Starting phenix.real_space_refine
on Sat Jun 21 00:56:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jma_36411/06_2025/8jma_36411_neut_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jma_36411/06_2025/8jma_36411.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jma_36411/06_2025/8jma_36411.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jma_36411/06_2025/8jma_36411.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jma_36411/06_2025/8jma_36411_neut_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jma_36411/06_2025/8jma_36411_neut_trim.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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      72      5.16       5
     C    7848      2.51       5
     N    2056      2.21       5
     O    2120      1.98       5
     H   12472      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 24568
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 6130
          Classifications: {'peptide': 381}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 374}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 12
          Unusual residues: {'FRU': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 14.99, per 1000 atoms: 0.61
  Number of scatterers: 24568
  At special positions: 0
  Unit cell: (110.67, 110.67, 105.09, 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      72     16.00
     O    2120      8.00
     N    2056      7.00
     C    7848      6.00
     H   12472      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: 6.47
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2904

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 8 sheets defined
      85.0% alpha, 2.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 17
    Processing helix  chain 'A' and resid 37 through 65
    Processing helix  chain 'A' and resid 73 through 100
      removed outlier: 3.550A  pdb=" N   VAL A  87 " --> pdb=" O   ASP A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 119
    Processing helix  chain 'A' and resid 120 through 123
    Processing helix  chain 'A' and resid 124 through 161
    Processing helix  chain 'A' and resid 168 through 174
      removed outlier: 3.509A  pdb=" N   VAL A 172 " --> pdb=" O   THR A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 215
    Processing helix  chain 'A' and resid 263 through 321
      removed outlier: 6.068A  pdb=" N   ILE A 294 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
      removed outlier: 5.756A  pdb=" N   ALA A 295 " --> pdb=" O   SER A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 357
      Proline residue:  A 347  - end of helix
    Processing helix  chain 'A' and resid 357 through 368
      removed outlier: 3.764A  pdb=" N   ILE A 361 " --> pdb=" O   LYS A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 387
      removed outlier: 3.945A  pdb=" N   VAL A 387 " --> pdb=" O   GLN A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 425
      removed outlier: 3.708A  pdb=" N   THR A 406 " --> pdb=" O   ARG A 402 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 17
    Processing helix  chain 'B' and resid 37 through 65
    Processing helix  chain 'B' and resid 73 through 100
      removed outlier: 3.550A  pdb=" N   VAL B  87 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 119
    Processing helix  chain 'B' and resid 120 through 123
    Processing helix  chain 'B' and resid 124 through 161
    Processing helix  chain 'B' and resid 168 through 174
      removed outlier: 3.509A  pdb=" N   VAL B 172 " --> pdb=" O   THR B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 215
    Processing helix  chain 'B' and resid 263 through 321
      removed outlier: 6.068A  pdb=" N   ILE B 294 " --> pdb=" O   ASN B 290 " (cutoff:3.500A)
      removed outlier: 5.757A  pdb=" N   ALA B 295 " --> pdb=" O   SER B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 323 through 357
      Proline residue:  B 347  - end of helix
    Processing helix  chain 'B' and resid 357 through 368
      removed outlier: 3.764A  pdb=" N   ILE B 361 " --> pdb=" O   LYS B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 387
      removed outlier: 3.945A  pdb=" N   VAL B 387 " --> pdb=" O   GLN B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 425
      removed outlier: 3.710A  pdb=" N   THR B 406 " --> pdb=" O   ARG B 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 7 through 17
    Processing helix  chain 'C' and resid 37 through 65
    Processing helix  chain 'C' and resid 73 through 100
      removed outlier: 3.550A  pdb=" N   VAL C  87 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 119
    Processing helix  chain 'C' and resid 120 through 123
    Processing helix  chain 'C' and resid 124 through 161
    Processing helix  chain 'C' and resid 168 through 174
      removed outlier: 3.509A  pdb=" N   VAL C 172 " --> pdb=" O   THR C 168 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 175 through 215
    Processing helix  chain 'C' and resid 263 through 321
      removed outlier: 6.068A  pdb=" N   ILE C 294 " --> pdb=" O   ASN C 290 " (cutoff:3.500A)
      removed outlier: 5.756A  pdb=" N   ALA C 295 " --> pdb=" O   SER C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 323 through 357
      Proline residue:  C 347  - end of helix
    Processing helix  chain 'C' and resid 357 through 368
      removed outlier: 3.763A  pdb=" N   ILE C 361 " --> pdb=" O   LYS C 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 371 through 387
      removed outlier: 3.945A  pdb=" N   VAL C 387 " --> pdb=" O   GLN C 383 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 402 through 425
      removed outlier: 3.708A  pdb=" N   THR C 406 " --> pdb=" O   ARG C 402 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 17
