Starting phenix.real_space_refine
on Fri Aug 22 19:42:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h86_34530/08_2025/8h86_34530.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h86_34530/08_2025/8h86_34530.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h86_34530/08_2025/8h86_34530.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h86_34530/08_2025/8h86_34530.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h86_34530/08_2025/8h86_34530.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h86_34530/08_2025/8h86_34530.map"
  }
  resolution = 2.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.115
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       9      5.49       5
     S      60      5.16       5
     C    4896      2.51       5
     N     957      2.21       5
     O    1158      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7080
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2090
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 255, 2071
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 16, 'TRANS': 238}
      Conformer: "B"
        Number of residues, atoms: 255, 2071
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 16, 'TRANS': 238}
          bond proxies already assigned to first conformer: 2129
    Chain: "A"
      Number of atoms: 270
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 270
          Unusual residues: {'PLM': 5, 'PSC': 10, 'RET': 1}
          Classifications: {'undetermined': 16, 'water': 21}
          Link IDs: {None: 36}
          Unresolved non-hydrogen bonds: 382
          Unresolved non-hydrogen angles: 459
          Unresolved non-hydrogen dihedrals: 335
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'RET:plan-5': 1, 'PSC:plan-3': 6, 'PSC:plan-4': 6, 'PLM:plan-1': 5, 'PSC:plan-1': 6, 'PSC:plan-2': 6}
          Unresolved non-hydrogen planarities: 105
    Chain: "B"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 21
          Classifications: {'water': 21}
          Link IDs: {None: 20}
    Chain: "C"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 21
          Classifications: {'water': 21}
          Link IDs: {None: 20}
  Restraints were copied for chains:
    B, C
  Residues with excluded nonbonded symmetry interactions: 3
    residue:
      pdb=" N  APHE A 144 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 144 " occ=0.50
    residue:
      pdb=" N  APHE B 144 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE B 144 " occ=0.50
    residue:
      pdb=" N  APHE C 144 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE C 144 " occ=0.50
  Time building chain proxies: 1.94, per 1000 atoms: 0.27
  Number of scatterers: 7080
  At special positions: 0
  Unit cell: (78.02, 76.36, 82.17, 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      60     16.00
     P       9     15.00
     O    1158      8.00
     N     957      7.00
     C    4896      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=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.58
  Conformation dependent library (CDL) restraints added in 511.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1422

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 0 sheets defined
      75.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 49
    Processing helix  chain 'A' and resid 64 through 67
    Processing helix  chain 'A' and resid 68 through 90
    Processing helix  chain 'A' and resid 103 through 122
      removed outlier: 3.992A  pdb=" N   PHE A 108 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      Proline residue:  A 111  - end of helix
    Processing helix  chain 'A' and resid 125 through 146
    Processing helix  chain 'A' and resid 149 through 177
      removed outlier: 3.802A  pdb=" N   ALA A 153 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
      Proline residue:  A 164  - end of helix
    Processing helix  chain 'A' and resid 181 through 199
      removed outlier: 4.003A  pdb=" N   TRP A 187 " --> pdb=" O   LYS A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 209
      removed outlier: 3.663A  pdb=" N   PHE A 208 " --> pdb=" O   ILE A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 252
      removed outlier: 3.633A  pdb=" N   ILE A 235 " --> pdb=" O   THR A 231 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   PHE A 236 " --> pdb=" O   CYS A 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 49
    Processing helix  chain 'B' and resid 64 through 67
    Processing helix  chain 'B' and resid 68 through 90
    Processing helix  chain 'B' and resid 103 through 122
      removed outlier: 3.992A  pdb=" N   PHE B 108 " --> pdb=" O   LEU B 104 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
    Processing helix  chain 'B' and resid 125 through 146
