Starting phenix.real_space_refine
on Mon Apr  6 03:10:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wu2_21903/04_2026/6wu2_21903_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wu2_21903/04_2026/6wu2_21903.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wu2_21903/04_2026/6wu2_21903_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wu2_21903/04_2026/6wu2_21903_neut_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wu2_21903/04_2026/6wu2_21903.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wu2_21903/04_2026/6wu2_21903.map"
  }
  resolution = 3.36
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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
     S      50      5.16       5
     C    5106      2.51       5
     N    1176      2.21       5
     O    1260      1.98       5
     H    7812      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15404
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7666
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 489, 7666
          Classifications: {'peptide': 489}
          Link IDs: {'PTRANS': 22, 'TRANS': 466}
    Chain: "B"
      Number of atoms: 7666
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 489, 7666
          Classifications: {'peptide': 489}
          Link IDs: {'PTRANS': 22, 'TRANS': 466}
    Chain: "A"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 36
          Unusual residues: {'D10': 1, 'HEX': 3, 'OCT': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 36
          Unusual residues: {'D10': 1, 'HEX': 3, 'OCT': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 3.17, per 1000 atoms: 0.21
  Number of scatterers: 15404
  At special positions: 0
  Unit cell: (78.8955, 102.723, 76.7775, 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      50     16.00
     O    1260      8.00
     N    1176      7.00
     C    5106      6.00
     H    7812      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.51
  Conformation dependent library (CDL) restraints added in 520.8 milliseconds
  

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1784

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 0 sheets defined
      81.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 11
    Processing helix  chain 'A' and resid 12 through 26
      removed outlier: 3.599A  pdb=" N   LEU A  16 " --> pdb=" O   PHE A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 27 through 29
      No H-bonds generated for 'chain 'A' and resid 27 through 29'
    Processing helix  chain 'A' and resid 34 through 54
    Processing helix  chain 'A' and resid 57 through 72
    Processing helix  chain 'A' and resid 98 through 118
      removed outlier: 3.614A  pdb=" N   TRP A 102 " --> pdb=" O   ASN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 132
    Processing helix  chain 'A' and resid 135 through 151
      removed outlier: 4.173A  pdb=" N   ALA A 151 " --> pdb=" O   LEU A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 163
    Processing helix  chain 'A' and resid 163 through 175
    Processing helix  chain 'A' and resid 181 through 185
      removed outlier: 3.595A  pdb=" N   LYS A 185 " --> pdb=" O   PRO A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 206
    Processing helix  chain 'A' and resid 207 through 209
      No H-bonds generated for 'chain 'A' and resid 207 through 209'
    Processing helix  chain 'A' and resid 210 through 223
      removed outlier: 3.733A  pdb=" N   LEU A 214 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 255
      removed outlier: 5.196A  pdb=" N   VAL A 238 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      Proline residue:  A 239  - end of helix
      Proline residue:  A 248  - end of helix
    Processing helix  chain 'A' and resid 264 through 277
      removed outlier: 3.663A  pdb=" N   GLY A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 300
    Processing helix  chain 'A' and resid 305 through 309
    Processing helix  chain 'A' and resid 311 through 325
    Processing helix  chain 'A' and resid 328 through 334
    Processing helix  chain 'A' and resid 335 through 358
      removed outlier: 4.356A  pdb=" N   TRP A 339 " --> pdb=" O   GLU A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 372
    Processing helix  chain 'A' and resid 376 through 391
    Processing helix  chain 'A' and resid 392 through 395
    Processing helix  chain 'A' and resid 398 through 416
      removed outlier: 4.025A  pdb=" N   MET A 402 " --> pdb=" O   GLY A 398 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   LEU A 407 " --> pdb=" O   THR A 403 " (cutoff:3.500A)
      Proline residue:  A 408  - end of helix
    Processing helix  chain 'A' and resid 419 through 434
    Processing helix  chain 'A' and resid 442 through 449