    Processing helix  chain 'D' and resid 37 through 65
    Processing helix  chain 'D' and resid 73 through 100
      removed outlier: 3.550A  pdb=" N   VAL D  87 " --> pdb=" O   ASP D  83 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 119
    Processing helix  chain 'D' and resid 120 through 123
    Processing helix  chain 'D' and resid 124 through 161
    Processing helix  chain 'D' and resid 168 through 174
      removed outlier: 3.509A  pdb=" N   VAL D 172 " --> pdb=" O   THR D 168 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 175 through 215
    Processing helix  chain 'D' and resid 263 through 321
      removed outlier: 6.068A  pdb=" N   ILE D 294 " --> pdb=" O   ASN D 290 " (cutoff:3.500A)
      removed outlier: 5.756A  pdb=" N   ALA D 295 " --> pdb=" O   SER D 291 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 323 through 357
      Proline residue:  D 347  - end of helix
    Processing helix  chain 'D' and resid 357 through 368
      removed outlier: 3.764A  pdb=" N   ILE D 361 " --> pdb=" O   LYS D 357 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 371 through 387
      removed outlier: 3.945A  pdb=" N   VAL D 387 " --> pdb=" O   GLN D 383 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 402 through 425
      removed outlier: 3.708A  pdb=" N   THR D 406 " --> pdb=" O   ARG D 402 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 26
    Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 393
      removed outlier: 4.635A  pdb=" N   PHE A 392 " --> pdb=" O   VAL A 400 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 26
    Processing sheet with id=AA4, first strand: chain 'B' and resid 392 through 393
      removed outlier: 4.635A  pdb=" N   PHE B 392 " --> pdb=" O   VAL B 400 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26
    Processing sheet with id=AA6, first strand: chain 'C' and resid 392 through 393
      removed outlier: 4.635A  pdb=" N   PHE C 392 " --> pdb=" O   VAL C 400 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 26
    Processing sheet with id=AA8, first strand: chain 'D' and resid 392 through 393
      removed outlier: 4.635A  pdb=" N   PHE D 392 " --> pdb=" O   VAL D 400 " (cutoff:3.500A)

    1072 hydrogen bonds defined for protein.
    3204 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: 9.30

  Time building geometry restraints manager: 7.83 seconds

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

  Histogram of bond lengths:
        0.82 -     1.02: 12440
        1.02 -     1.21: 32
        1.21 -     1.41: 5022
        1.41 -     1.61: 7194
        1.61 -     1.81: 112
  Bond restraints: 24800
  Sorted by residual:
  bond pdb=" C2  FRU C 501 "
       pdb=" O5  FRU C 501 "
    ideal  model  delta    sigma   weight residual
    1.412  1.483 -0.071 2.00e-02 2.50e+03 1.27e+01
  bond pdb=" C2  FRU B 501 "
       pdb=" O5  FRU B 501 "
    ideal  model  delta    sigma   weight residual
    1.412  1.483 -0.071 2.00e-02 2.50e+03 1.27e+01
  bond pdb=" C2  FRU D 501 "
       pdb=" O5  FRU D 501 "
    ideal  model  delta    sigma   weight residual
    1.412  1.483 -0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" C2  FRU A 501 "
       pdb=" O5  FRU A 501 "
    ideal  model  delta    sigma   weight residual
    1.412  1.483 -0.071 2.00e-02 2.50e+03 1.25e+01
  bond pdb=" C5  FRU B 501 "
       pdb=" O5  FRU B 501 "
    ideal  model  delta    sigma   weight residual
    1.420  1.486 -0.066 2.00e-02 2.50e+03 1.08e+01
  ... (remaining 24795 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.16: 42733
        1.16 -     2.33: 1910
        2.33 -     3.49: 106
        3.49 -     4.65: 31
        4.65 -     5.81: 12
  Bond angle restraints: 44792
  Sorted by residual:
  angle pdb=" C   ILE A 418 "
        pdb=" CA  ILE A 418 "
        pdb=" CB  ILE A 418 "
      ideal   model   delta    sigma   weight residual
     112.02  107.82    4.20 1.31e+00 5.83e-01 1.03e+01
  angle pdb=" C   ILE D 418 "
        pdb=" CA  ILE D 418 "
        pdb=" CB  ILE D 418 "
      ideal   model   delta    sigma   weight residual
     112.02  107.85    4.17 1.31e+00 5.83e-01 1.01e+01
  angle pdb=" C   ILE C 418 "
        pdb=" CA  ILE C 418 "
        pdb=" CB  ILE C 418 "
      ideal   model   delta    sigma   weight residual
     112.02  107.87    4.15 1.31e+00 5.83e-01 1.00e+01
  angle pdb=" C   ILE B 418 "
        pdb=" CA  ILE B 418 "
        pdb=" CB  ILE B 418 "
      ideal   model   delta    sigma   weight residual
     112.02  107.91    4.11 1.31e+00 5.83e-01 9.86e+00
  angle pdb=" C   VAL A 417 "
        pdb=" CA  VAL A 417 "
        pdb=" CB  VAL A 417 "
      ideal   model   delta    sigma   weight residual
     112.14  108.36    3.78 1.35e+00 5.49e-01 7.85e+00
  ... (remaining 44787 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.25: 10306
       17.25 -    34.50: 910
       34.50 -    51.75: 220
       51.75 -    69.00: 160
       69.00 -    86.25: 8
  Dihedral angle restraints: 11604
    sinusoidal: 6272
      harmonic: 5332
  Sorted by residual:
  dihedral pdb=" CB  GLU B  66 "
           pdb=" CG  GLU B  66 "
           pdb=" CD  GLU B  66 "
           pdb=" OE1 GLU B  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.25  -86.25     1      3.00e+01 1.11e-03 9.97e+00
  dihedral pdb=" CB  GLU A  66 "
           pdb=" CG  GLU A  66 "
           pdb=" CD  GLU A  66 "
           pdb=" OE1 GLU A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.20  -86.20     1      3.00e+01 1.11e-03 9.96e+00
  dihedral pdb=" CB  GLU D  66 "
           pdb=" CG  GLU D  66 "
           pdb=" CD  GLU D  66 "
           pdb=" OE1 GLU D  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.20  -86.20     1      3.00e+01 1.11e-03 9.96e+00
  ... (remaining 11601 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 1212