    Processing helix  chain 'B' and resid 149 through 177
      removed outlier: 3.802A  pdb=" N   ALA B 153 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
      Proline residue:  B 164  - end of helix
    Processing helix  chain 'B' and resid 181 through 199
      removed outlier: 4.003A  pdb=" N   TRP B 187 " --> pdb=" O   LYS B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 209
      removed outlier: 3.663A  pdb=" N   PHE B 208 " --> pdb=" O   ILE B 204 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 252
      removed outlier: 3.634A  pdb=" N   ILE B 235 " --> pdb=" O   THR B 231 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   PHE B 236 " --> pdb=" O   CYS B 232 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 49
    Processing helix  chain 'C' and resid 64 through 67
    Processing helix  chain 'C' and resid 68 through 90
    Processing helix  chain 'C' and resid 103 through 122
      removed outlier: 3.992A  pdb=" N   PHE C 108 " --> pdb=" O   LEU C 104 " (cutoff:3.500A)
      Proline residue:  C 111  - end of helix
    Processing helix  chain 'C' and resid 125 through 146
    Processing helix  chain 'C' and resid 149 through 177
      removed outlier: 3.802A  pdb=" N   ALA C 153 " --> pdb=" O   ALA C 149 " (cutoff:3.500A)
      Proline residue:  C 164  - end of helix
    Processing helix  chain 'C' and resid 181 through 199
      removed outlier: 4.003A  pdb=" N   TRP C 187 " --> pdb=" O   LYS C 183 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 209
      removed outlier: 3.663A  pdb=" N   PHE C 208 " --> pdb=" O   ILE C 204 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 217 through 252
      removed outlier: 3.633A  pdb=" N   ILE C 235 " --> pdb=" O   THR C 231 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   PHE C 236 " --> pdb=" O   CYS C 232 " (cutoff:3.500A)

    438 hydrogen bonds defined for protein.
    1305 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.20

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1031
        1.32 -     1.45: 2428
        1.45 -     1.58: 3672
        1.58 -     1.71: 15
        1.71 -     1.84: 81
  Bond restraints: 7227
  Sorted by residual:
  bond pdb=" C7  PSC A 311 "
       pdb=" C8  PSC A 311 "
    ideal  model  delta    sigma   weight residual
    1.530  1.322  0.208 2.00e-02 2.50e+03 1.08e+02
  bond pdb=" C7  PSC C 311 "
       pdb=" C8  PSC C 311 "
    ideal  model  delta    sigma   weight residual
    1.530  1.322  0.208 2.00e-02 2.50e+03 1.08e+02
  bond pdb=" C7  PSC B 311 "
       pdb=" C8  PSC B 311 "
    ideal  model  delta    sigma   weight residual
    1.530  1.323  0.207 2.00e-02 2.50e+03 1.08e+02
  bond pdb=" C6  PSC A 313 "
       pdb=" C7  PSC A 313 "
    ideal  model  delta    sigma   weight residual
    1.523  1.319  0.204 2.00e-02 2.50e+03 1.05e+02
  bond pdb=" C6  PSC C 313 "
       pdb=" C7  PSC C 313 "
    ideal  model  delta    sigma   weight residual
    1.523  1.319  0.204 2.00e-02 2.50e+03 1.05e+02
  ... (remaining 7222 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.95: 9173
        2.95 -     5.91: 403
        5.91 -     8.86: 15
        8.86 -    11.82: 21
       11.82 -    14.77: 21
  Bond angle restraints: 9633
  Sorted by residual:
  angle pdb=" C10 PSC C 311 "
        pdb=" C11 PSC C 311 "
        pdb=" C12 PSC C 311 "
      ideal   model   delta    sigma   weight residual
     111.07  125.84  -14.77 3.00e+00 1.11e-01 2.42e+01
  angle pdb=" C10 PSC A 311 "
        pdb=" C11 PSC A 311 "
        pdb=" C12 PSC A 311 "
      ideal   model   delta    sigma   weight residual
     111.07  125.82  -14.75 3.00e+00 1.11e-01 2.42e+01
  angle pdb=" C10 PSC B 311 "
        pdb=" C11 PSC B 311 "
        pdb=" C12 PSC B 311 "
      ideal   model   delta    sigma   weight residual
     111.07  125.82  -14.75 3.00e+00 1.11e-01 2.42e+01
  angle pdb=" C2  PSC B 312 "
        pdb=" C3  PSC B 312 "
        pdb=" C4  PSC B 312 "
      ideal   model   delta    sigma   weight residual
     111.73  125.94  -14.21 3.00e+00 1.11e-01 2.24e+01
  angle pdb=" C2  PSC C 312 "
        pdb=" C3  PSC C 312 "
        pdb=" C4  PSC C 312 "
      ideal   model   delta    sigma   weight residual
     111.73  125.93  -14.20 3.00e+00 1.11e-01 2.24e+01
  ... (remaining 9628 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.23: 3785
       25.23 -    50.45: 322
       50.45 -    75.68: 66
       75.68 -   100.90: 0
      100.90 -   126.12: 6
  Dihedral angle restraints: 4179
    sinusoidal: 1938
      harmonic: 2241
  Sorted by residual:
  dihedral pdb=" C02 PSC C 303 "
           pdb=" C03 PSC C 303 "
           pdb=" O11 PSC C 303 "
           pdb=" P   PSC C 303 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.62   54.50  126.12     1      3.00e+01 1.11e-03 1.70e+01
