angle     :  0.563  10.505  13953  Z= 0.274
  Chirality :  0.032   0.254   1674
  Planarity :  0.004   0.040   1157
  Dihedral  : 21.263 103.230   3367
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.83 %
    Favored  : 80.42 %
  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: -1.02 (0.33), residues: 694
  helix:  0.26 (0.28), residues: 394
  sheet: -1.23 (0.88), residues: 42
  loop : -2.00 (0.34), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  98 
 HIS   0.010   0.002   HIS A 358 
 PHE   0.014   0.002   PHE B  35 
 TYR   0.020   0.002   TYR A 123 
 ARG   0.003   0.000   ARG B  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04130 (  392)
  hydrogen bonds       : angle       4.18120 ( 1002)
  covalent geometry    : bond        0.00238 ( 9738)
  covalent geometry    : angle       0.56329 (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
  112 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.699 
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   64 TYR cc_start: 0.7624 (p90) cc_final: 0.7351 (p90)
REVERT: A  133 MET cc_start: 0.4728 (mmt) cc_final: 0.3487 (mmt)
REVERT: A  166 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8621 (ttmm)
REVERT: A  179 MET cc_start: 0.4623 (tpp) cc_final: 0.3791 (tpp)
REVERT: A  265 MET cc_start: 0.8525 (mmm) cc_final: 0.8009 (mmm)
REVERT: B   33 GLU cc_start: 0.9293 (OUTLIER) cc_final: 0.8919 (pm20)
REVERT: B   80 MET cc_start: 0.8582 (tpp) cc_final: 0.7868 (mtp)
REVERT: B   86 ASN cc_start: 0.9095 (m110) cc_final: 0.8775 (p0)
REVERT: B  228 ASP cc_start: 0.8313 (m-30) cc_final: 0.8036 (m-30)
REVERT: B  229 ASP cc_start: 0.8246 (m-30) cc_final: 0.7970 (m-30)
REVERT: B  254 MET cc_start: 0.5169 (mmp) cc_final: 0.4544 (mmp)
  outliers start: 17
  outliers final: 11
  residues processed: 112
  average time/residue: 0.2462
  time to fit residues: 36.6595
Evaluate side-chains
  98 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
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  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   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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 18 optimal weight:    0.3980
   chunk 59 optimal weight:    0.6980
   chunk 53 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 21 optimal weight:   20.0000
   chunk 83 optimal weight:    9.9990
   chunk 48 optimal weight:   10.0000
   overall best weight:    3.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 GLN
** B 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4659 r_free = 0.4659 target = 0.136974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.109907 restraints weight = 50182.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.111825 restraints weight = 43004.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.111868 restraints weight = 35568.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.4202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          0.6661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063   9738  Z= 0.252
  Angle     :  0.789  18.153  13953  Z= 0.393
  Chirality :  0.039   0.224   1674
  Planarity :  0.005   0.044   1157
  Dihedral  : 22.200  98.857   3367
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 30.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 15.21 %
    Favored  : 79.61 %
  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: -1.63 (0.31), residues: 694
  helix: -0.29 (0.26), residues: 386
  sheet: -2.34 (0.77), residues: 46
  loop : -1.95 (0.34), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 302 
 HIS   0.007   0.002   HIS A 358 
 PHE   0.037   0.004   PHE B 359 
 TYR   0.019   0.003   TYR A 123 
 ARG   0.009   0.001   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08927 (  392)
  hydrogen bonds       : angle       5.00273 ( 1002)
  covalent geometry    : bond        0.00504 ( 9738)
  covalent geometry    : angle       0.78936 (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
  131 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 99
  time to evaluate  : 1.212 
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  129 LYS cc_start: 0.9303 (tttt) cc_final: 0.8978 (tppt)
REVERT: A  133 MET cc_start: 0.5940 (mmt) cc_final: 0.3854 (mmt)
REVERT: A  166 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.8572 (ttmt)
REVERT: A  179 MET cc_start: 0.5802 (tpp) cc_final: 0.5265 (tpt)