       0.025 -    0.050: 474
       0.050 -    0.075: 252
       0.075 -    0.100: 50
       0.100 -    0.125: 24
  Chirality restraints: 2012
  Sorted by residual:
  chirality pdb=" CA  ILE A   3 "
            pdb=" N   ILE A   3 "
            pdb=" C   ILE A   3 "
            pdb=" CB  ILE A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.92e-01
  chirality pdb=" CA  ILE B   3 "
            pdb=" N   ILE B   3 "
            pdb=" C   ILE B   3 "
            pdb=" CB  ILE B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.87e-01
  chirality pdb=" CA  ILE D   3 "
            pdb=" N   ILE D   3 "
            pdb=" C   ILE D   3 "
            pdb=" CB  ILE D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.84e-01
  ... (remaining 2009 not shown)

  Planarity restraints: 3532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 413 "    0.011 2.00e-02 2.50e+03   2.24e-02 5.01e+00
        pdb=" C   ALA A 413 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ALA A 413 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR A 414 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D 413 "    0.011 2.00e-02 2.50e+03   2.24e-02 5.01e+00
        pdb=" C   ALA D 413 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ALA D 413 "    0.015 2.00e-02 2.50e+03
        pdb=" N   THR D 414 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 413 "   -0.011 2.00e-02 2.50e+03   2.24e-02 5.01e+00
        pdb=" C   ALA B 413 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ALA B 413 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   THR B 414 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 3529 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 1675
        2.21 -     2.80: 52319
        2.80 -     3.40: 73625
        3.40 -     4.00: 94551
        4.00 -     4.60: 147383
  Nonbonded interactions: 369553
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 401 "
            pdb=" HG1 THR A 403 "
     model   vdw
     1.607 2.450
  nonbonded pdb=" OD1 ASN D 401 "
            pdb=" HG1 THR D 403 "
     model   vdw
     1.608 2.450
  nonbonded pdb=" OD1 ASN B 401 "
            pdb=" HG1 THR B 403 "
     model   vdw
     1.608 2.450
  nonbonded pdb=" OD1 ASN C 401 "
            pdb=" HG1 THR C 403 "
     model   vdw
     1.608 2.450
  nonbonded pdb=" H   ASN C  27 "
            pdb=" O   ARG C  31 "
     model   vdw
     1.615 2.450
  ... (remaining 369548 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: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

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:             0.780
  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:             0.410
  Extract box with map and model:          0.940
  Check model and map are aligned:         0.180
  Set scattering table:                    0.230
  Process input model:                     56.130
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   70.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
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      :  0.004   0.071  12328  Z= 0.219
  Angle     :  0.512   5.813  16728  Z= 0.282
  Chirality :  0.035   0.125   2012
  Planarity :  0.004   0.022   2040
  Dihedral  : 16.386  86.254   4472
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 17.93 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.05 (0.21), residues: 1508
  helix:  2.43 (0.14), residues: 1264
  sheet:  1.30 (0.74), residues: 48
  loop : -0.65 (0.46), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 328 
 HIS   0.003   0.001   HIS C 337 
 PHE   0.011   0.001   PHE A 298 
 TYR   0.007   0.001   TYR A 415 
 ARG   0.004   0.000   ARG B 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09802 ( 1072)
  hydrogen bonds       : angle       4.78280 ( 3204)
  covalent geometry    : bond        0.00443 (12328)
  covalent geometry    : angle       0.51192 (16728)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 160
  time to evaluate  : 1.975 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.7560 (mp0) cc_final: 0.7336 (mp0)
REVERT: B   33 GLU cc_start: 0.7560 (mp0) cc_final: 0.7335 (mp0)
REVERT: C   33 GLU cc_start: 0.7562 (mp0) cc_final: 0.7333 (mp0)
REVERT: D   33 GLU cc_start: 0.7559 (mp0) cc_final: 0.7334 (mp0)
  outliers start: 8
  outliers final: 8
  residues processed: 168
  average time/residue: 2.5879
  time to fit residues: 475.9970
Evaluate side-chains
  168 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 160
  time to evaluate  : 2.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  410 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  410 SER
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  410 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 128 optimal weight:    0.7980
   chunk 115 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 77 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 119 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 88 optimal weight:   10.0000
   chunk 138 optimal weight:    3.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 383 GLN
A 423 GLN
B 383 GLN
B 423 GLN
C 383 GLN
C 423 GLN
D 383 GLN
D 423 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.138184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.098918 restraints weight = 35755.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 1.68
r_work: 0.2892 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2759 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.0486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12328  Z= 0.172
  Angle     :  0.465   4.022  16728  Z= 0.258
  Chirality :  0.035   0.132   2012
  Planarity :  0.003   0.030   2040
  Dihedral  :  4.328  25.693   1764