    Processing helix  chain 'A' and resid 455 through 486
    Processing helix  chain 'B' and resid 8 through 11
    Processing helix  chain 'B' and resid 12 through 26
      removed outlier: 3.600A  pdb=" N   LEU B  16 " --> pdb=" O   PHE B  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 29
      No H-bonds generated for 'chain 'B' and resid 27 through 29'
    Processing helix  chain 'B' and resid 34 through 54
    Processing helix  chain 'B' and resid 57 through 72
    Processing helix  chain 'B' and resid 98 through 118
      removed outlier: 3.614A  pdb=" N   TRP B 102 " --> pdb=" O   ASN B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 132
    Processing helix  chain 'B' and resid 135 through 151
      removed outlier: 4.171A  pdb=" N   ALA B 151 " --> pdb=" O   LEU B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 163
    Processing helix  chain 'B' and resid 163 through 175
    Processing helix  chain 'B' and resid 181 through 185
      removed outlier: 3.596A  pdb=" N   LYS B 185 " --> pdb=" O   PRO B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 206
    Processing helix  chain 'B' and resid 207 through 209
      No H-bonds generated for 'chain 'B' and resid 207 through 209'
    Processing helix  chain 'B' and resid 210 through 223
      removed outlier: 3.732A  pdb=" N   LEU B 214 " --> pdb=" O   ALA B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 255
      removed outlier: 5.197A  pdb=" N   VAL B 238 " --> pdb=" O   TRP B 234 " (cutoff:3.500A)
      Proline residue:  B 239  - end of helix
      Proline residue:  B 248  - end of helix
    Processing helix  chain 'B' and resid 264 through 277
      removed outlier: 3.665A  pdb=" N   GLY B 277 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 300
    Processing helix  chain 'B' and resid 305 through 309
    Processing helix  chain 'B' and resid 311 through 325
    Processing helix  chain 'B' and resid 328 through 334
    Processing helix  chain 'B' and resid 335 through 358
      removed outlier: 4.355A  pdb=" N   TRP B 339 " --> pdb=" O   GLU B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 372
    Processing helix  chain 'B' and resid 376 through 391
    Processing helix  chain 'B' and resid 392 through 395
    Processing helix  chain 'B' and resid 398 through 416
      removed outlier: 4.025A  pdb=" N   MET B 402 " --> pdb=" O   GLY B 398 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   LEU B 407 " --> pdb=" O   THR B 403 " (cutoff:3.500A)
      Proline residue:  B 408  - end of helix
    Processing helix  chain 'B' and resid 419 through 434
    Processing helix  chain 'B' and resid 442 through 449
    Processing helix  chain 'B' and resid 455 through 486

    548 hydrogen bonds defined for protein.
    1614 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: 3.64

  Time building geometry restraints manager: 2.09 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 7808
        1.03 -     1.22: 4
        1.22 -     1.42: 3156
        1.42 -     1.61: 4544
        1.61 -     1.81: 96
  Bond restraints: 15608
  Sorted by residual:
  bond pdb=" C   SER B 177 "
       pdb=" N   LYS B 178 "
    ideal  model  delta    sigma   weight residual
    1.331  1.269  0.062 2.07e-02 2.33e+03 8.92e+00
  bond pdb=" C   SER A 177 "
       pdb=" N   LYS A 178 "
    ideal  model  delta    sigma   weight residual
    1.331  1.269  0.062 2.07e-02 2.33e+03 8.90e+00
  bond pdb=" C3  D10 A 503 "
       pdb=" C4  D10 A 503 "
    ideal  model  delta    sigma   weight residual
    1.523  1.484  0.039 2.00e-02 2.50e+03 3.78e+00
  bond pdb=" C6  D10 A 503 "
       pdb=" C7  D10 A 503 "
    ideal  model  delta    sigma   weight residual
    1.524  1.490  0.034 2.00e-02 2.50e+03 2.90e+00
  bond pdb=" C3  D10 B 503 "
       pdb=" C4  D10 B 503 "
    ideal  model  delta    sigma   weight residual
    1.523  1.489  0.034 2.00e-02 2.50e+03 2.86e+00
  ... (remaining 15603 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.51: 28193
        2.51 -     5.02: 123
        5.02 -     7.53: 8
        7.53 -    10.04: 8
       10.04 -    12.55: 2
  Bond angle restraints: 28334
  Sorted by residual:
  angle pdb=" C4  D10 A 503 "
        pdb=" C5  D10 A 503 "
        pdb=" C6  D10 A 503 "
      ideal   model   delta    sigma   weight residual
     113.31  100.76   12.55 3.00e+00 1.11e-01 1.75e+01
  angle pdb=" C4  D10 B 503 "
        pdb=" C5  D10 B 503 "
        pdb=" C6  D10 B 503 "
      ideal   model   delta    sigma   weight residual
     113.31  102.22   11.09 3.00e+00 1.11e-01 1.37e+01
  angle pdb=" N   GLY A 398 "
        pdb=" CA  GLY A 398 "
        pdb=" C   GLY A 398 "
      ideal   model   delta    sigma   weight residual
     114.67  109.62    5.05 1.41e+00 5.03e-01 1.28e+01
