Starting phenix.real_space_refine
on Sat May 10 16:12:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9n0x_48797/05_2025/9n0x_48797.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9n0x_48797/05_2025/9n0x_48797.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9n0x_48797/05_2025/9n0x_48797.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9n0x_48797/05_2025/9n0x_48797.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9n0x_48797/05_2025/9n0x_48797.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9n0x_48797/05_2025/9n0x_48797.cif"
  }
  resolution = 3.3
  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=   0.004 sd=   0.021
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: 6
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     P       6      5.49       5
     S      40      5.16       5
     C    4432      2.51       5
     N    1008      2.21       5
     O    1100      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 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: 6588
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 3181
          Classifications: {'peptide': 380}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 358}
    Chain: "B"
      Number of atoms: 3181
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 380, 3181
          Classifications: {'peptide': 380}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 358}
    Chain: "A"
      Number of atoms: 113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 113
          Unusual residues: {' CA': 1, 'RXY': 1}
          Classifications: {'peptide': 2, 'undetermined': 2}
          Link IDs: {'TRANS': 1, None: 2}
            Not linked:
              pdbres="P5S A 502 "
              pdbres=" CA A 503 "
            Not linked:
              pdbres=" CA A 503 "
              pdbres="RXY A 504 "
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 45
    Chain: "B"
      Number of atoms: 113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 113
          Unusual residues: {' CA': 1, 'RXY': 1}
          Classifications: {'peptide': 2, 'undetermined': 2}
          Link IDs: {'TRANS': 1, None: 2}
            Not linked:
              pdbres="P5S B 502 "
              pdbres=" CA B 503 "
            Not linked:
              pdbres=" CA B 503 "
              pdbres="RXY B 504 "
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 45
  Time building chain proxies: 4.89, per 1000 atoms: 0.74
  Number of scatterers: 6588
  At special positions: 0
  Unit cell: (107.748, 118.818, 69.372, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      2     19.99
     S      40     16.00
     P       6     15.00
     O    1100      8.00
     N    1008      7.00
     C    4432      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 174 " - pdb=" SG  CYS A 241 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 174 " - pdb=" SG  CYS B 241 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.59
  Conformation dependent library (CDL) restraints added in 915.5 milliseconds
  

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1448

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 0 sheets defined
      73.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 65 through 82
    Processing helix  chain 'A' and resid 88 through 112
      removed outlier: 3.851A  pdb=" N   LYS A  94 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 144
      removed outlier: 3.950A  pdb=" N   TRP A 125 " --> pdb=" O   HIS A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 158
    Processing helix  chain 'A' and resid 186 through 193
      removed outlier: 4.047A  pdb=" N   ASP A 191 " --> pdb=" O   HIS A 187 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LYS A 192 " --> pdb=" O   ASN A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 212
      removed outlier: 3.663A  pdb=" N   LEU A 202 " --> pdb=" O   PRO A 198 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE A 211 " --> pdb=" O   LYS A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 231
      removed outlier: 3.509A  pdb=" N   CYS A 217 " --> pdb=" O   ASP A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 247
    Processing helix  chain 'A' and resid 249 through 256
    Processing helix  chain 'A' and resid 256 through 269
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 311 through 338
      removed outlier: 3.609A  pdb=" N   GLU A 328 " --> pdb=" O   PHE A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 371
      removed outlier: 3.613A  pdb=" N   LEU A 348 " --> pdb=" O   HIS A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 400
      removed outlier: 3.558A  pdb=" N   ASP A 400 " --> pdb=" O   VAL A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 405
      removed outlier: 3.605A  pdb=" N   LEU A 404 " --> pdb=" O   ASP A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 437
      removed outlier: 3.874A  pdb=" N   CYS A 415 " --> pdb=" O   TYR A 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 82
    Processing helix  chain 'B' and resid 88 through 112
      removed outlier: 3.916A  pdb=" N   LYS B  94 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 144
      removed outlier: 3.953A  pdb=" N   TRP B 125 " --> pdb=" O   HIS B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 158
    Processing helix  chain 'B' and resid 186 through 193
      removed outlier: 4.013A  pdb=" N   ASP B 191 " --> pdb=" O   HIS B 187 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LYS B 192 " --> pdb=" O   ASN B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 212
      removed outlier: 3.548A  pdb=" N   PHE B 201 " --> pdb=" O   VAL B 197 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU B 202 " --> pdb=" O   PRO B 198 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE B 211 " --> pdb=" O   LYS B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 231
      removed outlier: 3.513A  pdb=" N   CYS B 217 " --> pdb=" O   ASP B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 247
    Processing helix  chain 'B' and resid 249 through 256
    Processing helix  chain 'B' and resid 256 through 269
    Processing helix  chain 'B' and resid 283 through 294
    Processing helix  chain 'B' and resid 311 through 338
      removed outlier: 3.607A  pdb=" N   GLU B 328 " --> pdb=" O   PHE B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 370
      removed outlier: 3.632A  pdb=" N   LEU B 348 " --> pdb=" O   HIS B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 400
      removed outlier: 3.560A  pdb=" N   ASP B 400 " --> pdb=" O   VAL B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 405
      removed outlier: 3.618A  pdb=" N   LEU B 404 " --> pdb=" O   ASP B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 437
      removed outlier: 3.875A  pdb=" N   CYS B 415 " --> pdb=" O   TYR B 411 " (cutoff:3.500A)

    404 hydrogen bonds defined for protein.