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 2.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.72 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.46 (0.21), residues: 1508
  helix:  2.73 (0.13), residues: 1264
  sheet:  0.81 (0.79), residues: 48
  loop : -0.46 (0.49), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 154 
 HIS   0.003   0.001   HIS B 337 
 PHE   0.010   0.001   PHE A 298 
 TYR   0.011   0.001   TYR D 415 
 ARG   0.002   0.000   ARG C 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04599 ( 1072)
  hydrogen bonds       : angle       4.14962 ( 3204)
  covalent geometry    : bond        0.00355 (12328)
  covalent geometry    : angle       0.46494 (16728)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 180
  time to evaluate  : 1.714 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7863 (mp0) cc_final: 0.7592 (mp0)
REVERT: A  420 ILE cc_start: 0.8759 (mm) cc_final: 0.8505 (mt)
REVERT: B   33 GLU cc_start: 0.7853 (mp0) cc_final: 0.7581 (mp0)
REVERT: B  420 ILE cc_start: 0.8751 (mm) cc_final: 0.8494 (mt)
REVERT: C   33 GLU cc_start: 0.7858 (mp0) cc_final: 0.7586 (mp0)
REVERT: C  420 ILE cc_start: 0.8752 (mm) cc_final: 0.8492 (mt)
REVERT: D   33 GLU cc_start: 0.7844 (mp0) cc_final: 0.7576 (mp0)
REVERT: D  420 ILE cc_start: 0.8754 (mm) cc_final: 0.8498 (mt)
  outliers start: 20
  outliers final: 12
  residues processed: 192
  average time/residue: 2.7737
  time to fit residues: 579.1584
Evaluate side-chains
  184 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 172
  time to evaluate  : 1.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain C residue  404 ILE
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  182 TYR
Chi-restraints excluded: chain D residue  404 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 118 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 122 optimal weight:    3.9990
   chunk 116 optimal weight:    0.9990
   chunk 151 optimal weight:    3.9990
   chunk 117 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 101 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   overall best weight:    1.7788

-------------------------------------------------------------------------------
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 = 0.3618 r_free = 0.3618 target = 0.140272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.101332 restraints weight = 35309.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 1.67
r_work: 0.2897 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.0687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12328  Z= 0.159
  Angle     :  0.452   3.918  16728  Z= 0.248
  Chirality :  0.035   0.130   2012
  Planarity :  0.003   0.030   2040
  Dihedral  :  4.028  22.860   1760
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 1.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.72 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.55 (0.21), residues: 1508
  helix:  2.81 (0.14), residues: 1264
  sheet:  0.57 (0.79), residues: 48
  loop : -0.52 (0.49), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 328 
 HIS   0.004   0.001   HIS B 337 
 PHE   0.013   0.002   PHE C 125 
 TYR   0.008   0.001   TYR D 182 
 ARG   0.002   0.000   ARG A 340 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04390 ( 1072)
  hydrogen bonds       : angle       4.09517 ( 3204)
  covalent geometry    : bond        0.00325 (12328)
  covalent geometry    : angle       0.45249 (16728)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 160
  time to evaluate  : 1.980 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.7869 (mp0) cc_final: 0.7547 (mp0)
REVERT: A  354 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8304 (mm-30)
REVERT: A  420 ILE cc_start: 0.8774 (mm) cc_final: 0.8548 (mt)
REVERT: B   33 GLU cc_start: 0.7857 (mp0) cc_final: 0.7535 (mp0)
REVERT: B  354 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8304 (mm-30)
REVERT: B  420 ILE cc_start: 0.8777 (mm) cc_final: 0.8550 (mt)
REVERT: C   33 GLU cc_start: 0.7858 (mp0) cc_final: 0.7535 (mp0)
REVERT: C  354 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8302 (mm-30)
REVERT: C  420 ILE cc_start: 0.8773 (mm) cc_final: 0.8544 (mt)
REVERT: D   33 GLU cc_start: 0.7848 (mp0) cc_final: 0.7526 (mp0)
REVERT: D  354 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8310 (mm-30)
REVERT: D  420 ILE cc_start: 0.8771 (mm) cc_final: 0.8545 (mt)
  outliers start: 24
  outliers final: 12
  residues processed: 184
  average time/residue: 2.4969
  time to fit residues: 505.7666
Evaluate side-chains
  174 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 162
  time to evaluate  : 1.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  182 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   chunk 148 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
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 = 0.3578 r_free = 0.3578 target = 0.137414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.097537 restraints weight = 35896.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 1.71
r_work: 0.2881 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2746 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.0718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12328  Z= 0.191
  Angle     :  0.472   4.385  16728  Z= 0.260
  Chirality :  0.036   0.129   2012
  Planarity :  0.004   0.039   2040
  Dihedral  :  4.135  24.008   1760
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.93 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.38 (0.21), residues: 1508
  helix:  2.70 (0.14), residues: 1264
  sheet:  0.54 (0.80), residues: 48
  loop : -0.60 (0.49), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 328 
 HIS   0.004   0.001   HIS D 337 
 PHE   0.012   0.002   PHE A 298 
 TYR   0.008   0.001   TYR A 182 