  angle pdb=" N   GLY B 398 "
        pdb=" CA  GLY B 398 "
        pdb=" C   GLY B 398 "
      ideal   model   delta    sigma   weight residual
     114.67  109.65    5.02 1.41e+00 5.03e-01 1.27e+01
  angle pdb=" C6  D10 A 503 "
        pdb=" C7  D10 A 503 "
        pdb=" C8  D10 A 503 "
      ideal   model   delta    sigma   weight residual
     113.25  103.67    9.58 3.00e+00 1.11e-01 1.02e+01
  ... (remaining 28329 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 6301
       17.43 -    34.86: 699
       34.86 -    52.29: 232
       52.29 -    69.72: 67
       69.72 -    87.15: 17
  Dihedral angle restraints: 7316
    sinusoidal: 3890
      harmonic: 3426
  Sorted by residual:
  dihedral pdb=" CA  LYS B  54 "
           pdb=" C   LYS B  54 "
           pdb=" N   PRO B  55 "
           pdb=" CA  PRO B  55 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.87   23.13     0      5.00e+00 4.00e-02 2.14e+01
  dihedral pdb=" CA  LYS A  54 "
           pdb=" C   LYS A  54 "
           pdb=" N   PRO A  55 "
           pdb=" CA  PRO A  55 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.03   22.97     0      5.00e+00 4.00e-02 2.11e+01
  dihedral pdb=" CA  PRO A  57 "
           pdb=" C   PRO A  57 "
           pdb=" N   ILE A  58 "
           pdb=" CA  ILE A  58 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.78  -20.22     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 7313 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 557
       0.027 -    0.053: 347
       0.053 -    0.080: 242
       0.080 -    0.106: 78
       0.106 -    0.133: 18
  Chirality restraints: 1242
  Sorted by residual:
  chirality pdb=" CA  ILE A 305 "
            pdb=" N   ILE A 305 "
            pdb=" C   ILE A 305 "
            pdb=" CB  ILE A 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.43e-01
  chirality pdb=" CA  ILE B 305 "
            pdb=" N   ILE B 305 "
            pdb=" C   ILE B 305 "
            pdb=" CB  ILE B 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.24e-01
  chirality pdb=" CA  ILE B 153 "
            pdb=" N   ILE B 153 "
            pdb=" C   ILE B 153 "
            pdb=" CB  ILE B 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.74e-01
  ... (remaining 1239 not shown)

  Planarity restraints: 2186
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 475 "   -0.009 2.00e-02 2.50e+03   1.78e-02 3.16e+00
        pdb=" C   GLY A 475 "    0.031 2.00e-02 2.50e+03
        pdb=" O   GLY A 475 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ILE A 476 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 475 "    0.009 2.00e-02 2.50e+03   1.72e-02 2.97e+00
        pdb=" C   GLY B 475 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   GLY B 475 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ILE B 476 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 342 "    0.007 2.00e-02 2.50e+03   1.45e-02 2.10e+00
        pdb=" C   LEU B 342 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   LEU B 342 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ILE B 343 "    0.008 2.00e-02 2.50e+03
  ... (remaining 2183 not shown)

  Histogram of nonbonded interaction distances:
        1.43 -     2.07: 234
        2.07 -     2.70: 25566
        2.70 -     3.33: 46384
        3.33 -     3.97: 57537
        3.97 -     4.60: 93580
  Nonbonded interactions: 223301
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 134 "
            pdb=" H   GLY A 137 "
     model   vdw
     1.431 2.450
  nonbonded pdb=" O   ARG B 134 "
            pdb=" H   GLY B 137 "
     model   vdw
     1.431 2.450
  nonbonded pdb=" O   LEU A 387 "
            pdb=" HG1 THR A 391 "
     model   vdw
     1.562 2.450
  nonbonded pdb=" O   GLY B 443 "
            pdb=" HG  SER B 446 "
     model   vdw
     1.585 2.450
  nonbonded pdb=" O   TRP A 234 "
            pdb=" HE1 TRP A 481 "
     model   vdw
     1.591 2.450
  ... (remaining 223296 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'
}

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:             5.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.090
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     17.450
  Find NCS groups from input model:        0.180
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
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      :  0.010   0.062   7796  Z= 0.395
  Angle     :  0.767  12.550  10602  Z= 0.411
  Chirality :  0.045   0.133   1242
  Planarity :  0.004   0.031   1254
  Dihedral  : 14.776  72.458   2692
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  7.80 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 14.56 %
    Favored  : 84.68 %
  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 are not related in a simple way.