    1212 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: 1.61

  Time building geometry restraints manager: 1.81 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 950
        1.30 -     1.43: 2022
        1.43 -     1.56: 3766
        1.56 -     1.69: 18
        1.69 -     1.81: 60
  Bond restraints: 6816
  Sorted by residual:
  bond pdb=" CBJ RXY A 504 "
       pdb=" CBK RXY A 504 "
    ideal  model  delta    sigma   weight residual
    1.533  1.317  0.216 2.00e-02 2.50e+03 1.16e+02
  bond pdb=" CBJ RXY B 504 "
       pdb=" CBK RXY B 504 "
    ideal  model  delta    sigma   weight residual
    1.533  1.318  0.215 2.00e-02 2.50e+03 1.16e+02
  bond pdb=" CBG RXY B 504 "
       pdb=" CBH RXY B 504 "
    ideal  model  delta    sigma   weight residual
    1.525  1.318  0.207 2.00e-02 2.50e+03 1.07e+02
  bond pdb=" CBG RXY A 504 "
       pdb=" CBH RXY A 504 "
    ideal  model  delta    sigma   weight residual
    1.525  1.318  0.207 2.00e-02 2.50e+03 1.07e+02
  bond pdb=" CAK RXY A 504 "
       pdb=" CAL RXY A 504 "
    ideal  model  delta    sigma   weight residual
    1.333  1.529 -0.196 2.00e-02 2.50e+03 9.59e+01
  ... (remaining 6811 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.82: 9088
        2.82 -     5.64: 130
        5.64 -     8.47: 34
        8.47 -    11.29: 14
       11.29 -    14.11: 8
  Bond angle restraints: 9274
  Sorted by residual:
  angle pdb=" CAK RXY B 504 "
        pdb=" CAL RXY B 504 "
        pdb=" CAM RXY B 504 "
      ideal   model   delta    sigma   weight residual
     126.11  112.00   14.11 3.00e+00 1.11e-01 2.21e+01
  angle pdb=" CAK RXY A 504 "
        pdb=" CAL RXY A 504 "
        pdb=" CAM RXY A 504 "
      ideal   model   delta    sigma   weight residual
     126.11  112.03   14.08 3.00e+00 1.11e-01 2.20e+01
  angle pdb=" OAB RXY A 504 "
        pdb=" PAZ RXY A 504 "
        pdb=" OBX RXY A 504 "
      ideal   model   delta    sigma   weight residual
     123.18  109.25   13.93 3.00e+00 1.11e-01 2.16e+01
  angle pdb=" OAB RXY B 504 "
        pdb=" PAZ RXY B 504 "
        pdb=" OBX RXY B 504 "
      ideal   model   delta    sigma   weight residual
     123.18  109.29   13.89 3.00e+00 1.11e-01 2.14e+01
  angle pdb=" CAJ RXY A 504 "
        pdb=" CAK RXY A 504 "
        pdb=" CAL RXY A 504 "
      ideal   model   delta    sigma   weight residual
     125.80  112.37   13.43 3.00e+00 1.11e-01 2.00e+01
  ... (remaining 9269 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.80: 3752
       35.80 -    71.60: 180
       71.60 -   107.40: 24
      107.40 -   143.20: 7
      143.20 -   179.00: 11
  Dihedral angle restraints: 3974
    sinusoidal: 1732
      harmonic: 2242
  Sorted by residual:
  dihedral pdb=" C38 P5S A 502 "
           pdb=" C39 P5S A 502 "
           pdb=" C40 P5S A 502 "
           pdb=" C41 P5S A 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
      64.51 -114.49  179.00     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C38 P5S B 502 "
           pdb=" C39 P5S B 502 "
           pdb=" C40 P5S B 502 "
           pdb=" C41 P5S B 502 "
      ideal   model   delta sinusoidal    sigma   weight residual
      64.51 -114.47  178.98     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" CBF RXY B 504 "
           pdb=" CBG RXY B 504 "
           pdb=" CBH RXY B 504 "
           pdb=" CBI RXY B 504 "
      ideal   model   delta sinusoidal    sigma   weight residual
     178.53   -0.14  178.67     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 3971 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 841
       0.056 -    0.112: 132
       0.112 -    0.167: 9
       0.167 -    0.223: 2
       0.223 -    0.279: 2
  Chirality restraints: 986
  Sorted by residual:
  chirality pdb=" CAW RXY B 504 "
            pdb=" CAV RXY B 504 "
            pdb=" CAX RXY B 504 "
            pdb=" OBW RXY B 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.21    2.49   -0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" CAW RXY A 504 "
            pdb=" CAV RXY A 504 "
            pdb=" CAX RXY A 504 "
            pdb=" OBW RXY A 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.21    2.49   -0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CA  P5S B 501 "
            pdb=" N   P5S B 501 "
            pdb=" C   P5S B 501 "
            pdb=" CB  P5S B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.59   -0.19 2.00e-01 2.50e+01 9.09e-01
  ... (remaining 983 not shown)

  Planarity restraints: 1108
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAJ RXY B 504 "   -0.142 2.00e-02 2.50e+03   2.39e-01 5.73e+02
        pdb=" CAK RXY B 504 "    0.308 2.00e-02 2.50e+03
        pdb=" CAL RXY B 504 "   -0.307 2.00e-02 2.50e+03
        pdb=" CAM RXY B 504 "    0.140 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CAJ RXY A 504 "    0.141 2.00e-02 2.50e+03   2.37e-01 5.62e+02