REVERT: A  243 MET cc_start: 0.8973 (pmm) cc_final: 0.8455 (mpp)
REVERT: A  251 GLN cc_start: 0.5130 (OUTLIER) cc_final: 0.2965 (pp30)
REVERT: A  265 MET cc_start: 0.8865 (mmm) cc_final: 0.8440 (mmm)
REVERT: B   33 GLU cc_start: 0.9481 (OUTLIER) cc_final: 0.9027 (pm20)
REVERT: B   58 LYS cc_start: 0.6129 (OUTLIER) cc_final: 0.5767 (pttp)
REVERT: B   73 MET cc_start: 0.6748 (ppp) cc_final: 0.6134 (ppp)
REVERT: B  179 MET cc_start: 0.7486 (ttt) cc_final: 0.6897 (tpp)
REVERT: B  228 ASP cc_start: 0.8829 (m-30) cc_final: 0.8468 (m-30)
REVERT: B  229 ASP cc_start: 0.8721 (m-30) cc_final: 0.8465 (m-30)
REVERT: B  254 MET cc_start: 0.5804 (OUTLIER) cc_final: 0.5303 (mmp)
  outliers start: 32
  outliers final: 20
  residues processed: 123
  average time/residue: 0.2651
  time to fit residues: 43.1946
Evaluate side-chains
  112 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
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  166 LYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  251 GLN
Chi-restraints excluded: chain A residue  254 MET
Chi-restraints excluded: chain A residue  256 LYS
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain B residue   33 GLU
Chi-restraints excluded: chain B residue   35 PHE
Chi-restraints excluded: chain B residue   58 LYS
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  254 MET
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  304 ASN
Chi-restraints excluded: chain B residue  306 PHE
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:    0.0170
   chunk 51 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0980
   chunk 6 optimal weight:    9.9990
   chunk 69 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 75 optimal weight:   10.0000
   chunk 25 optimal weight:    0.0470
   chunk 78 optimal weight:    5.9990
   overall best weight:    0.8320

-------------------------------------------------------------------------------
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**
A 251 GLN
** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4736 r_free = 0.4736 target = 0.144038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.115893 restraints weight = 50105.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.118146 restraints weight = 38847.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.119700 restraints weight = 32760.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.4327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          0.6571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9738  Z= 0.133
  Angle     :  0.670  13.320  13953  Z= 0.330
  Chirality :  0.035   0.245   1674
  Planarity :  0.004   0.045   1157
  Dihedral  : 21.915 102.217   3363
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 20.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 19.09 %
    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: -1.03 (0.32), residues: 694
  helix:  0.16 (0.27), residues: 390
  sheet: -2.13 (0.82), residues: 42
  loop : -1.64 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 102 
 HIS   0.007   0.001   HIS A 358 
 PHE   0.025   0.002   PHE B 359 
 TYR   0.021   0.002   TYR A 123 
 ARG   0.003   0.001   ARG A 152 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05059 (  392)
  hydrogen bonds       : angle       4.64021 ( 1002)
  covalent geometry    : bond        0.00300 ( 9738)
  covalent geometry    : angle       0.67035 (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
  117 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.769 
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  129 LYS cc_start: 0.9219 (tttt) cc_final: 0.8901 (tppt)
REVERT: A  133 MET cc_start: 0.6122 (mmt) cc_final: 0.3869 (mmt)
REVERT: A  166 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.9029 (mtpp)
REVERT: A  242 HIS cc_start: 0.7367 (OUTLIER) cc_final: 0.6619 (p90)
REVERT: A  243 MET cc_start: 0.8988 (pmm) cc_final: 0.8206 (mpp)
REVERT: A  251 GLN cc_start: 0.4271 (OUTLIER) cc_final: 0.2572 (pp30)
REVERT: A  265 MET cc_start: 0.8663 (mmm) cc_final: 0.8194 (mmm)
REVERT: B   33 GLU cc_start: 0.9430 (OUTLIER) cc_final: 0.8959 (pm20)
REVERT: B  197 MET cc_start: 0.6661 (mpp) cc_final: 0.6402 (mpp)
REVERT: B  214 MET cc_start: 0.7303 (pmm) cc_final: 0.6739 (mmm)
REVERT: B  228 ASP cc_start: 0.8637 (m-30) cc_final: 0.8239 (m-30)
REVERT: B  229 ASP cc_start: 0.8571 (m-30) cc_final: 0.8292 (m-30)