  whole: -3.14 (0.23), residues: 974
  helix: -1.56 (0.16), residues: 754
  sheet:  None (None), residues: 0
  loop : -3.36 (0.33), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 159 
 TYR   0.011   0.001   TYR B 140 
 PHE   0.013   0.001   PHE B 360 
 TRP   0.017   0.001   TRP A 344 
 HIS   0.005   0.001   HIS B 439 

Details of bonding type rmsd
  covalent geometry    : bond        0.00970 ( 7796)
  covalent geometry    : angle       0.76672 (10602)
  hydrogen bonds       : bond        0.12771 (  548)
  hydrogen bonds       : angle       6.51599 ( 1614)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 115
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
REVERT: A  234 TRP cc_start: 0.6608 (t-100) cc_final: 0.6338 (t60)
REVERT: A  356 ILE cc_start: 0.8895 (tt) cc_final: 0.8679 (mt)
REVERT: A  369 GLN cc_start: 0.8509 (tt0) cc_final: 0.8143 (mt0)
REVERT: B  103 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8451 (tp)
REVERT: B  234 TRP cc_start: 0.6634 (t-100) cc_final: 0.6341 (t60)
REVERT: B  356 ILE cc_start: 0.8880 (tt) cc_final: 0.8667 (mt)
REVERT: B  369 GLN cc_start: 0.8511 (tt0) cc_final: 0.8163 (mt0)
  outliers start: 6
  outliers final: 4
  residues processed: 119
  average time/residue: 0.1664
  time to fit residues: 28.8696
Evaluate side-chains
  101 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  368 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 180 ASN
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 456 GLN
** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 180 ASN
B 226 GLN
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 456 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.142417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.130708 restraints weight = 30805.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 1.99
r_work: 0.3525 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3400 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7796  Z= 0.134
  Angle     :  0.559   4.935  10602  Z= 0.302
  Chirality :  0.040   0.149   1242
  Planarity :  0.005   0.044   1254
  Dihedral  :  5.974  57.867   1066
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.65 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 13.80 %
    Favored  : 84.43 %
  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 are not related in a simple way.
  whole: -0.98 (0.25), residues: 974
  helix: -0.05 (0.18), residues: 762
  sheet:  None (None), residues: 0
  loop : -2.57 (0.38), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 184 
 TYR   0.006   0.001   TYR A 255 
 PHE   0.012   0.001   PHE A 474 
 TRP   0.014   0.001   TRP A 344 
 HIS   0.005   0.001   HIS B 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 7796)
  covalent geometry    : angle       0.55897 (10602)
  hydrogen bonds       : bond        0.04415 (  548)
  hydrogen bonds       : angle       5.03987 ( 1614)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 ASN cc_start: 0.8215 (t0) cc_final: 0.7886 (t0)
REVERT: A  234 TRP cc_start: 0.7199 (t-100) cc_final: 0.6330 (t60)
REVERT: A  264 ASN cc_start: 0.7800 (t0) cc_final: 0.7490 (t0)
REVERT: A  331 ASP cc_start: 0.8483 (m-30) cc_final: 0.8033 (m-30)
REVERT: A  356 ILE cc_start: 0.8890 (tt) cc_final: 0.8649 (mt)
REVERT: B    8 ASN cc_start: 0.8189 (t0) cc_final: 0.7888 (t0)
REVERT: B  234 TRP cc_start: 0.7228 (t-100) cc_final: 0.6364 (t60)
REVERT: B  264 ASN cc_start: 0.7825 (t0) cc_final: 0.7537 (t0)
REVERT: B  331 ASP cc_start: 0.8416 (m-30) cc_final: 0.8021 (m-30)
REVERT: B  356 ILE cc_start: 0.8890 (tt) cc_final: 0.8668 (mt)
  outliers start: 14
  outliers final: 8
  residues processed: 138
  average time/residue: 0.1328
  time to fit residues: 28.6877
Evaluate side-chains
  115 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  328 SER
Chi-restraints excluded: chain B residue  368 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 463 ASN
** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 213 ASN
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 456 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.147547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.135474 restraints weight = 32840.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.10
r_work: 0.3412 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3290 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.2084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   7796  Z= 0.212
  Angle     :  0.583   5.076  10602  Z= 0.319
  Chirality :  0.041   0.140   1242
  Planarity :  0.005   0.047   1254
  Dihedral  :  5.809  47.441   1064
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.26 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 15.57 %
    Favored  : 82.78 %
  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 are not related in a simple way.