        pdb=" CAK RXY A 504 "   -0.305 2.00e-02 2.50e+03
        pdb=" CAL RXY A 504 "    0.304 2.00e-02 2.50e+03
        pdb=" CAM RXY A 504 "   -0.140 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 296 "    0.048 5.00e-02 4.00e+02   7.13e-02 8.13e+00
        pdb=" N   PRO B 297 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO B 297 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 297 "    0.040 5.00e-02 4.00e+02
  ... (remaining 1105 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 781
        2.75 -     3.29: 6415
        3.29 -     3.82: 11099
        3.82 -     4.36: 11856
        4.36 -     4.90: 21679
  Nonbonded interactions: 51830
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 293 "
            pdb=" OG1 THR B 296 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   PHE A 293 "
            pdb=" OG1 THR A 296 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OG1 THR A 331 "
            pdb=" NH1 ARG A 350 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" OG1 THR B 331 "
            pdb=" NH1 ARG B 350 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" O   LEU A 268 "
            pdb=" OH  TYR A 273 "
     model   vdw
     2.284 3.040
  ... (remaining 51825 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: 0.03
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=1.00 max=1.00 mean=1.00
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:             2.400
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.460
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
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      :  0.008   0.216   6818  Z= 0.405
  Angle     :  0.961  14.112   9278  Z= 0.399
  Chirality :  0.041   0.279    986
  Planarity :  0.011   0.239   1108
  Dihedral  : 23.177 178.998   2520
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 15.84 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.18 (0.30), residues: 756
  helix:  2.05 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -2.00 (0.35), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 204 
 HIS   0.004   0.001   HIS A  64 
 PHE   0.008   0.001   PHE A 303 
 TYR   0.019   0.001   TYR B 366 
 ARG   0.002   0.001   ARG B 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09318 (  404)
  hydrogen bonds       : angle       4.62007 ( 1212)
  SS BOND              : bond        0.00227 (    2)
  SS BOND              : angle       0.67024 (    4)
  covalent geometry    : bond        0.00812 ( 6816)
  covalent geometry    : angle       0.96130 ( 9274)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.616 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.6820 (t80) cc_final: 0.6572 (t80)
REVERT: B  224 PHE cc_start: 0.6909 (t80) cc_final: 0.6588 (t80)
  outliers start: 2
  outliers final: 2
  residues processed: 55
  average time/residue: 0.1343
  time to fit residues: 11.2806
Evaluate side-chains
  56 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain B residue  188 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 57 optimal weight:    7.9990
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 59 optimal weight:    9.9990
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    6.9990
   chunk 44 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.214840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 104)---------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.174765 restraints weight = 8502.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.4157 rms_B_bonded: 2.00
r_work: 0.3974 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3853 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.0659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6818  Z= 0.129
  Angle     :  0.535   6.287   9278  Z= 0.270
  Chirality :  0.039   0.133    986
  Planarity :  0.005   0.048   1108
  Dihedral  : 23.647 176.024   1059
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.41 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.13 (0.30), residues: 756
  helix:  1.95 (0.23), residues: 502
  sheet:  None (None), residues: 0
  loop : -1.83 (0.35), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 204 
 HIS   0.004   0.001   HIS B 233 
 PHE   0.008   0.001   PHE A 303 
 TYR   0.017   0.001   TYR A 366 
 ARG   0.003   0.001   ARG B 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05040 (  404)
  hydrogen bonds       : angle       4.15834 ( 1212)
  SS BOND              : bond        0.00229 (    2)
  SS BOND              : angle       0.62250 (    4)
  covalent geometry    : bond        0.00283 ( 6816)
  covalent geometry    : angle       0.53519 ( 9274)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.644 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.7027 (t80) cc_final: 0.6677 (t80)
REVERT: A  260 CYS cc_start: 0.7878 (m) cc_final: 0.7256 (m)