  dihedral pdb=" C02 PSC B 303 "
           pdb=" C03 PSC B 303 "
           pdb=" O11 PSC B 303 "
           pdb=" P   PSC B 303 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.62   54.51  126.11     1      3.00e+01 1.11e-03 1.70e+01
  dihedral pdb=" C02 PSC A 303 "
           pdb=" C03 PSC A 303 "
           pdb=" O11 PSC A 303 "
           pdb=" P   PSC A 303 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.62   54.54  126.08     1      3.00e+01 1.11e-03 1.69e+01
  ... (remaining 4176 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 458
       0.052 -    0.105: 299
       0.105 -    0.157: 109
       0.157 -    0.209: 58
       0.209 -    0.261: 9
  Chirality restraints: 933
  Sorted by residual:
  chirality pdb=" CA  TYR B  81 "
            pdb=" N   TYR B  81 "
            pdb=" C   TYR B  81 "
            pdb=" CB  TYR B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CA  TYR C  81 "
            pdb=" N   TYR C  81 "
            pdb=" C   TYR C  81 "
            pdb=" CB  TYR C  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" CA  TYR A  81 "
            pdb=" N   TYR A  81 "
            pdb=" C   TYR A  81 "
            pdb=" CB  TYR A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.66e+00
  ... (remaining 930 not shown)

  Planarity restraints: 1155
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C11 PSC B 311 "    0.268 2.00e-02 2.50e+03   2.81e-01 7.87e+02
        pdb=" C12 PSC B 311 "   -0.238 2.00e-02 2.50e+03
        pdb=" C13 PSC B 311 "   -0.320 2.00e-02 2.50e+03
        pdb=" C14 PSC B 311 "    0.290 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C11 PSC C 311 "   -0.268 2.00e-02 2.50e+03   2.80e-01 7.87e+02
        pdb=" C12 PSC C 311 "    0.238 2.00e-02 2.50e+03
        pdb=" C13 PSC C 311 "    0.320 2.00e-02 2.50e+03
        pdb=" C14 PSC C 311 "   -0.290 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C11 PSC A 311 "   -0.268 2.00e-02 2.50e+03   2.80e-01 7.86e+02
        pdb=" C12 PSC A 311 "    0.238 2.00e-02 2.50e+03
        pdb=" C13 PSC A 311 "    0.320 2.00e-02 2.50e+03
        pdb=" C14 PSC A 311 "   -0.289 2.00e-02 2.50e+03
  ... (remaining 1152 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1904
        2.82 -     3.34: 6804
        3.34 -     3.86: 12425
        3.86 -     4.38: 15633
        4.38 -     4.90: 25093
  Nonbonded interactions: 61859
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  68 "
            pdb=" O   HOH A 401 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OG  SER C  68 "
            pdb=" O   HOH C 401 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OG  SER B  68 "
            pdb=" O   HOH B 401 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OG1 THR A 146 "
            pdb=" O   HOH A 402 "
     model   vdw
     2.385 3.040
  nonbonded pdb=" NH2 ARG C 171 "
            pdb=" O13 PSC C 310 "
     model   vdw
     2.385 3.120
  ... (remaining 61854 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     9.190
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6882
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      :  0.015   0.208   7230  Z= 0.868
  Angle     :  1.563  14.769   9633  Z= 0.928
  Chirality :  0.082   0.261    933
  Planarity :  0.030   0.281   1155
  Dihedral  : 18.473 126.125   2757
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  2.26 %
    Favored  : 97.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.67 (0.28), residues: 771
  helix: -0.49 (0.18), residues: 537
  sheet:  None (None), residues: 0
  loop :  0.15 (0.46), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.027   0.003   ARG C  62 
 TYR   0.043   0.009   TYR C 155 
 PHE   0.047   0.010   PHE A  86 
 TRP   0.047   0.009   TRP B 190 
 HIS   0.014   0.004   HIS A 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.01434 ( 7227)
  covalent geometry    : angle       1.56274 ( 9633)
  hydrogen bonds       : bond        0.19337 (  438)
  hydrogen bonds       : angle       7.43519 ( 1305)
  Misc. bond           : bond        0.16901 (    3)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.280 
Fit side-chains
REVERT: A   20 MET cc_start: 0.7679 (mtm) cc_final: 0.7391 (mtm)
REVERT: A  170 MET cc_start: 0.6515 (mtm) cc_final: 0.6266 (mtt)
REVERT: B   60 SER cc_start: 0.7505 (m) cc_final: 0.7289 (t)
REVERT: B  170 MET cc_start: 0.6548 (mtm) cc_final: 0.6181 (mtt)
REVERT: B  186 ARG cc_start: 0.6295 (ttm170) cc_final: 0.5676 (ttt180)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.7065
  time to fit residues: 71.5007
Evaluate side-chains
  85 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    0.0970
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    0.0980
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS
B 125 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.136664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.108776 restraints weight = 14332.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 1.58
r_work: 0.2812 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2675 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2632
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2632 r_free = 0.2632    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2631 r_free = 0.2631    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2631
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8705
moved from start:          0.1543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   7230  Z= 0.254
  Angle     :  1.297  46.757   9633  Z= 0.604
  Chirality :  0.066   0.579    933
  Planarity :  0.013   0.226   1155
  Dihedral  : 21.014 117.891   1380
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  4.08 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  6.49 %
    Favored  : 92.16 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.30), residues: 771
  helix:  0.12 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.03 (0.46), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.069   0.003   ARG C 128 
 TYR   0.124   0.007   TYR C  45 
 PHE   0.093   0.007   PHE C 131 
 TRP   0.071   0.007   TRP B 190 
 HIS   0.033   0.005   HIS B 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 7227)
  covalent geometry    : angle       1.29721 ( 9633)
  hydrogen bonds       : bond        0.08578 (  438)
  hydrogen bonds       : angle       5.35688 ( 1305)
  Misc. bond           : bond        0.00115 (    3)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A   20 MET cc_start: 0.8757 (mtm) cc_final: 0.8549 (mtm)
REVERT: A  174 LYS cc_start: 0.8460 (tttp) cc_final: 0.7947 (mtmt)
REVERT: B   60 SER cc_start: 0.8722 (m) cc_final: 0.8453 (t)
REVERT: B   87 ASP cc_start: 0.9032 (t70) cc_final: 0.8767 (t70)
REVERT: B  170 MET cc_start: 0.8760 (mtm) cc_final: 0.8367 (mtt)
REVERT: B  174 LYS cc_start: 0.8341 (tttt) cc_final: 0.7765 (mtmt)
REVERT: B  183 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7147 (tttt)
  outliers start: 7
  outliers final: 1
  residues processed: 95
  average time/residue: 0.5581
  time to fit residues: 55.6721
Evaluate side-chains
  84 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 82
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  183 LYS
Chi-restraints excluded: chain C residue   60 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 21 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 41 optimal weight:    6.9990
   chunk 54 optimal weight:    0.5980
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
B 218 GLN
C 218 GLN
C 219 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.134366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.104869 restraints weight = 22410.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 1.94
r_work: 0.2968 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2956
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2956 r_free = 0.2956    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2956 r_free = 0.2956    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2956
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7230  Z= 0.120
  Angle     :  0.547   8.178   9633  Z= 0.270
  Chirality :  0.039   0.126    933
  Planarity :  0.005   0.038   1155
  Dihedral  : 17.229  73.376   1380
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  6.79 %
    Favored  : 92.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.55 (0.30), residues: 771
  helix:  2.08 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop :  0.88 (0.46), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 171 
 TYR   0.013   0.001   TYR C 155 
 PHE   0.023   0.002   PHE C 221 
 TRP   0.024   0.002   TRP B  42 
 HIS   0.003   0.001   HIS C 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 7227)
  covalent geometry    : angle       0.54688 ( 9633)
  hydrogen bonds       : bond        0.04590 (  438)
  hydrogen bonds       : angle       4.06732 ( 1305)
  Misc. bond           : bond        0.00035 (    3)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A  170 MET cc_start: 0.8467 (mtp) cc_final: 0.8203 (mtt)
REVERT: A  171 ARG cc_start: 0.8505 (ttp80) cc_final: 0.8298 (ttp-110)
REVERT: A  174 LYS cc_start: 0.8423 (tttp) cc_final: 0.8202 (tmtp)
REVERT: A  248 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8282 (mt-10)
REVERT: B  170 MET cc_start: 0.8678 (mtm) cc_final: 0.8229 (mtt)
  outliers start: 4
  outliers final: 1
  residues processed: 82
  average time/residue: 0.7033
  time to fit residues: 60.0199
Evaluate side-chains
  72 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 8 optimal weight:    9.9990