  whole: -0.26 (0.26), residues: 974
  helix:  0.48 (0.18), residues: 774
  sheet:  None (None), residues: 0
  loop : -2.55 (0.41), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 184 
 TYR   0.007   0.001   TYR B 140 
 PHE   0.013   0.001   PHE B 474 
 TRP   0.015   0.001   TRP A 344 
 HIS   0.005   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 7796)
  covalent geometry    : angle       0.58304 (10602)
  hydrogen bonds       : bond        0.04399 (  548)
  hydrogen bonds       : angle       4.98275 ( 1614)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: A  234 TRP cc_start: 0.7314 (t-100) cc_final: 0.6416 (t60)
REVERT: A  331 ASP cc_start: 0.8583 (m-30) cc_final: 0.8115 (m-30)
REVERT: B  234 TRP cc_start: 0.7308 (t-100) cc_final: 0.6433 (t60)
REVERT: B  331 ASP cc_start: 0.8498 (m-30) cc_final: 0.8103 (m-30)
REVERT: B  456 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7575 (mm-40)
  outliers start: 13
  outliers final: 10
  residues processed: 127
  average time/residue: 0.1289
  time to fit residues: 25.8462
Evaluate side-chains
  121 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  456 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 463 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.130111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.118298 restraints weight = 32880.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.06
r_work: 0.3359 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8649
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   7796  Z= 0.231
  Angle     :  0.600   5.018  10602  Z= 0.331
  Chirality :  0.042   0.154   1242
  Planarity :  0.005   0.049   1254
  Dihedral  :  5.736  46.228   1062
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.26 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.20 %
    Favored  : 81.65 %
  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 are not related in a simple way.
  whole:  0.20 (0.27), residues: 974
  helix:  0.80 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop : -2.37 (0.43), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 122 
 TYR   0.007   0.001   TYR A 390 
 PHE   0.012   0.001   PHE A 474 
 TRP   0.015   0.001   TRP A 344 
 HIS   0.011   0.002   HIS B 439 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 ( 7796)
  covalent geometry    : angle       0.60030 (10602)
  hydrogen bonds       : bond        0.04405 (  548)
  hydrogen bonds       : angle       4.95125 ( 1614)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 ASP cc_start: 0.8801 (t0) cc_final: 0.8400 (t0)
REVERT: A  234 TRP cc_start: 0.7360 (t-100) cc_final: 0.6831 (t60)
REVERT: A  331 ASP cc_start: 0.8613 (m-30) cc_final: 0.8126 (m-30)
REVERT: A  402 MET cc_start: 0.8367 (mmm) cc_final: 0.8104 (mmp)
REVERT: B  234 TRP cc_start: 0.7351 (t-100) cc_final: 0.6829 (t60)
REVERT: B  331 ASP cc_start: 0.8565 (m-30) cc_final: 0.8124 (m-30)
REVERT: B  402 MET cc_start: 0.8423 (mmm) cc_final: 0.8140 (mmp)
  outliers start: 17
  outliers final: 15
  residues processed: 130
  average time/residue: 0.1276
  time to fit residues: 26.3033
Evaluate side-chains
  120 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  375 ILE
Chi-restraints excluded: chain B residue  432 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 92 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 79 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.132770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.120926 restraints weight = 32568.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 2.07
r_work: 0.3389 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3271 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8616
moved from start:          0.2852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7796  Z= 0.135
  Angle     :  0.540   4.662  10602  Z= 0.291
  Chirality :  0.039   0.145   1242
  Planarity :  0.005   0.046   1254
  Dihedral  :  5.354  45.736   1062
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.85 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.46 %
    Favored  : 81.14 %
  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 are not related in a simple way.
