Starting phenix.real_space_refine
on Tue May 13 18:07:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cl3_16711/05_2025/8cl3_16711.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cl3_16711/05_2025/8cl3_16711.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cl3_16711/05_2025/8cl3_16711.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cl3_16711/05_2025/8cl3_16711.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cl3_16711/05_2025/8cl3_16711.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cl3_16711/05_2025/8cl3_16711.cif"
  }
  resolution = 3.14
  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=   0.001 sd=   0.041
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 774 atoms to isotropic.
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: 4
    Type Number    sf(0)   Gaussians
     S      72      5.16       5
     C    6498      2.51       5
     N    1770      2.21       5
     O    1932      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 10272
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1633
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1633
          Classifications: {'peptide': 213}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 55
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "B"
      Number of atoms: 79
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 79
          Classifications: {'peptide': 12}
          Link IDs: {'PTRANS': 3, 'TRANS': 8}
  Restraints were copied for chains:
    C, E, G, I, K, D, F, H, J, L
  Time building chain proxies: 4.52, per 1000 atoms: 0.44
  Number of scatterers: 10272
  At special positions: 0
  Unit cell: (112.53, 112.53, 70.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      72     16.00
     O    1932      8.00
     N    1770      7.00
     C    6498      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.59
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2496

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 6 sheets defined
      66.7% alpha, 1.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 31
    Processing helix  chain 'A' and resid 35 through 44
    Processing helix  chain 'A' and resid 48 through 58
    Processing helix  chain 'A' and resid 62 through 84
    Processing helix  chain 'A' and resid 100 through 105
    Processing helix  chain 'A' and resid 110 through 120
    Processing helix  chain 'A' and resid 125 through 146
    Processing helix  chain 'A' and resid 160 through 173
    Processing helix  chain 'A' and resid 178 through 193
      removed outlier: 3.665A  pdb=" N   LEU A 190 " --> pdb=" O   THR A 186 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   VAL A 191 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 206
    Processing helix  chain 'A' and resid 210 through 218
    Processing helix  chain 'C' and resid 16 through 31
    Processing helix  chain 'C' and resid 35 through 44
    Processing helix  chain 'C' and resid 48 through 58
    Processing helix  chain 'C' and resid 62 through 84
    Processing helix  chain 'C' and resid 100 through 105
    Processing helix  chain 'C' and resid 110 through 120
    Processing helix  chain 'C' and resid 125 through 146
    Processing helix  chain 'C' and resid 160 through 173
    Processing helix  chain 'C' and resid 178 through 193
      removed outlier: 3.665A  pdb=" N   LEU C 190 " --> pdb=" O   THR C 186 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   VAL C 191 " --> pdb=" O   GLU C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 195 through 206
    Processing helix  chain 'C' and resid 210 through 218
    Processing helix  chain 'E' and resid 16 through 31
    Processing helix  chain 'E' and resid 35 through 44
    Processing helix  chain 'E' and resid 48 through 58
    Processing helix  chain 'E' and resid 62 through 84
    Processing helix  chain 'E' and resid 100 through 105
    Processing helix  chain 'E' and resid 110 through 120
    Processing helix  chain 'E' and resid 125 through 146
    Processing helix  chain 'E' and resid 160 through 173
    Processing helix  chain 'E' and resid 178 through 193
      removed outlier: 3.665A  pdb=" N   LEU E 190 " --> pdb=" O   THR E 186 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   VAL E 191 " --> pdb=" O   GLU E 187 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 195 through 206
    Processing helix  chain 'E' and resid 210 through 218
    Processing helix  chain 'G' and resid 16 through 31
    Processing helix  chain 'G' and resid 35 through 44
    Processing helix  chain 'G' and resid 48 through 58
    Processing helix  chain 'G' and resid 62 through 84
    Processing helix  chain 'G' and resid 100 through 105
    Processing helix  chain 'G' and resid 110 through 120
    Processing helix  chain 'G' and resid 125 through 146
    Processing helix  chain 'G' and resid 160 through 173
    Processing helix  chain 'G' and resid 178 through 193
      removed outlier: 3.665A  pdb=" N   LEU G 190 " --> pdb=" O   THR G 186 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   VAL G 191 " --> pdb=" O   GLU G 187 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 195 through 206
    Processing helix  chain 'G' and resid 210 through 218
    Processing helix  chain 'I' and resid 16 through 31
    Processing helix  chain 'I' and resid 35 through 44
    Processing helix  chain 'I' and resid 48 through 58
    Processing helix  chain 'I' and resid 62 through 84
    Processing helix  chain 'I' and resid 100 through 105
    Processing helix  chain 'I' and resid 110 through 120
    Processing helix  chain 'I' and resid 125 through 146
    Processing helix  chain 'I' and resid 160 through 173
    Processing helix  chain 'I' and resid 178 through 193
      removed outlier: 3.665A  pdb=" N   LEU I 190 " --> pdb=" O   THR I 186 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   VAL I 191 " --> pdb=" O   GLU I 187 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 195 through 206
    Processing helix  chain 'I' and resid 210 through 218
    Processing helix  chain 'K' and resid 16 through 31
    Processing helix  chain 'K' and resid 35 through 44
    Processing helix  chain 'K' and resid 48 through 58
    Processing helix  chain 'K' and resid 62 through 84
    Processing helix  chain 'K' and resid 100 through 105
    Processing helix  chain 'K' and resid 110 through 120
    Processing helix  chain 'K' and resid 125 through 146
    Processing helix  chain 'K' and resid 160 through 173
    Processing helix  chain 'K' and resid 178 through 193
      removed outlier: 3.665A  pdb=" N   LEU K 190 " --> pdb=" O   THR K 186 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   VAL K 191 " --> pdb=" O   GLU K 187 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 195 through 206
    Processing helix  chain 'K' and resid 210 through 218
    Processing sheet with id=1, first strand: chain 'A' and resid 2 through 4
    Processing sheet with id=2, first strand: chain 'C' and resid 2 through 4
    Processing sheet with id=3, first strand: chain 'E' and resid 2 through 4
    Processing sheet with id=4, first strand: chain 'G' and resid 2 through 4
    Processing sheet with id=5, first strand: chain 'I' and resid 2 through 4
    Processing sheet with id=6, first strand: chain 'K' and resid 2 through 4