   chunk 66 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   chunk 68 optimal weight:   10.0000
   chunk 46 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 20 optimal weight:    8.9990
   chunk 54 optimal weight:    8.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 218 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.131832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.100393 restraints weight = 20683.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.2949 rms_B_bonded: 1.98
r_work: 0.2788 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2653 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2772
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2772 r_free = 0.2772    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2772 r_free = 0.2772    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2772
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   7230  Z= 0.125
  Angle     :  0.532   6.673   9633  Z= 0.263
  Chirality :  0.039   0.122    933
  Planarity :  0.005   0.032   1155
  Dihedral  : 14.352  59.911   1380
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  7.09 %
    Favored  : 91.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.06 (0.30), residues: 771
  helix:  2.47 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop :  1.02 (0.45), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 171 
 TYR   0.014   0.001   TYR C 154 
 PHE   0.020   0.002   PHE C 221 
 TRP   0.020   0.002   TRP B  42 
 HIS   0.003   0.001   HIS C 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 7227)
  covalent geometry    : angle       0.53236 ( 9633)
  hydrogen bonds       : bond        0.05025 (  438)
  hydrogen bonds       : angle       3.98926 ( 1305)
  Misc. bond           : bond        0.00057 (    3)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8071 (tttp) cc_final: 0.7741 (tttt)
REVERT: A  105 ASP cc_start: 0.8577 (p0) cc_final: 0.8373 (p0)
REVERT: A  170 MET cc_start: 0.8621 (mtp) cc_final: 0.8349 (mtt)
REVERT: A  174 LYS cc_start: 0.8384 (tttp) cc_final: 0.8182 (tmtp)
REVERT: B  170 MET cc_start: 0.8781 (mtm) cc_final: 0.8336 (mtt)
REVERT: C  174 LYS cc_start: 0.8400 (ttpt) cc_final: 0.8172 (tttp)
  outliers start: 5
  outliers final: 3
  residues processed: 84
  average time/residue: 0.6981
  time to fit residues: 61.1988
Evaluate side-chains
  72 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain C residue   60 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 53 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 31 optimal weight:    9.9990
   chunk 56 optimal weight:    3.9990
   chunk 22 optimal weight:    5.9990
   chunk 74 optimal weight:    9.9990
   chunk 67 optimal weight:    4.9990
   chunk 45 optimal weight:   10.0000
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 215 HIS
B 215 HIS
C 125 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.127357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.095506 restraints weight = 19844.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.2983 rms_B_bonded: 1.91
r_work: 0.2842 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2712 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2566
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2566 r_free = 0.2566    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2565 r_free = 0.2565    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2565
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8768
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7230  Z= 0.206
  Angle     :  0.629   6.320   9633  Z= 0.315
  Chirality :  0.044   0.131    933
  Planarity :  0.005   0.034   1155
  Dihedral  : 14.929  59.867   1380
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  7.09 %
    Favored  : 91.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.56 (0.29), residues: 771
  helix:  2.13 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop :  0.76 (0.44), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 171 
 TYR   0.021   0.002   TYR C  81 
 PHE   0.021   0.002   PHE C 221 
 TRP   0.019   0.002   TRP B  42 
 HIS   0.007   0.002   HIS C 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 7227)
  covalent geometry    : angle       0.62947 ( 9633)
  hydrogen bonds       : bond        0.06696 (  438)
  hydrogen bonds       : angle       4.25494 ( 1305)
  Misc. bond           : bond        0.00137 (    3)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8063 (tttp) cc_final: 0.7784 (tttt)
REVERT: A  174 LYS cc_start: 0.8563 (tttp) cc_final: 0.8112 (ttpt)
REVERT: B  170 MET cc_start: 0.8779 (mtm) cc_final: 0.8342 (mtt)
  outliers start: 6
  outliers final: 3
  residues processed: 82
  average time/residue: 0.7387
  time to fit residues: 63.1299