  whole:  0.66 (0.27), residues: 974
  helix:  1.07 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop : -2.02 (0.45), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 184 
 TYR   0.006   0.001   TYR B 470 
 PHE   0.011   0.001   PHE B 474 
 TRP   0.013   0.001   TRP A 344 
 HIS   0.005   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 7796)
  covalent geometry    : angle       0.54030 (10602)
  hydrogen bonds       : bond        0.04052 (  548)
  hydrogen bonds       : angle       4.70663 ( 1614)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
REVERT: A  234 TRP cc_start: 0.7334 (t-100) cc_final: 0.6762 (t60)
REVERT: A  331 ASP cc_start: 0.8546 (m-30) cc_final: 0.8050 (m-30)
REVERT: B  234 TRP cc_start: 0.7328 (t-100) cc_final: 0.6766 (t60)
REVERT: B  331 ASP cc_start: 0.8504 (m-30) cc_final: 0.8057 (m-30)
  outliers start: 19
  outliers final: 15
  residues processed: 122
  average time/residue: 0.1291
  time to fit residues: 24.9826
Evaluate side-chains
  113 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  207 ILE
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  328 SER
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  456 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 72 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.144319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.132320 restraints weight = 32988.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 2.12
r_work: 0.3371 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3252 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8634
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7796  Z= 0.158
  Angle     :  0.548   4.690  10602  Z= 0.295
  Chirality :  0.040   0.175   1242
  Planarity :  0.005   0.044   1254
  Dihedral  :  5.287  45.267   1062
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.47 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 16.71 %
    Favored  : 81.27 %
  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 are not related in a simple way.
  whole:  0.90 (0.28), residues: 974
  helix:  1.22 (0.19), residues: 778
  sheet:  None (None), residues: 0
  loop : -1.84 (0.47), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 184 
 TYR   0.007   0.001   TYR B 470 
 PHE   0.011   0.001   PHE A 474 
 TRP   0.014   0.001   TRP A 344 
 HIS   0.011   0.002   HIS A 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7796)
  covalent geometry    : angle       0.54831 (10602)
  hydrogen bonds       : bond        0.03978 (  548)
  hydrogen bonds       : angle       4.61476 ( 1614)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 ASP cc_start: 0.8800 (t0) cc_final: 0.8389 (t0)
REVERT: A  234 TRP cc_start: 0.7350 (t-100) cc_final: 0.6753 (t60)
REVERT: A  331 ASP cc_start: 0.8530 (m-30) cc_final: 0.8023 (m-30)
REVERT: B  176 ASP cc_start: 0.8839 (t0) cc_final: 0.8435 (t0)
REVERT: B  234 TRP cc_start: 0.7325 (t-100) cc_final: 0.6729 (t60)
REVERT: B  331 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8043 (m-30)
  outliers start: 16
  outliers final: 15
  residues processed: 121
  average time/residue: 0.1308
  time to fit residues: 25.0463
Evaluate side-chains
  120 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  331 ASP
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  456 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 75 optimal weight:    8.9990
   chunk 91 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0370
   chunk 28 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   overall best weight:    0.6860

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

Flipped N/Q/H residues before XYZ refinement:
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.134161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.122432 restraints weight = 32185.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 2.07
r_work: 0.3399 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3287 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7796  Z= 0.110
  Angle     :  0.516   4.489  10602  Z= 0.273
  Chirality :  0.039   0.159   1242
  Planarity :  0.004   0.042   1254
  Dihedral  :  4.989  45.049   1062
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.34 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 17.22 %
    Favored  : 81.14 %
  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 are not related in a simple way.