REVERT: B  254 MET cc_start: 0.5749 (OUTLIER) cc_final: 0.5231 (mmp)
  outliers start: 24
  outliers final: 14
  residues processed: 112
  average time/residue: 0.2555
  time to fit residues: 39.4289
Evaluate side-chains
  105 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  166 LYS
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  242 HIS
Chi-restraints excluded: chain A residue  251 GLN
Chi-restraints excluded: chain A residue  254 MET
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   99 ILE
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  254 MET
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  340 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 33 optimal weight:   20.0000
   chunk 51 optimal weight:    5.9990
   chunk 43 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   chunk 17 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0070
   chunk 62 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    1.9604

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4676 r_free = 0.4676 target = 0.138366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.110076 restraints weight = 49730.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.112113 restraints weight = 37879.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.113642 restraints weight = 32269.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.4245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.7222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9738  Z= 0.173
  Angle     :  0.702  13.077  13953  Z= 0.344
  Chirality :  0.037   0.400   1674
  Planarity :  0.004   0.052   1157
  Dihedral  : 22.047 101.797   3363
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 27.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 18.61 %
    Favored  : 77.35 %
  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: -1.04 (0.32), residues: 694
  helix:  0.10 (0.27), residues: 388
  sheet: -2.37 (0.76), residues: 46
  loop : -1.47 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 102 
 HIS   0.006   0.001   HIS A 358 
 PHE   0.049   0.003   PHE B 359 
 TYR   0.024   0.002   TYR A 294 
 ARG   0.006   0.001   ARG B  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06343 (  392)
  hydrogen bonds       : angle       4.78253 ( 1002)
  covalent geometry    : bond        0.00367 ( 9738)
  covalent geometry    : angle       0.70184 (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
  116 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 91
  time to evaluate  : 0.721 
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  129 LYS cc_start: 0.9242 (tttt) cc_final: 0.8933 (tppt)
REVERT: A  133 MET cc_start: 0.6141 (mmt) cc_final: 0.3915 (mmt)
REVERT: A  166 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.8544 (ttmt)
REVERT: A  179 MET cc_start: 0.5109 (tpp) cc_final: 0.4557 (tpp)
REVERT: A  243 MET cc_start: 0.8996 (pmm) cc_final: 0.8423 (mpp)
REVERT: A  251 GLN cc_start: 0.4645 (OUTLIER) cc_final: 0.4334 (pt0)
REVERT: A  265 MET cc_start: 0.8758 (mmm) cc_final: 0.8193 (mmm)
REVERT: B   33 GLU cc_start: 0.9505 (OUTLIER) cc_final: 0.9155 (pm20)
REVERT: B   48 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8443 (pm20)
REVERT: B   81 LYS cc_start: 0.9206 (tptt) cc_final: 0.8905 (mmmt)
REVERT: B  122 ARG cc_start: 0.8755 (mmm-85) cc_final: 0.8525 (mmm-85)
REVERT: B  179 MET cc_start: 0.7755 (ttt) cc_final: 0.6056 (tpp)
REVERT: B  197 MET cc_start: 0.6815 (mpp) cc_final: 0.6584 (mpp)
REVERT: B  225 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7690 (mt-10)
REVERT: B  228 ASP cc_start: 0.8747 (m-30) cc_final: 0.8388 (m-30)
REVERT: B  229 ASP cc_start: 0.8728 (m-30) cc_final: 0.8472 (m-30)
REVERT: B  254 MET cc_start: 0.6129 (OUTLIER) cc_final: 0.5586 (mmp)
REVERT: B  297 TYR cc_start: 0.8372 (m-80) cc_final: 0.7142 (t80)
  outliers start: 25
  outliers final: 15
  residues processed: 110
  average time/residue: 0.2412
  time to fit residues: 35.4371
Evaluate side-chains
  109 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  159 LEU
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  286 VAL
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   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  295 ILE
Chi-restraints excluded: chain B residue  299 ILE
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:    7.9990