Evaluate side-chains
  75 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain B residue   33 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 49 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 51 optimal weight:    0.3980
   chunk 53 optimal weight:    0.8980
   chunk 45 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 73 optimal weight:    6.9990
   chunk 67 optimal weight:    0.0870
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.6760

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

Flipped N/Q/H residues before XYZ refinement:
A 215 HIS
C 225 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.135777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.104906 restraints weight = 18054.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 1.86
r_work: 0.3002 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2827
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2827 r_free = 0.2827    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2827 r_free = 0.2827    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2827
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   7230  Z= 0.104
  Angle     :  0.481   6.017   9633  Z= 0.239
  Chirality :  0.037   0.115    933
  Planarity :  0.005   0.033   1155
  Dihedral  : 12.371  58.767   1380
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  7.69 %
    Favored  : 91.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.19 (0.30), residues: 771
  helix:  2.61 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop :  0.93 (0.44), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 171 
 TYR   0.013   0.001   TYR C  81 
 PHE   0.016   0.001   PHE C 134 
 TRP   0.019   0.001   TRP B  42 
 HIS   0.002   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 7227)
  covalent geometry    : angle       0.48112 ( 9633)
  hydrogen bonds       : bond        0.04090 (  438)
  hydrogen bonds       : angle       3.79071 ( 1305)
  Misc. bond           : bond        0.00041 (    3)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8014 (tttp) cc_final: 0.7752 (tttt)
REVERT: A  170 MET cc_start: 0.8590 (mtp) cc_final: 0.8323 (mtt)
REVERT: A  174 LYS cc_start: 0.8384 (tttp) cc_final: 0.8182 (tmtp)
REVERT: B  170 MET cc_start: 0.8701 (mtm) cc_final: 0.8234 (mtt)
REVERT: C  174 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8250 (tttp)
  outliers start: 3
  outliers final: 3
  residues processed: 84
  average time/residue: 0.7403
  time to fit residues: 64.8497
Evaluate side-chains
  81 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain B residue   33 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 14 optimal weight:    9.9990
   chunk 12 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0020
   chunk 66 optimal weight:    8.9990
   chunk 55 optimal weight:    0.4980
   chunk 51 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 38 optimal weight:    9.9990
   overall best weight:    1.2790

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

Flipped N/Q/H residues before XYZ refinement:
A 215 HIS
C 215 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.132783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.101580 restraints weight = 26915.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3093 rms_B_bonded: 2.18
r_work: 0.2905 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2869
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2869 r_free = 0.2869    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2869
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.2808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   7230  Z= 0.120
  Angle     :  0.510   6.031   9633  Z= 0.252
  Chirality :  0.038   0.120    933
  Planarity :  0.005   0.035   1155
  Dihedral  : 12.088  59.795   1380
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  8.75 %
    Favored  : 90.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.18 (0.30), residues: 771
  helix:  2.61 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop :  0.91 (0.44), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 171 
 TYR   0.013   0.001   TYR C  81 
 PHE   0.016   0.001   PHE B 134 
 TRP   0.016   0.002   TRP B  42 
 HIS   0.003   0.001   HIS C 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 7227)
  covalent geometry    : angle       0.51045 ( 9633)
  hydrogen bonds       : bond        0.04751 (  438)
  hydrogen bonds       : angle       3.88201 ( 1305)
  Misc. bond           : bond        0.00054 (    3)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8076 (tttp) cc_final: 0.7815 (tttt)
REVERT: A  170 MET cc_start: 0.8528 (mtp) cc_final: 0.8256 (mtt)
REVERT: A  174 LYS cc_start: 0.8348 (tttp) cc_final: 0.8137 (tmtp)
REVERT: B   87 ASP cc_start: 0.9083 (t70) cc_final: 0.8881 (t70)