REVERT: B  223 MET cc_start: 0.6890 (mmm) cc_final: 0.6612 (mmm)
  outliers start: 13
  outliers final: 12
  residues processed: 66
  average time/residue: 0.1434
  time to fit residues: 14.8620
Evaluate side-chains
  65 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  188 ASN
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  248 MET
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  260 CYS
Chi-restraints excluded: chain B residue  264 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 12 optimal weight:    0.2980
   chunk 48 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.214355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 99)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.173686 restraints weight = 8523.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.4142 rms_B_bonded: 2.03
r_work: 0.3956 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3836 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.0965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6818  Z= 0.124
  Angle     :  0.502   6.158   9278  Z= 0.258
  Chirality :  0.038   0.127    986
  Planarity :  0.004   0.040   1108
  Dihedral  : 20.009 170.945   1056
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.28 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.26 (0.30), residues: 756
  helix:  2.00 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -1.70 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 204 
 HIS   0.005   0.001   HIS A 233 
 PHE   0.006   0.001   PHE B 354 
 TYR   0.017   0.001   TYR A 366 
 ARG   0.003   0.001   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04958 (  404)
  hydrogen bonds       : angle       4.16491 ( 1212)
  SS BOND              : bond        0.00146 (    2)
  SS BOND              : angle       0.62366 (    4)
  covalent geometry    : bond        0.00269 ( 6816)
  covalent geometry    : angle       0.50241 ( 9274)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 55
  time to evaluate  : 0.692 
Fit side-chains
REVERT: A  223 MET cc_start: 0.6874 (mmm) cc_final: 0.6570 (mmm)
REVERT: A  224 PHE cc_start: 0.7027 (t80) cc_final: 0.6757 (t80)
REVERT: A  260 CYS cc_start: 0.7807 (m) cc_final: 0.7158 (m)
REVERT: B  224 PHE cc_start: 0.6987 (t80) cc_final: 0.6661 (t80)
REVERT: B  231 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7382 (mp)
REVERT: B  234 GLN cc_start: 0.7140 (mt0) cc_final: 0.6916 (mt0)
REVERT: B  260 CYS cc_start: 0.7968 (m) cc_final: 0.7144 (m)
  outliers start: 17
  outliers final: 14
  residues processed: 66
  average time/residue: 0.1263
  time to fit residues: 13.0039
Evaluate side-chains
  70 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  188 ASN
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  248 MET
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  357 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 66 optimal weight:    0.4980
   chunk 23 optimal weight:    0.4980
   chunk 75 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.215010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 115)---------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.179496 restraints weight = 8611.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.4212 rms_B_bonded: 1.47
r_work: 0.4013 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3914 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.1128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6818  Z= 0.113
  Angle     :  0.481   6.043   9278  Z= 0.246
  Chirality :  0.038   0.126    986
  Planarity :  0.004   0.035   1108
  Dihedral  : 19.417 167.338   1056
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 17.01 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.40 (0.30), residues: 756
  helix:  2.09 (0.23), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.67 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 204 
 HIS   0.004   0.001   HIS A 233 
 PHE   0.008   0.001   PHE A 354 
 TYR   0.014   0.001   TYR B 366 
 ARG   0.003   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04715 (  404)
  hydrogen bonds       : angle       4.10080 ( 1212)
  SS BOND              : bond        0.00131 (    2)
  SS BOND              : angle       0.54886 (    4)
  covalent geometry    : bond        0.00243 ( 6816)
  covalent geometry    : angle       0.48053 ( 9274)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.695 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.6898 (t80) cc_final: 0.6616 (t80)
REVERT: A  260 CYS cc_start: 0.7540 (m) cc_final: 0.6876 (m)
REVERT: A  324 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7864 (t80)
REVERT: B  224 PHE cc_start: 0.6942 (t80) cc_final: 0.6640 (t80)
REVERT: B  231 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7359 (mp)
REVERT: B  234 GLN cc_start: 0.7081 (mt0) cc_final: 0.6835 (mt0)
REVERT: B  324 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.7865 (t80)