   chunk 81 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 29 optimal weight:    0.2980
   chunk 12 optimal weight:    0.8980
   chunk 64 optimal weight:    0.4980
   chunk 37 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   chunk 73 optimal weight:   10.0000
   chunk 65 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.5384

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4686 r_free = 0.4686 target = 0.139197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.111759 restraints weight = 46699.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.113985 restraints weight = 35693.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.115164 restraints weight = 29707.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.4284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.7421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9738  Z= 0.149
  Angle     :  0.692  16.011  13953  Z= 0.338
  Chirality :  0.036   0.306   1674
  Planarity :  0.004   0.043   1157
  Dihedral  : 22.071 103.750   3363
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 23.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 19.42 %
    Favored  : 77.51 %
  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: -0.92 (0.33), residues: 694
  helix:  0.18 (0.28), residues: 392
  sheet: -2.15 (0.85), residues: 42
  loop : -1.47 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 102 
 HIS   0.006   0.001   HIS A 358 
 PHE   0.017   0.002   PHE B 359 
 TYR   0.022   0.002   TYR A 294 
 ARG   0.004   0.000   ARG B 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05561 (  392)
  hydrogen bonds       : angle       4.72481 ( 1002)
  covalent geometry    : bond        0.00322 ( 9738)
  covalent geometry    : angle       0.69191 (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
  113 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.764 
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  129 LYS cc_start: 0.9242 (tttt) cc_final: 0.8950 (tppt)
REVERT: A  133 MET cc_start: 0.6089 (mmt) cc_final: 0.3848 (mmt)
REVERT: A  166 LYS cc_start: 0.9391 (OUTLIER) cc_final: 0.8539 (ttmm)
REVERT: A  179 MET cc_start: 0.5329 (tpp) cc_final: 0.4715 (tpp)
REVERT: A  243 MET cc_start: 0.8990 (pmm) cc_final: 0.8455 (mpp)
REVERT: A  251 GLN cc_start: 0.4394 (OUTLIER) cc_final: 0.2456 (pp30)
REVERT: A  265 MET cc_start: 0.8584 (mmm) cc_final: 0.8134 (mmm)
REVERT: B   33 GLU cc_start: 0.9470 (OUTLIER) cc_final: 0.9148 (pm20)
REVERT: B   49 ASP cc_start: 0.9251 (t0) cc_final: 0.8743 (p0)
REVERT: B   53 ASN cc_start: 0.9488 (m110) cc_final: 0.9143 (p0)
REVERT: B  179 MET cc_start: 0.7755 (ttt) cc_final: 0.6263 (tpp)
REVERT: B  225 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7674 (mt-10)
REVERT: B  228 ASP cc_start: 0.8728 (m-30) cc_final: 0.8365 (m-30)
REVERT: B  229 ASP cc_start: 0.8678 (m-30) cc_final: 0.8410 (m-30)
REVERT: B  254 MET cc_start: 0.5913 (mmp) cc_final: 0.5327 (mmp)
  outliers start: 19
  outliers final: 14
  residues processed: 110
  average time/residue: 0.2573
  time to fit residues: 37.7269
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  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  159 LEU
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  286 VAL
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   67 PHE
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  194 TYR
Chi-restraints excluded: chain B residue  242 HIS
Chi-restraints excluded: chain B residue  263 VAL
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  299 ILE
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:    9.9990
   chunk 5 optimal weight:    7.9990
   chunk 46 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0770
   chunk 6 optimal weight:    9.9990
   chunk 18 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9980
   chunk 67 optimal weight:    9.9990
   chunk 63 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   overall best weight:    1.1740

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4701 r_free = 0.4701 target = 0.140237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.112393 restraints weight = 46699.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.114724 restraints weight = 35199.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.116440 restraints weight = 29090.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.4299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.7522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9738  Z= 0.139