    636 hydrogen bonds defined for protein.
    1908 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: 2.74

  Time building geometry restraints manager: 3.03 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1752
        1.32 -     1.44: 2538
        1.44 -     1.56: 6078
        1.56 -     1.68: 0
        1.68 -     1.81: 132
  Bond restraints: 10500
  Sorted by residual:
  bond pdb=" C   ARG G 143 "
       pdb=" O   ARG G 143 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.044 1.25e-02 6.40e+03 1.23e+01
  bond pdb=" C   ARG A 143 "
       pdb=" O   ARG A 143 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.044 1.25e-02 6.40e+03 1.23e+01
  bond pdb=" C   ARG I 143 "
       pdb=" O   ARG I 143 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.044 1.25e-02 6.40e+03 1.22e+01
  bond pdb=" C   ARG C 143 "
       pdb=" O   ARG C 143 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.044 1.25e-02 6.40e+03 1.22e+01
  bond pdb=" C   ARG E 143 "
       pdb=" O   ARG E 143 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.044 1.25e-02 6.40e+03 1.22e+01
  ... (remaining 10495 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 13950
        2.52 -     5.04: 294
        5.04 -     7.56: 12
        7.56 -    10.07: 12
       10.07 -    12.59: 12
  Bond angle restraints: 14280
  Sorted by residual:
  angle pdb=" CB  LEU E   6 "
        pdb=" CG  LEU E   6 "
        pdb=" CD1 LEU E   6 "
      ideal   model   delta    sigma   weight residual
     110.70  123.29  -12.59 3.00e+00 1.11e-01 1.76e+01
  angle pdb=" CB  LEU K   6 "
        pdb=" CG  LEU K   6 "
        pdb=" CD1 LEU K   6 "
      ideal   model   delta    sigma   weight residual
     110.70  123.29  -12.59 3.00e+00 1.11e-01 1.76e+01
  angle pdb=" CB  LEU C   6 "
        pdb=" CG  LEU C   6 "
        pdb=" CD1 LEU C   6 "
      ideal   model   delta    sigma   weight residual
     110.70  123.29  -12.59 3.00e+00 1.11e-01 1.76e+01
  angle pdb=" CB  LEU I   6 "
        pdb=" CG  LEU I   6 "
        pdb=" CD1 LEU I   6 "
      ideal   model   delta    sigma   weight residual
     110.70  123.29  -12.59 3.00e+00 1.11e-01 1.76e+01
  angle pdb=" CB  LEU A   6 "
        pdb=" CG  LEU A   6 "
        pdb=" CD1 LEU A   6 "
      ideal   model   delta    sigma   weight residual
     110.70  123.27  -12.57 3.00e+00 1.11e-01 1.76e+01
  ... (remaining 14275 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.20: 5874
       17.20 -    34.39: 420
       34.39 -    51.59: 72
       51.59 -    68.79: 12
       68.79 -    85.98: 6
  Dihedral angle restraints: 6384
    sinusoidal: 2532
      harmonic: 3852
  Sorted by residual:
  dihedral pdb=" CA  PHE C  32 "
           pdb=" C   PHE C  32 "
           pdb=" N   SER C  33 "
           pdb=" CA  SER C  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.00   29.00     0      5.00e+00 4.00e-02 3.36e+01
  dihedral pdb=" CA  PHE I  32 "
           pdb=" C   PHE I  32 "
           pdb=" N   SER I  33 "
           pdb=" CA  SER I  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.00   29.00     0      5.00e+00 4.00e-02 3.36e+01