REVERT: B  170 MET cc_start: 0.8612 (mtm) cc_final: 0.8119 (mtt)
  outliers start: 3
  outliers final: 3
  residues processed: 84
  average time/residue: 0.7789
  time to fit residues: 68.1336
Evaluate side-chains
  82 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain B residue   33 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 0 optimal weight:   30.0000
   chunk 9 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 58 optimal weight:   10.0000
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 215 HIS
C 215 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.129370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.097439 restraints weight = 22917.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 2.06
r_work: 0.2860 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.2731 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2582
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2582 r_free = 0.2582    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2582 r_free = 0.2582    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2582
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8744
moved from start:          0.2578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7230  Z= 0.163
  Angle     :  0.568   6.181   9633  Z= 0.283
  Chirality :  0.041   0.125    933
  Planarity :  0.005   0.032   1155
  Dihedral  : 12.638  57.973   1380
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  9.05 %
    Favored  : 89.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.85 (0.30), residues: 771
  helix:  2.37 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop :  0.80 (0.44), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 151 
 TYR   0.017   0.001   TYR C  81 
 PHE   0.018   0.002   PHE B 134 
 TRP   0.017   0.002   TRP B  42 
 HIS   0.005   0.002   HIS C 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 7227)
  covalent geometry    : angle       0.56832 ( 9633)
  hydrogen bonds       : bond        0.05852 (  438)
  hydrogen bonds       : angle       4.10019 ( 1305)
  Misc. bond           : bond        0.00097 (    3)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8105 (tttp) cc_final: 0.7791 (tttt)
REVERT: A  170 MET cc_start: 0.8680 (mtp) cc_final: 0.8399 (mtt)
REVERT: A  174 LYS cc_start: 0.8544 (tttp) cc_final: 0.8087 (ttpt)
REVERT: B  170 MET cc_start: 0.8796 (mtm) cc_final: 0.8335 (mtt)
  outliers start: 4
  outliers final: 4
  residues processed: 80
  average time/residue: 0.7176
  time to fit residues: 59.8641
Evaluate side-chains
  76 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain B residue   33 CYS
Chi-restraints excluded: chain B residue  145 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 54 optimal weight:    8.9990
   chunk 41 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 215 HIS
C 215 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.130751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.099330 restraints weight = 19026.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3048 rms_B_bonded: 1.88
r_work: 0.2912 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2784 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2639
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2639 r_free = 0.2639    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2639 r_free = 0.2639    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8720
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7230  Z= 0.141
  Angle     :  0.538   5.963   9633  Z= 0.269
  Chirality :  0.040   0.122    933
  Planarity :  0.005   0.041   1155
  Dihedral  : 12.237  59.252   1380
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  8.60 %
    Favored  : 90.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.93 (0.30), residues: 771
  helix:  2.43 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop :  0.80 (0.44), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 171 
 TYR   0.016   0.001   TYR C  81 
 PHE   0.017   0.001   PHE B 134 
 TRP   0.015   0.002   TRP B  42 
 HIS   0.004   0.001   HIS C 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 7227)
  covalent geometry    : angle       0.53800 ( 9633)
  hydrogen bonds       : bond        0.05283 (  438)
  hydrogen bonds       : angle       4.00707 ( 1305)
  Misc. bond           : bond        0.00079 (    3)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8100 (tttp) cc_final: 0.7807 (tttt)
REVERT: A  170 MET cc_start: 0.8666 (mtp) cc_final: 0.8373 (mtt)
REVERT: B  170 MET cc_start: 0.8744 (mtm) cc_final: 0.8309 (mtt)
REVERT: B  176 ARG cc_start: 0.7955 (mtp85) cc_final: 0.7575 (ttm-80)
  outliers start: 5
  outliers final: 4
  residues processed: 77
  average time/residue: 0.7498
  time to fit residues: 60.1730