  outliers start: 20
  outliers final: 14
  residues processed: 72
  average time/residue: 0.1519
  time to fit residues: 15.8920
Evaluate side-chains
  71 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  324 PHE
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  248 MET
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  324 PHE
Chi-restraints excluded: chain B residue  357 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 63 optimal weight:    0.0470
   chunk 61 optimal weight:   10.0000
   chunk 50 optimal weight:    0.4980
   chunk 2 optimal weight:    0.0470
   chunk 3 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 20 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.3776

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.216560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 100)---------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.181862 restraints weight = 8579.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.4231 rms_B_bonded: 1.42
r_work: 0.4032 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3931 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6818  Z= 0.102
  Angle     :  0.467   7.527   9278  Z= 0.238
  Chirality :  0.037   0.126    986
  Planarity :  0.004   0.035   1108
  Dihedral  : 19.055 167.420   1056
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.86 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.61 (0.30), residues: 756
  helix:  2.25 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.58 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 204 
 HIS   0.003   0.001   HIS A 233 
 PHE   0.007   0.001   PHE B 354 
 TYR   0.014   0.001   TYR B 366 
 ARG   0.003   0.000   ARG B 119 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04363 (  404)
  hydrogen bonds       : angle       4.02590 ( 1212)
  SS BOND              : bond        0.00183 (    2)
  SS BOND              : angle       0.61466 (    4)
  covalent geometry    : bond        0.00213 ( 6816)
  covalent geometry    : angle       0.46707 ( 9274)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.702 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.6809 (t80) cc_final: 0.6555 (t80)
REVERT: A  260 CYS cc_start: 0.7610 (m) cc_final: 0.6940 (m)
REVERT: A  324 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.7833 (t80)
REVERT: B  224 PHE cc_start: 0.6809 (t80) cc_final: 0.6540 (t80)
REVERT: B  231 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7359 (mp)
REVERT: B  234 GLN cc_start: 0.7062 (mt0) cc_final: 0.6784 (mt0)
REVERT: B  260 CYS cc_start: 0.7722 (m) cc_final: 0.6871 (m)
REVERT: B  324 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7838 (t80)
  outliers start: 17
  outliers final: 13
  residues processed: 70
  average time/residue: 0.1275
  time to fit residues: 13.7901
Evaluate side-chains
  71 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  188 ASN
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  324 PHE
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  248 MET
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  324 PHE
Chi-restraints excluded: chain B residue  357 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 11 optimal weight:    0.4980
   chunk 50 optimal weight:    0.0020
   chunk 60 optimal weight:   20.0000
   chunk 2 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 18 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    0.5388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.215709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 102)---------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.175042 restraints weight = 8459.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.4160 rms_B_bonded: 2.19
r_work: 0.3975 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3861 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.1370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6818  Z= 0.110
  Angle     :  0.474   7.084   9278  Z= 0.242
  Chirality :  0.037   0.126    986
  Planarity :  0.004   0.035   1108
  Dihedral  : 18.871 166.257   1056
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.30 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.61 (0.30), residues: 756
  helix:  2.24 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.56 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 204 
 HIS   0.004   0.001   HIS A 233 
 PHE   0.007   0.001   PHE A 354 
 TYR   0.013   0.001   TYR B 366 
 ARG   0.003   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04537 (  404)
  hydrogen bonds       : angle       4.01663 ( 1212)
  SS BOND              : bond        0.00086 (    2)
  SS BOND              : angle       0.41556 (    4)
  covalent geometry    : bond        0.00234 ( 6816)
  covalent geometry    : angle       0.47375 ( 9274)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 55