  whole:  1.27 (0.28), residues: 974
  helix:  1.48 (0.19), residues: 774
  sheet:  None (None), residues: 0
  loop : -1.64 (0.47), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 184 
 TYR   0.006   0.001   TYR A 255 
 PHE   0.010   0.001   PHE B 474 
 TRP   0.012   0.001   TRP A 344 
 HIS   0.006   0.001   HIS B 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 7796)
  covalent geometry    : angle       0.51603 (10602)
  hydrogen bonds       : bond        0.03695 (  548)
  hydrogen bonds       : angle       4.44516 ( 1614)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 MET cc_start: 0.8718 (tpt) cc_final: 0.8512 (tpt)
REVERT: A  176 ASP cc_start: 0.8759 (t0) cc_final: 0.8344 (t0)
REVERT: A  234 TRP cc_start: 0.7248 (t-100) cc_final: 0.6633 (t60)
REVERT: A  331 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8028 (m-30)
REVERT: B  176 ASP cc_start: 0.8817 (t0) cc_final: 0.8418 (t0)
REVERT: B  234 TRP cc_start: 0.7244 (t-100) cc_final: 0.6638 (t60)
REVERT: B  331 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8031 (m-30)
  outliers start: 13
  outliers final: 11
  residues processed: 125
  average time/residue: 0.1257
  time to fit residues: 25.1306
Evaluate side-chains
  119 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  331 ASP
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  331 ASP
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  375 ILE
Chi-restraints excluded: chain B residue  432 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 74 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 92 optimal weight:    0.2980
   chunk 38 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 83 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 85 optimal weight:    4.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.132423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.120655 restraints weight = 33000.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 2.09
r_work: 0.3377 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.3370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7796  Z= 0.134
  Angle     :  0.527   4.592  10602  Z= 0.280
  Chirality :  0.039   0.167   1242
  Planarity :  0.005   0.042   1254
  Dihedral  :  5.000  45.157   1062
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.85 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 17.72 %
    Favored  : 80.38 %
  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 are not related in a simple way.
  whole:  1.31 (0.28), residues: 974
  helix:  1.50 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop : -1.61 (0.48), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 184 
 TYR   0.007   0.001   TYR A 390 
 PHE   0.018   0.001   PHE A 131 
 TRP   0.013   0.001   TRP A 344 
 HIS   0.007   0.001   HIS B 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7796)
  covalent geometry    : angle       0.52746 (10602)
  hydrogen bonds       : bond        0.03728 (  548)
  hydrogen bonds       : angle       4.47119 ( 1614)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 ASP cc_start: 0.8781 (t0) cc_final: 0.8361 (t0)
REVERT: A  234 TRP cc_start: 0.7272 (t-100) cc_final: 0.6654 (t60)
REVERT: A  331 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8030 (m-30)
REVERT: B  176 ASP cc_start: 0.8839 (t0) cc_final: 0.8432 (t0)
REVERT: B  234 TRP cc_start: 0.7250 (t-100) cc_final: 0.6621 (t60)
REVERT: B  331 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8067 (m-30)
  outliers start: 15
  outliers final: 12
  residues processed: 119
  average time/residue: 0.1278
  time to fit residues: 24.2377
Evaluate side-chains
  119 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  331 ASP
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  331 ASP
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  375 ILE
Chi-restraints excluded: chain B residue  432 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 91 optimal weight:    0.7980
   chunk 27 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.132771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.121006 restraints weight = 32749.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.08
r_work: 0.3382 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3270 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8585
moved from start:          0.3472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7796  Z= 0.126
  Angle     :  0.522   4.602  10602  Z= 0.277
  Chirality :  0.040   0.179   1242
  Planarity :  0.005   0.041   1254
  Dihedral  :  4.955  45.167   1062
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.95 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 17.85 %
    Favored  : 80.00 %
  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 are not related in a simple way.