Evaluate side-chains
  75 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain B residue   33 CYS
Chi-restraints excluded: chain B residue  145 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 4 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 63 optimal weight:    8.9990
   chunk 25 optimal weight:   30.0000
   chunk 67 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   overall best weight:    3.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 215 HIS
C 215 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.128422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.097108 restraints weight = 26599.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3032 rms_B_bonded: 2.12
r_work: 0.2852 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2701
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2701 r_free = 0.2701    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2701 r_free = 0.2701    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2701
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8703
moved from start:          0.2535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7230  Z= 0.190
  Angle     :  0.606   5.999   9633  Z= 0.304
  Chirality :  0.043   0.129    933
  Planarity :  0.005   0.061   1155
  Dihedral  : 12.858  58.607   1380
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  8.90 %
    Favored  : 89.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.65 (0.29), residues: 771
  helix:  2.23 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop :  0.68 (0.43), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 171 
 TYR   0.020   0.002   TYR C  81 
 PHE   0.018   0.002   PHE B 134 
 TRP   0.016   0.002   TRP B  42 
 HIS   0.006   0.002   HIS C 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 7227)
  covalent geometry    : angle       0.60578 ( 9633)
  hydrogen bonds       : bond        0.06284 (  438)
  hydrogen bonds       : angle       4.17957 ( 1305)
  Misc. bond           : bond        0.00118 (    3)

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

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

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1542 Ramachandran restraints generated.
    771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8128 (tttp) cc_final: 0.7837 (tttt)
REVERT: A  170 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8237 (mtt)
REVERT: A  174 LYS cc_start: 0.8482 (tttp) cc_final: 0.8022 (ttpt)
REVERT: B  170 MET cc_start: 0.8664 (mtm) cc_final: 0.8201 (mtt)
REVERT: C  171 ARG cc_start: 0.8476 (ttp-170) cc_final: 0.8229 (ttp-170)
  outliers start: 5
  outliers final: 4
  residues processed: 77
  average time/residue: 0.7751
  time to fit residues: 62.3256
Evaluate side-chains
  76 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  170 MET
Chi-restraints excluded: chain B residue   33 CYS
Chi-restraints excluded: chain B residue  145 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 17 optimal weight:    0.1980
   chunk 35 optimal weight:    2.9990
   chunk 16 optimal weight:    8.9990
   chunk 7 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 215 HIS
C 215 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.134199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.103257 restraints weight = 22971.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 2.07
r_work: 0.2939 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2904
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2904 r_free = 0.2904    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2904 r_free = 0.2904    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2904
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.2907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7230  Z= 0.111
  Angle     :  0.498   5.733   9633  Z= 0.248
  Chirality :  0.038   0.120    933
  Planarity :  0.005   0.045   1155
  Dihedral  : 11.731  59.497   1380
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  9.05 %
    Favored  : 89.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.13 (0.30), residues: 771
  helix:  2.58 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop :  0.88 (0.43), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 171 
 TYR   0.011   0.001   TYR C  81 
 PHE   0.015   0.001   PHE B 134 
 TRP   0.017   0.001   TRP B  42 
 HIS   0.003   0.001   HIS A 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 7227)
  covalent geometry    : angle       0.49761 ( 9633)
  hydrogen bonds       : bond        0.04447 (  438)
  hydrogen bonds       : angle       3.88235 ( 1305)
  Misc. bond           : bond        0.00033 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2607.39 seconds
wall clock time: 45 minutes 9.54 seconds (2709.54 seconds total)