  dihedral pdb=" CA  PHE G  32 "
           pdb=" C   PHE G  32 "
           pdb=" N   SER G  33 "
           pdb=" CA  SER G  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.01   28.99     0      5.00e+00 4.00e-02 3.36e+01
  ... (remaining 6381 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.273: 1596
       0.273 -    0.547: 0
       0.547 -    0.820: 0
       0.820 -    1.093: 0
       1.093 -    1.367: 12
  Chirality restraints: 1608
  Sorted by residual:
  chirality pdb=" CG  LEU K   6 "
            pdb=" CB  LEU K   6 "
            pdb=" CD1 LEU K   6 "
            pdb=" CD2 LEU K   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.22   -1.37 2.00e-01 2.50e+01 4.67e+01
  chirality pdb=" CG  LEU E   6 "
            pdb=" CB  LEU E   6 "
            pdb=" CD1 LEU E   6 "
            pdb=" CD2 LEU E   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.22   -1.37 2.00e-01 2.50e+01 4.67e+01
  chirality pdb=" CG  LEU G   6 "
            pdb=" CB  LEU G   6 "
            pdb=" CD1 LEU G   6 "
            pdb=" CD2 LEU G   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.22   -1.37 2.00e-01 2.50e+01 4.67e+01
  ... (remaining 1605 not shown)

  Planarity restraints: 1860
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 136 "    0.014 2.00e-02 2.50e+03   2.77e-02 7.68e+00
        pdb=" C   LEU A 136 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   LEU A 136 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLY A 137 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU G 136 "   -0.014 2.00e-02 2.50e+03   2.77e-02 7.68e+00
        pdb=" C   LEU G 136 "    0.048 2.00e-02 2.50e+03
        pdb=" O   LEU G 136 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   GLY G 137 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E 136 "    0.014 2.00e-02 2.50e+03   2.77e-02 7.68e+00
        pdb=" C   LEU E 136 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   LEU E 136 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLY E 137 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1857 not shown)

  Histogram of nonbonded interaction distances:
        0.98 -     1.77: 6
        1.77 -     2.55: 36
        2.55 -     3.33: 13324
        3.33 -     4.12: 25712
        4.12 -     4.90: 47520
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 86598
  Sorted by model distance:
  nonbonded pdb=" CD2 LEU E   6 "
            pdb=" CA  GLY G   8 "
     model   vdw
     0.985 3.860
  nonbonded pdb=" CA  GLY A   8 "
            pdb=" CD2 LEU K   6 "
     model   vdw
     0.985 3.860
  nonbonded pdb=" CD2 LEU G   6 "
            pdb=" CA  GLY I   8 "
     model   vdw
     0.985 3.860
  nonbonded pdb=" CD2 LEU A   6 "
            pdb=" CA  GLY C   8 "
     model   vdw
     0.985 3.860
  nonbonded pdb=" CD2 LEU C   6 "
            pdb=" CA  GLY E   8 "
     model   vdw
     0.985 3.860
  ... (remaining 86593 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: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'I'
  selection = chain 'K'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
  selection = chain 'J'
  selection = chain 'L'
}