  whole:  1.38 (0.28), residues: 974
  helix:  1.53 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop : -1.53 (0.48), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 184 
 TYR   0.006   0.001   TYR B 470 
 PHE   0.013   0.001   PHE A 131 
 TRP   0.013   0.001   TRP A 344 
 HIS   0.007   0.001   HIS B 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 7796)
  covalent geometry    : angle       0.52185 (10602)
  hydrogen bonds       : bond        0.03711 (  548)
  hydrogen bonds       : angle       4.43531 ( 1614)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  176 ASP cc_start: 0.8787 (t0) cc_final: 0.8368 (t0)
REVERT: A  234 TRP cc_start: 0.7272 (t-100) cc_final: 0.6633 (t60)
REVERT: A  331 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8019 (m-30)
REVERT: B  176 ASP cc_start: 0.8846 (t0) cc_final: 0.8445 (t0)
REVERT: B  234 TRP cc_start: 0.7282 (t-100) cc_final: 0.6628 (t60)
REVERT: B  331 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8043 (m-30)
  outliers start: 17
  outliers final: 15
  residues processed: 121
  average time/residue: 0.1313
  time to fit residues: 25.1876
Evaluate side-chains
  120 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  331 ASP
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  331 ASP
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  375 ILE
Chi-restraints excluded: chain B residue  432 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.144290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.132124 restraints weight = 33112.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 2.12
r_work: 0.3354 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7796  Z= 0.181
  Angle     :  0.563   4.772  10602  Z= 0.303
  Chirality :  0.041   0.185   1242
  Planarity :  0.005   0.041   1254
  Dihedral  :  5.202  49.343   1062
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.57 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.48 %
    Favored  : 79.49 %
  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 are not related in a simple way.
  whole:  1.25 (0.28), residues: 974
  helix:  1.47 (0.19), residues: 776
  sheet:  None (None), residues: 0
  loop : -1.71 (0.47), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 159 
 TYR   0.008   0.001   TYR A 390 
 PHE   0.010   0.001   PHE A 131 
 TRP   0.015   0.001   TRP A 344 
 HIS   0.013   0.002   HIS B 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 7796)
  covalent geometry    : angle       0.56282 (10602)
  hydrogen bonds       : bond        0.03940 (  548)
  hydrogen bonds       : angle       4.54374 ( 1614)

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 ASP cc_start: 0.8802 (t0) cc_final: 0.8391 (t0)
REVERT: A  234 TRP cc_start: 0.7324 (t-100) cc_final: 0.6629 (t60)
REVERT: A  331 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8045 (m-30)
REVERT: A  364 PHE cc_start: 0.8491 (t80) cc_final: 0.7916 (t80)
REVERT: B  176 ASP cc_start: 0.8881 (t0) cc_final: 0.8480 (t0)
REVERT: B  234 TRP cc_start: 0.7306 (t-100) cc_final: 0.6614 (t60)
REVERT: B  331 ASP cc_start: 0.8572 (m-30) cc_final: 0.8058 (m-30)
REVERT: B  364 PHE cc_start: 0.8501 (t80) cc_final: 0.7970 (t80)
  outliers start: 16
  outliers final: 15
  residues processed: 121
  average time/residue: 0.1325
  time to fit residues: 25.3949
Evaluate side-chains
  121 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   34 SER
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  291 CYS
Chi-restraints excluded: chain A residue  331 ASP
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  432 VAL
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   34 SER
Chi-restraints excluded: chain B residue  262 THR
Chi-restraints excluded: chain B residue  291 CYS
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  375 ILE
Chi-restraints excluded: chain B residue  432 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 89 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 72 optimal weight:    0.5980
   chunk 95 optimal weight:    2.9990
   chunk 80 optimal weight:    0.3980
   chunk 42 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 66 optimal weight:    0.4980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.134117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.122244 restraints weight = 32363.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 2.08
r_work: 0.3403 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.3659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7796  Z= 0.113
  Angle     :  0.522   4.969  10602  Z= 0.275
  Chirality :  0.039   0.149   1242
  Planarity :  0.004   0.041   1254
  Dihedral  :  5.034  50.272   1062
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  5.24 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 18.99 %
    Favored  : 79.37 %
  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 are not related in a simple way.
  whole:  1.40 (0.28), residues: 974
  helix:  1.54 (0.19), residues: 778
  sheet:  None (None), residues: 0
  loop : -1.52 (0.48), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 184 
 TYR   0.006   0.001   TYR A 255 
 PHE   0.011   0.001   PHE A 131 
 TRP   0.013   0.001   TRP A 344 
 HIS   0.015   0.002   HIS B 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 7796)
  covalent geometry    : angle       0.52220 (10602)
  hydrogen bonds       : bond        0.03692 (  548)
  hydrogen bonds       : angle       4.41555 ( 1614)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3666.24 seconds
wall clock time: 62 minutes 54.35 seconds (3774.35 seconds total)