 ARG   0.004   0.000   ARG A 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04531 ( 1072)
  hydrogen bonds       : angle       4.14355 ( 3204)
  covalent geometry    : bond        0.00407 (12328)
  covalent geometry    : angle       0.47239 (16728)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 176
  time to evaluate  : 1.931 
Fit side-chains
REVERT: A   33 GLU cc_start: 0.7811 (mp0) cc_final: 0.7474 (mp0)
REVERT: A  354 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8319 (mm-30)
REVERT: A  420 ILE cc_start: 0.8781 (mm) cc_final: 0.8564 (mt)
REVERT: A  423 GLN cc_start: 0.5954 (mm110) cc_final: 0.4956 (pt0)
REVERT: B   33 GLU cc_start: 0.7802 (mp0) cc_final: 0.7459 (mp0)
REVERT: B  354 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8329 (mm-30)
REVERT: B  420 ILE cc_start: 0.8775 (mm) cc_final: 0.8545 (mt)
REVERT: B  423 GLN cc_start: 0.5935 (mm110) cc_final: 0.4945 (pt0)
REVERT: C   33 GLU cc_start: 0.7797 (mp0) cc_final: 0.7457 (mp0)
REVERT: C  354 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8324 (mm-30)
REVERT: C  420 ILE cc_start: 0.8768 (mm) cc_final: 0.8537 (mt)
REVERT: C  423 GLN cc_start: 0.5938 (mm110) cc_final: 0.4940 (pt0)
REVERT: D   33 GLU cc_start: 0.7795 (mp0) cc_final: 0.7456 (mp0)
REVERT: D  354 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8332 (mm-30)
REVERT: D  420 ILE cc_start: 0.8768 (mm) cc_final: 0.8538 (mt)
REVERT: D  423 GLN cc_start: 0.5940 (mm110) cc_final: 0.4935 (pt0)
  outliers start: 24
  outliers final: 8
  residues processed: 192
  average time/residue: 2.6789
  time to fit residues: 561.0729
Evaluate side-chains
  182 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 174
  time to evaluate  : 1.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue  182 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 118 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9990
   chunk 116 optimal weight:    6.9990
   chunk 84 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 113 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9990
   overall best weight:    1.3988

-------------------------------------------------------------------------------
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 = 0.3585 r_free = 0.3585 target = 0.138297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.098814 restraints weight = 35985.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 1.70
r_work: 0.2905 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2770 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.0831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12328  Z= 0.139
  Angle     :  0.442   4.032  16728  Z= 0.242
  Chirality :  0.034   0.130   2012
  Planarity :  0.003   0.031   2040
  Dihedral  :  3.801  19.785   1756
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 17.93 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.59 (0.21), residues: 1508
  helix:  2.84 (0.14), residues: 1264
  sheet:  0.49 (0.81), residues: 48
  loop : -0.50 (0.50), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 328 
 HIS   0.004   0.001   HIS A 337 
 PHE   0.010   0.001   PHE A  11 
 TYR   0.006   0.001   TYR C 182 
 ARG   0.004   0.000   ARG B 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04183 ( 1072)
  hydrogen bonds       : angle       4.04518 ( 3204)
  covalent geometry    : bond        0.00278 (12328)
  covalent geometry    : angle       0.44241 (16728)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 1.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 ASN cc_start: 0.7372 (OUTLIER) cc_final: 0.7156 (t160)
REVERT: A  354 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8177 (mm-30)
REVERT: A  420 ILE cc_start: 0.8790 (mm) cc_final: 0.8571 (mt)
REVERT: A  423 GLN cc_start: 0.5944 (mm110) cc_final: 0.4930 (pt0)
REVERT: B  120 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.7155 (t160)
REVERT: B  354 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8186 (mm-30)
REVERT: B  420 ILE cc_start: 0.8798 (mm) cc_final: 0.8559 (mt)
REVERT: B  423 GLN cc_start: 0.5923 (mm110) cc_final: 0.4919 (pt0)
REVERT: C  120 ASN cc_start: 0.7369 (OUTLIER) cc_final: 0.7153 (t160)
REVERT: C  354 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8187 (mm-30)
REVERT: C  420 ILE cc_start: 0.8792 (mm) cc_final: 0.8554 (mt)
REVERT: C  423 GLN cc_start: 0.5931 (mm110) cc_final: 0.4916 (pt0)
REVERT: D  120 ASN cc_start: 0.7375 (OUTLIER) cc_final: 0.7161 (t160)
REVERT: D  354 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8192 (mm-30)
REVERT: D  420 ILE cc_start: 0.8800 (mm) cc_final: 0.8564 (mt)
REVERT: D  423 GLN cc_start: 0.5938 (mm110) cc_final: 0.4921 (pt0)
  outliers start: 26
  outliers final: 12
  residues processed: 190
  average time/residue: 2.7518
  time to fit residues: 568.1211
Evaluate side-chains
  184 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 168
  time to evaluate  : 1.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  120 ASN
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  120 ASN
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  120 ASN
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  120 ASN
Chi-restraints excluded: chain D residue  182 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 81 optimal weight:    5.9990
   chunk 104 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   chunk 94 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
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 = 0.3578 r_free = 0.3578 target = 0.137591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.098182 restraints weight = 35774.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 1.69
r_work: 0.2895 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2760 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.0815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12328  Z= 0.170