  time to evaluate  : 0.714 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.6901 (t80) cc_final: 0.6644 (t80)
REVERT: A  238 PHE cc_start: 0.4630 (OUTLIER) cc_final: 0.4382 (m-80)
REVERT: A  260 CYS cc_start: 0.7829 (m) cc_final: 0.7173 (m)
REVERT: A  324 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.7884 (t80)
REVERT: B  224 PHE cc_start: 0.6949 (t80) cc_final: 0.6682 (t80)
REVERT: B  231 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7301 (mp)
REVERT: B  234 GLN cc_start: 0.7155 (mt0) cc_final: 0.6840 (mt0)
REVERT: B  260 CYS cc_start: 0.7908 (m) cc_final: 0.7069 (m)
REVERT: B  324 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.7947 (t80)
  outliers start: 24
  outliers final: 14
  residues processed: 74
  average time/residue: 0.1209
  time to fit residues: 13.8351
Evaluate side-chains
  74 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  324 PHE
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  248 MET
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  324 PHE
Chi-restraints excluded: chain B residue  357 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 12 optimal weight:    0.0980
   chunk 41 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 60 optimal weight:   20.0000
   chunk 51 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 2 optimal weight:    0.1980
   chunk 40 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.7784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.214306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 92)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.179541 restraints weight = 8479.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.4213 rms_B_bonded: 1.44
r_work: 0.3995 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3890 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6818  Z= 0.124
  Angle     :  0.496   8.924   9278  Z= 0.250
  Chirality :  0.038   0.127    986
  Planarity :  0.004   0.034   1108
  Dihedral  : 18.777 165.224   1056
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 17.01 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.53 (0.30), residues: 756
  helix:  2.17 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.55 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 204 
 HIS   0.004   0.001   HIS A 233 
 PHE   0.008   0.001   PHE A 354 
 TYR   0.013   0.001   TYR B 366 
 ARG   0.003   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04866 (  404)
  hydrogen bonds       : angle       4.07343 ( 1212)
  SS BOND              : bond        0.00143 (    2)
  SS BOND              : angle       0.42967 (    4)
  covalent geometry    : bond        0.00274 ( 6816)
  covalent geometry    : angle       0.49583 ( 9274)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 56
  time to evaluate  : 0.633 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.7006 (t80) cc_final: 0.6727 (t80)
REVERT: A  238 PHE cc_start: 0.4755 (OUTLIER) cc_final: 0.4518 (m-80)
REVERT: A  260 CYS cc_start: 0.7688 (m) cc_final: 0.7034 (m)
REVERT: A  324 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.7878 (t80)
REVERT: B  223 MET cc_start: 0.6798 (mmm) cc_final: 0.6507 (mmm)
REVERT: B  224 PHE cc_start: 0.7011 (t80) cc_final: 0.6754 (t80)
REVERT: B  231 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7408 (mp)
REVERT: B  234 GLN cc_start: 0.7108 (mt0) cc_final: 0.6834 (mt0)
REVERT: B  260 CYS cc_start: 0.7789 (m) cc_final: 0.6943 (m)
REVERT: B  324 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.7943 (t80)
  outliers start: 26
  outliers final: 17
  residues processed: 76
  average time/residue: 0.1186
  time to fit residues: 13.9227
Evaluate side-chains
  76 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 55
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  188 ASN
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  324 PHE
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  248 MET
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  324 PHE
Chi-restraints excluded: chain B residue  357 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 39 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 36 optimal weight:   30.0000
   chunk 31 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 57 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.214575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 117)---------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.173498 restraints weight = 8508.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.4135 rms_B_bonded: 1.99
r_work: 0.3956 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.3836 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6818  Z= 0.118
  Angle     :  0.490   7.918   9278  Z= 0.247
  Chirality :  0.038   0.126    986
  Planarity :  0.004   0.034   1108
  Dihedral  : 18.661 164.890   1056