  Angle     :  0.706  18.640  13953  Z= 0.343
  Chirality :  0.037   0.442   1674
  Planarity :  0.004   0.039   1157
  Dihedral  : 22.013 103.713   3363
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 22.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 19.74 %
    Favored  : 77.18 %
  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: -0.86 (0.33), residues: 694
  helix:  0.19 (0.27), residues: 392
  sheet: -2.02 (0.87), residues: 42
  loop : -1.39 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 102 
 HIS   0.006   0.001   HIS A 358 
 PHE   0.017   0.002   PHE B  35 
 TYR   0.020   0.002   TYR A 123 
 ARG   0.003   0.000   ARG B  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05385 (  392)
  hydrogen bonds       : angle       4.64785 ( 1002)
  covalent geometry    : bond        0.00302 ( 9738)
  covalent geometry    : angle       0.70623 (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
  111 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.720 
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  129 LYS cc_start: 0.9233 (tttt) cc_final: 0.8909 (tppt)
REVERT: A  133 MET cc_start: 0.6105 (mmt) cc_final: 0.3835 (mmt)
REVERT: A  166 LYS cc_start: 0.9385 (OUTLIER) cc_final: 0.8548 (ttmm)
REVERT: A  179 MET cc_start: 0.5248 (tpp) cc_final: 0.4665 (tpp)
REVERT: A  243 MET cc_start: 0.8994 (pmm) cc_final: 0.8460 (mpp)
REVERT: A  251 GLN cc_start: 0.4521 (OUTLIER) cc_final: 0.2685 (pp30)
REVERT: A  265 MET cc_start: 0.8530 (mmm) cc_final: 0.8132 (mmm)
REVERT: B   48 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8487 (pm20)
REVERT: B   53 ASN cc_start: 0.9486 (m110) cc_final: 0.9245 (p0)
REVERT: B  179 MET cc_start: 0.7749 (ttt) cc_final: 0.6251 (tpp)
REVERT: B  225 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7773 (mt-10)
REVERT: B  228 ASP cc_start: 0.8705 (m-30) cc_final: 0.8340 (m-30)
REVERT: B  229 ASP cc_start: 0.8654 (m-30) cc_final: 0.8398 (m-30)
REVERT: B  254 MET cc_start: 0.5925 (mmp) cc_final: 0.5276 (mmp)
REVERT: B  297 TYR cc_start: 0.8301 (m-80) cc_final: 0.7106 (t80)
  outliers start: 19
  outliers final: 15
  residues processed: 108
  average time/residue: 0.2551
  time to fit residues: 36.5784
Evaluate side-chains
  107 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  159 LEU
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  286 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  124 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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 47 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 19 optimal weight:    6.9990
   chunk 75 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 23 optimal weight:    0.6980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 251 GLN
B 198 GLN
** B 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.140817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.112954 restraints weight = 48955.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.115279 restraints weight = 36953.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.117040 restraints weight = 30623.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.7625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9738  Z= 0.133
  Angle     :  0.694  18.390  13953  Z= 0.337
  Chirality :  0.036   0.427   1674
  Planarity :  0.004   0.040   1157
  Dihedral  : 21.889 103.628   3360
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 21.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 20.71 %
    Favored  : 76.70 %
  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: -0.75 (0.33), residues: 694
  helix:  0.28 (0.28), residues: 388
  sheet: -2.03 (0.82), residues: 46
  loop : -1.28 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 102 
 HIS   0.006   0.001   HIS A 358 
 PHE   0.021   0.003   PHE A 264 
 TYR   0.022   0.003   TYR B 226 
 ARG   0.004   0.000   ARG B  94 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05166 (  392)
  hydrogen bonds       : angle       4.58338 ( 1002)
  covalent geometry    : bond        0.00293 ( 9738)
  covalent geometry    : angle       0.69401 (13953)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3987.17 seconds
wall clock time: 70 minutes 59.46 seconds (4259.46 seconds total)