  Angle     :  0.459   4.126  16728  Z= 0.251
  Chirality :  0.035   0.129   2012
  Planarity :  0.004   0.036   2040
  Dihedral  :  3.839  20.310   1756
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 1.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 17.93 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.46 (0.21), residues: 1508
  helix:  2.75 (0.14), residues: 1264
  sheet:  0.45 (0.80), residues: 48
  loop : -0.53 (0.50), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 328 
 HIS   0.004   0.001   HIS A 337 
 PHE   0.019   0.002   PHE C 125 
 TYR   0.008   0.001   TYR C 182 
 ARG   0.004   0.000   ARG A 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04356 ( 1072)
  hydrogen bonds       : angle       4.09127 ( 3204)
  covalent geometry    : bond        0.00356 (12328)
  covalent geometry    : angle       0.45903 (16728)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 172
  time to evaluate  : 1.782 
Fit side-chains
REVERT: A  354 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8182 (mm-30)
REVERT: A  420 ILE cc_start: 0.8797 (mm) cc_final: 0.8576 (mt)
REVERT: A  423 GLN cc_start: 0.5993 (mm110) cc_final: 0.4936 (pt0)
REVERT: B  354 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8192 (mm-30)
REVERT: B  420 ILE cc_start: 0.8799 (mm) cc_final: 0.8564 (mt)
REVERT: B  423 GLN cc_start: 0.5971 (mm110) cc_final: 0.4915 (pt0)
REVERT: C  354 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8193 (mm-30)
REVERT: C  420 ILE cc_start: 0.8792 (mm) cc_final: 0.8547 (mt)
REVERT: C  423 GLN cc_start: 0.5980 (mm110) cc_final: 0.4909 (pt0)
REVERT: D  354 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8195 (mm-30)
REVERT: D  420 ILE cc_start: 0.8794 (mm) cc_final: 0.8553 (mt)
REVERT: D  423 GLN cc_start: 0.5986 (mm110) cc_final: 0.4914 (pt0)
  outliers start: 22
  outliers final: 12
  residues processed: 190
  average time/residue: 2.7866
  time to fit residues: 576.0213
Evaluate side-chains
  184 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 172
  time to evaluate  : 1.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  182 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 107 optimal weight:    3.9990
   chunk 134 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 148 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 128 optimal weight:    0.5980
   overall best weight:    2.5186

-------------------------------------------------------------------------------
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 = 0.3572 r_free = 0.3572 target = 0.137083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.097644 restraints weight = 35819.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 1.69
r_work: 0.2887 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.0788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12328  Z= 0.198
  Angle     :  0.482   4.534  16728  Z= 0.264
  Chirality :  0.036   0.128   2012
  Planarity :  0.004   0.040   2040
  Dihedral  :  3.984  23.176   1756
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.93 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.30 (0.21), residues: 1508
  helix:  2.64 (0.14), residues: 1264
  sheet:  0.44 (0.79), residues: 48
  loop : -0.60 (0.50), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 328 
 HIS   0.004   0.001   HIS A 337 
 PHE   0.012   0.002   PHE A 298 
 TYR   0.009   0.001   TYR B 182 
 ARG   0.004   0.000   ARG B 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04516 ( 1072)
  hydrogen bonds       : angle       4.15275 ( 3204)
  covalent geometry    : bond        0.00423 (12328)
  covalent geometry    : angle       0.48249 (16728)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 185
  time to evaluate  : 1.748 
Fit side-chains
REVERT: A  354 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8318 (mm-30)
REVERT: A  420 ILE cc_start: 0.8791 (mm) cc_final: 0.8564 (mt)
REVERT: A  423 GLN cc_start: 0.5957 (mm110) cc_final: 0.4906 (pt0)
REVERT: B  354 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8325 (mm-30)
REVERT: B  420 ILE cc_start: 0.8796 (mm) cc_final: 0.8556 (mt)
REVERT: B  423 GLN cc_start: 0.5935 (mm110) cc_final: 0.4889 (pt0)
REVERT: C  354 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8327 (mm-30)
REVERT: C  420 ILE cc_start: 0.8790 (mm) cc_final: 0.8539 (mt)
REVERT: C  423 GLN cc_start: 0.5942 (mm110) cc_final: 0.4888 (pt0)
REVERT: D  354 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8332 (mm-30)
REVERT: D  420 ILE cc_start: 0.8791 (mm) cc_final: 0.8545 (mt)
REVERT: D  423 GLN cc_start: 0.5949 (mm110) cc_final: 0.4889 (pt0)
  outliers start: 24
  outliers final: 12
  residues processed: 201
  average time/residue: 2.9735
  time to fit residues: 653.7031
Evaluate side-chains
  192 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 180
  time to evaluate  : 1.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  182 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 137 optimal weight:    2.9990
   chunk 141 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 62 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 138 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 98 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 40 optimal weight:    4.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.3592 r_free = 0.3592 target = 0.138902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.099652 restraints weight = 35790.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 1.70
r_work: 0.2911 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.0887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12328  Z= 0.134
  Angle     :  0.444   4.867  16728  Z= 0.241
  Chirality :  0.034   0.129   2012
  Planarity :  0.003   0.024   2040