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 17.73 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.54 (0.30), residues: 756
  helix:  2.18 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.57 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 204 
 HIS   0.004   0.001   HIS B 233 
 PHE   0.011   0.001   PHE B 238 
 TYR   0.013   0.001   TYR B 366 
 ARG   0.003   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04744 (  404)
  hydrogen bonds       : angle       4.06933 ( 1212)
  SS BOND              : bond        0.00060 (    2)
  SS BOND              : angle       0.30469 (    4)
  covalent geometry    : bond        0.00258 ( 6816)
  covalent geometry    : angle       0.48991 ( 9274)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 54
  time to evaluate  : 0.707 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.6983 (t80) cc_final: 0.6721 (t80)
REVERT: A  238 PHE cc_start: 0.4726 (OUTLIER) cc_final: 0.4477 (m-80)
REVERT: A  260 CYS cc_start: 0.7852 (m) cc_final: 0.7218 (m)
REVERT: A  324 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7901 (t80)
REVERT: B  224 PHE cc_start: 0.7011 (t80) cc_final: 0.6743 (t80)
REVERT: B  231 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7393 (mp)
REVERT: B  234 GLN cc_start: 0.7224 (mt0) cc_final: 0.6931 (mt0)
REVERT: B  260 CYS cc_start: 0.7922 (m) cc_final: 0.7090 (m)
REVERT: B  324 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7895 (t80)
  outliers start: 23
  outliers final: 17
  residues processed: 73
  average time/residue: 0.1265
  time to fit residues: 14.3687
Evaluate side-chains
  76 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 55
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  324 PHE
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  248 MET
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  324 PHE
Chi-restraints excluded: chain B residue  357 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 49 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 67 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 15 optimal weight:    0.3980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.213602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 99)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.173361 restraints weight = 8560.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.4138 rms_B_bonded: 1.92
r_work: 0.3951 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3835 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6818  Z= 0.127
  Angle     :  0.500   7.997   9278  Z= 0.253
  Chirality :  0.038   0.128    986
  Planarity :  0.004   0.033   1108
  Dihedral  : 18.532 163.882   1056
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 17.73 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.48 (0.30), residues: 756
  helix:  2.13 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.57 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 204 
 HIS   0.003   0.001   HIS A 233 
 PHE   0.007   0.001   PHE A 127 
 TYR   0.013   0.001   TYR B 366 
 ARG   0.003   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04954 (  404)
  hydrogen bonds       : angle       4.11835 ( 1212)
  SS BOND              : bond        0.00167 (    2)
  SS BOND              : angle       0.41987 (    4)
  covalent geometry    : bond        0.00283 ( 6816)
  covalent geometry    : angle       0.50027 ( 9274)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 55
  time to evaluate  : 0.687 
Fit side-chains
REVERT: A  224 PHE cc_start: 0.7041 (t80) cc_final: 0.6773 (t80)
REVERT: A  238 PHE cc_start: 0.4780 (OUTLIER) cc_final: 0.4540 (m-80)
REVERT: A  260 CYS cc_start: 0.7828 (m) cc_final: 0.7215 (m)
REVERT: A  324 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.7908 (t80)
REVERT: B  223 MET cc_start: 0.6855 (mmm) cc_final: 0.6563 (mmm)
REVERT: B  224 PHE cc_start: 0.6976 (t80) cc_final: 0.6716 (t80)
REVERT: B  231 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7414 (mp)
REVERT: B  234 GLN cc_start: 0.7233 (mt0) cc_final: 0.6933 (mt0)
REVERT: B  260 CYS cc_start: 0.7854 (m) cc_final: 0.7018 (m)
REVERT: B  324 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.7906 (t80)
  outliers start: 23
  outliers final: 19
  residues processed: 73
  average time/residue: 0.1247
  time to fit residues: 14.0441
Evaluate side-chains
  78 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 55
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  188 ASN
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  324 PHE
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  248 MET
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  324 PHE
Chi-restraints excluded: chain B residue  357 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 33 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 9 optimal weight:    0.1980