  Dihedral  :  3.750  18.218   1756
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 18.24 %
    Favored  : 80.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.58 (0.21), residues: 1508
  helix:  2.84 (0.14), residues: 1264
  sheet:  0.37 (0.81), residues: 48
  loop : -0.51 (0.51), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 328 
 HIS   0.004   0.001   HIS A 337 
 PHE   0.020   0.002   PHE C 125 
 TYR   0.006   0.001   TYR C 182 
 ARG   0.003   0.000   ARG C 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04109 ( 1072)
  hydrogen bonds       : angle       4.03719 ( 3204)
  covalent geometry    : bond        0.00266 (12328)
  covalent geometry    : angle       0.44374 (16728)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 164
  time to evaluate  : 1.963 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 ARG cc_start: 0.6376 (ttm-80) cc_final: 0.6118 (ttm-80)
REVERT: A  354 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8293 (mm-30)
REVERT: A  420 ILE cc_start: 0.8770 (mm) cc_final: 0.8562 (mt)
REVERT: A  423 GLN cc_start: 0.5945 (mm110) cc_final: 0.4872 (pt0)
REVERT: B   31 ARG cc_start: 0.6359 (ttm-80) cc_final: 0.6100 (ttm-80)
REVERT: B  354 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8189 (mm-30)
REVERT: B  420 ILE cc_start: 0.8782 (mm) cc_final: 0.8563 (mt)
REVERT: B  423 GLN cc_start: 0.5923 (mm110) cc_final: 0.4858 (pt0)
REVERT: C   31 ARG cc_start: 0.6354 (ttm-80) cc_final: 0.6091 (ttm-80)
REVERT: C  354 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8302 (mm-30)
REVERT: C  420 ILE cc_start: 0.8776 (mm) cc_final: 0.8557 (mt)
REVERT: C  423 GLN cc_start: 0.5932 (mm110) cc_final: 0.4861 (pt0)
REVERT: D   31 ARG cc_start: 0.6372 (ttm-80) cc_final: 0.6113 (ttm-80)
REVERT: D  354 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8309 (mm-30)
REVERT: D  420 ILE cc_start: 0.8781 (mm) cc_final: 0.8565 (mt)
REVERT: D  423 GLN cc_start: 0.5942 (mm110) cc_final: 0.4867 (pt0)
  outliers start: 20
  outliers final: 16
  residues processed: 180
  average time/residue: 3.0866
  time to fit residues: 601.7253
Evaluate side-chains
  178 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 162
  time to evaluate  : 2.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain A residue  404 ILE
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain B residue  404 ILE
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain C residue  404 ILE
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  182 TYR
Chi-restraints excluded: chain D residue  404 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 151 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 16 optimal weight:    8.9990
   chunk 102 optimal weight:    2.9990
   chunk 122 optimal weight:    3.9990
   chunk 84 optimal weight:    0.5980
   chunk 111 optimal weight:    0.9980
   chunk 141 optimal weight:    5.9990
   chunk 54 optimal weight:    9.9990
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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 = 0.3623 r_free = 0.3623 target = 0.140763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.102177 restraints weight = 35595.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 1.67
r_work: 0.2906 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.0852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12328  Z= 0.146
  Angle     :  0.444   4.578  16728  Z= 0.243
  Chirality :  0.034   0.128   2012
  Planarity :  0.004   0.064   2040
  Dihedral  :  3.710  16.995   1756
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 1.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 18.92 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.60 (0.21), residues: 1508
  helix:  2.85 (0.14), residues: 1264
  sheet:  0.37 (0.82), residues: 48
  loop : -0.48 (0.51), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 328 
 HIS   0.004   0.001   HIS C 337 
 PHE   0.010   0.001   PHE D  11 
 TYR   0.007   0.001   TYR C 182 
 ARG   0.009   0.000   ARG C 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04182 ( 1072)
  hydrogen bonds       : angle       4.02555 ( 3204)
  covalent geometry    : bond        0.00298 (12328)
  covalent geometry    : angle       0.44430 (16728)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 163
  time to evaluate  : 2.078 
Fit side-chains
REVERT: A   31 ARG cc_start: 0.6375 (ttm-80) cc_final: 0.6121 (ttm-80)
REVERT: A  120 ASN cc_start: 0.7391 (t0) cc_final: 0.7187 (t160)
REVERT: A  354 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8299 (mm-30)
REVERT: A  423 GLN cc_start: 0.6089 (mm110) cc_final: 0.4960 (pt0)
REVERT: B   31 ARG cc_start: 0.6357 (ttm-80) cc_final: 0.6104 (ttm-80)
REVERT: B  120 ASN cc_start: 0.7394 (t0) cc_final: 0.7192 (t160)
REVERT: B  354 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8309 (mm-30)
REVERT: B  420 ILE cc_start: 0.8785 (mm) cc_final: 0.8566 (mt)
REVERT: B  423 GLN cc_start: 0.6067 (mm110) cc_final: 0.4944 (pt0)
REVERT: C   31 ARG cc_start: 0.6354 (ttm-80) cc_final: 0.6097 (ttm-80)
REVERT: C  120 ASN cc_start: 0.7385 (t0) cc_final: 0.7180 (t160)
REVERT: C  354 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8308 (mm-30)
REVERT: C  420 ILE cc_start: 0.8778 (mm) cc_final: 0.8560 (mt)
REVERT: C  423 GLN cc_start: 0.6072 (mm110) cc_final: 0.4943 (pt0)
REVERT: D   31 ARG cc_start: 0.6370 (ttm-80) cc_final: 0.6115 (ttm-80)
REVERT: D  354 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8314 (mm-30)
REVERT: D  420 ILE cc_start: 0.8781 (mm) cc_final: 0.8565 (mt)
REVERT: D  423 GLN cc_start: 0.6095 (mm110) cc_final: 0.4955 (pt0)
  outliers start: 13
  outliers final: 12
  residues processed: 175
  average time/residue: 3.1550
  time to fit residues: 597.9810
Evaluate side-chains
  171 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 159
  time to evaluate  : 1.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  182 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 102 optimal weight:    5.9990
   chunk 64 optimal weight:    5.9990
   chunk 120 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 146 optimal weight:    5.9990
   chunk 109 optimal weight:    5.9990
   chunk 139 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 123 optimal weight:    0.9990
   chunk 124 optimal weight:    1.9990
   chunk 3 optimal weight:    0.4980
   overall best weight:    1.2786

-------------------------------------------------------------------------------
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 = 0.3614 r_free = 0.3614 target = 0.140273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.101537 restraints weight = 35847.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 1.68
r_work: 0.2912 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2779 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.0992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12328  Z= 0.133
  Angle     :  0.435   4.212  16728  Z= 0.238
  Chirality :  0.034   0.130   2012
  Planarity :  0.004   0.054   2040
  Dihedral  :  3.626  15.123   1756
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 1.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 19.07 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.70 (0.21), residues: 1508
  helix:  2.92 (0.14), residues: 1264
  sheet:  0.36 (0.82), residues: 48
  loop : -0.48 (0.51), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 328 
 HIS   0.004   0.001   HIS B 337 
 PHE   0.022   0.002   PHE A 125 
 TYR   0.006   0.001   TYR B 182 
 ARG   0.007   0.000   ARG C 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04077 ( 1072)
  hydrogen bonds       : angle       3.97886 ( 3204)
  covalent geometry    : bond        0.00265 (12328)
  covalent geometry    : angle       0.43498 (16728)

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

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

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3016 Ramachandran restraints generated.
    1508 Oldfield, 0 Emsley, 1508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 161
  time to evaluate  : 1.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 ARG cc_start: 0.6325 (ttm-80) cc_final: 0.6063 (ttm-80)
REVERT: A  354 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8300 (mm-30)
REVERT: A  423 GLN cc_start: 0.6119 (mm110) cc_final: 0.4959 (pt0)
REVERT: B   31 ARG cc_start: 0.6311 (ttm-80) cc_final: 0.6050 (ttm-80)
REVERT: B  120 ASN cc_start: 0.7392 (t0) cc_final: 0.7191 (t160)
REVERT: B  354 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8303 (mm-30)
REVERT: B  423 GLN cc_start: 0.6105 (mm110) cc_final: 0.4973 (pt0)
REVERT: C   31 ARG cc_start: 0.6307 (ttm-80) cc_final: 0.6044 (ttm-80)
REVERT: C  354 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8301 (mm-30)
REVERT: C  423 GLN cc_start: 0.6109 (mm110) cc_final: 0.4972 (pt0)
REVERT: D   31 ARG cc_start: 0.6321 (ttm-80) cc_final: 0.6059 (ttm-80)
REVERT: D  354 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8311 (mm-30)
REVERT: D  423 GLN cc_start: 0.6122 (mm110) cc_final: 0.4975 (pt0)
  outliers start: 12
  outliers final: 12
  residues processed: 173
  average time/residue: 3.0652
  time to fit residues: 573.3580
Evaluate side-chains
  173 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 161
  time to evaluate  : 1.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 SER
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  182 TYR
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue  182 TYR
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain C residue  182 TYR
Chi-restraints excluded: chain D residue    7 SER
Chi-restraints excluded: chain D residue   75 THR
Chi-restraints excluded: chain D residue  182 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 112 optimal weight:    3.9990
   chunk 49 optimal weight:    0.5980
   chunk 147 optimal weight:    5.9990
   chunk 107 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 138 optimal weight:    3.9990
   chunk 142 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 91 optimal weight:    0.4980
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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 = 0.3590 r_free = 0.3590 target = 0.138789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.099421 restraints weight = 35878.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 1.70
r_work: 0.2908 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2774 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.0978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12328  Z= 0.141
  Angle     :  0.440   4.063  16728  Z= 0.242
  Chirality :  0.034   0.129   2012
  Planarity :  0.004   0.053   2040
  Dihedral  :  3.609  14.427   1756
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 2.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 19.76 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.64 (0.21), residues: 1508
  helix:  2.88 (0.14), residues: 1264
  sheet:  0.37 (0.82), residues: 48
  loop : -0.49 (0.51), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 328 
 HIS   0.004   0.001   HIS A 337 
 PHE   0.010   0.001   PHE C  11 
 TYR   0.006   0.001   TYR A 182 
 ARG   0.007   0.000   ARG A 156 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04119 ( 1072)
  hydrogen bonds       : angle       4.01112 ( 3204)
  covalent geometry    : bond        0.00284 (12328)
  covalent geometry    : angle       0.44040 (16728)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 19537.93 seconds
wall clock time: 338 minutes 33.89 seconds (20313.89 seconds total)