   chunk 45 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0040
   overall best weight:    0.4392

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.215795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 90)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.181782 restraints weight = 8627.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.4235 rms_B_bonded: 1.46
r_work: 0.4017 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3906 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6818  Z= 0.104
  Angle     :  0.469   7.346   9278  Z= 0.238
  Chirality :  0.037   0.126    986
  Planarity :  0.004   0.036   1108
  Dihedral  : 18.178 164.379   1056
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 18.31 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.64 (0.30), residues: 756
  helix:  2.26 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.53 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 204 
 HIS   0.003   0.001   HIS B 233 
 PHE   0.007   0.001   PHE A 354 
 TYR   0.015   0.001   TYR B 366 
 ARG   0.002   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04387 (  404)
  hydrogen bonds       : angle       4.04862 ( 1212)
  SS BOND              : bond        0.00044 (    2)
  SS BOND              : angle       0.37556 (    4)
  covalent geometry    : bond        0.00215 ( 6816)
  covalent geometry    : angle       0.46933 ( 9274)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 54
  time to evaluate  : 0.697 
Fit side-chains
REVERT: A  223 MET cc_start: 0.6671 (mmm) cc_final: 0.6408 (mmm)
REVERT: A  224 PHE cc_start: 0.6859 (t80) cc_final: 0.6637 (t80)
REVERT: A  238 PHE cc_start: 0.4739 (OUTLIER) cc_final: 0.4537 (m-80)
REVERT: A  260 CYS cc_start: 0.7680 (m) cc_final: 0.7052 (m)
REVERT: A  324 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.7825 (t80)
REVERT: B  223 MET cc_start: 0.6698 (mmm) cc_final: 0.6438 (mmm)
REVERT: B  224 PHE cc_start: 0.6834 (t80) cc_final: 0.6611 (t80)
REVERT: B  231 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7396 (mp)
REVERT: B  234 GLN cc_start: 0.7181 (mt0) cc_final: 0.6893 (mt0)
REVERT: B  260 CYS cc_start: 0.7734 (m) cc_final: 0.6889 (m)
REVERT: B  324 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.7823 (t80)
  outliers start: 20
  outliers final: 15
  residues processed: 69
  average time/residue: 0.1231
  time to fit residues: 13.1433
Evaluate side-chains
  73 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 54
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 HIS
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  238 PHE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  324 PHE
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  165 LEU
Chi-restraints excluded: chain B residue  188 ASN
Chi-restraints excluded: chain B residue  218 MET
Chi-restraints excluded: chain B residue  231 LEU
Chi-restraints excluded: chain B residue  248 MET
Chi-restraints excluded: chain B residue  264 THR
Chi-restraints excluded: chain B residue  324 PHE
Chi-restraints excluded: chain B residue  357 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 31 optimal weight:    0.4980
   chunk 60 optimal weight:    9.9990
   chunk 10 optimal weight:    0.1980
   chunk 72 optimal weight:    0.0020
   chunk 62 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.4188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4568 r_free = 0.4568 target = 0.216162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 88)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.182124 restraints weight = 8568.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.4245 rms_B_bonded: 1.45
r_work: 0.4026 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3918 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.1759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6818  Z= 0.104
  Angle     :  0.469   7.564   9278  Z= 0.236
  Chirality :  0.037   0.125    986
  Planarity :  0.004   0.036   1108
  Dihedral  : 17.848 164.596   1056
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 18.46 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.73 (0.30), residues: 756
  helix:  2.32 (0.22), residues: 508
  sheet:  None (None), residues: 0
  loop : -1.47 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 204 
 HIS   0.003   0.001   HIS B 233 
 PHE   0.007   0.001   PHE A 354 
 TYR   0.013   0.001   TYR B 366 
 ARG   0.003   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04345 (  404)
  hydrogen bonds       : angle       4.00489 ( 1212)
  SS BOND              : bond        0.00123 (    2)
  SS BOND              : angle       0.55924 (    4)
  covalent geometry    : bond        0.00217 ( 6816)
  covalent geometry    : angle       0.46872 ( 9274)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3895.18 seconds
wall clock time: 68 minutes 0.48 seconds (4080.48 seconds total)