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:             8.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    1.250
  Process input model:                     22.270
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6695
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      :  0.005   0.068  10500  Z= 0.281
  Angle     :  0.974  12.594  14280  Z= 0.553
  Chirality :  0.126   1.367   1608
  Planarity :  0.009   0.056   1860
  Dihedral  : 12.731  85.982   3888
  Min Nonbonded Distance : 0.985

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.21), residues: 1314
  helix: -0.88 (0.15), residues: 870
  sheet:  None (None), residues: 0
  loop :  0.20 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP E 117 
 HIS   0.007   0.003   HIS E  62 
 PHE   0.013   0.003   PHE B   9 
 TYR   0.027   0.008   TYR K 164 
 ARG   0.014   0.002   ARG K 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12735 (  636)
  hydrogen bonds       : angle       6.48606 ( 1908)
  covalent geometry    : bond        0.00529 (10500)
  covalent geometry    : angle       0.97355 (14280)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 1.069 
Fit side-chains
REVERT: A  118 MET cc_start: 0.7654 (mtp) cc_final: 0.7411 (mtm)
REVERT: C  143 ARG cc_start: 0.7039 (mtt90) cc_final: 0.6837 (mtm-85)
REVERT: E  118 MET cc_start: 0.7680 (mtp) cc_final: 0.7449 (mtp)
REVERT: G  118 MET cc_start: 0.7651 (mtp) cc_final: 0.7409 (mtm)
REVERT: K  118 MET cc_start: 0.7674 (mtp) cc_final: 0.7444 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 224
  average time/residue: 0.2564
  time to fit residues: 77.1064
Evaluate side-chains
  160 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 103 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 77 optimal weight:    3.9990
   chunk 119 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** B   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L   7 GLN ** 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 = 0.4218 r_free = 0.4218 target = 0.212097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.162534 restraints weight = 9281.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 2.82
r_work: 0.3408 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6367
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10500  Z= 0.180
  Angle     :  0.626   7.456  14280  Z= 0.310
  Chirality :  0.046   0.154   1608
  Planarity :  0.005   0.038   1860
  Dihedral  :  4.814  19.779   1410
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  4.07 %
    Favored  : 93.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.22), residues: 1314
  helix:  0.71 (0.17), residues: 870
  sheet:  None (None), residues: 0
  loop :  0.35 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP I 117 
 HIS   0.003   0.001   HIS I 120 
 PHE   0.010   0.002   PHE A 161 
 TYR   0.010   0.001   TYR E 169 
 ARG   0.003   0.000   ARG I 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04377 (  636)
  hydrogen bonds       : angle       4.06889 ( 1908)
  covalent geometry    : bond        0.00444 (10500)
  covalent geometry    : angle       0.62608 (14280)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 155
  time to evaluate  : 1.116 
Fit side-chains
REVERT: A  128 GLU cc_start: 0.6416 (tp30) cc_final: 0.5836 (mp0)
REVERT: C  118 MET cc_start: 0.7167 (mtp) cc_final: 0.6796 (mtp)
REVERT: C  128 GLU cc_start: 0.6276 (tp30) cc_final: 0.5903 (tp30)
REVERT: C  175 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7091 (mm-30)
REVERT: C  191 VAL cc_start: 0.6206 (t) cc_final: 0.5973 (m)
REVERT: E   35 GLU cc_start: 0.6967 (pm20) cc_final: 0.6737 (pm20)
REVERT: E  128 GLU cc_start: 0.6244 (OUTLIER) cc_final: 0.6009 (mp0)
REVERT: G  128 GLU cc_start: 0.6399 (tp30) cc_final: 0.5818 (mp0)
REVERT: I  118 MET cc_start: 0.7162 (mtp) cc_final: 0.6792 (mtp)
REVERT: I  128 GLU cc_start: 0.6289 (tp30) cc_final: 0.5919 (tp30)
REVERT: I  191 VAL cc_start: 0.6209 (t) cc_final: 0.5978 (m)
REVERT: K   35 GLU cc_start: 0.6977 (pm20) cc_final: 0.6751 (pm20)
REVERT: K  128 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.6030 (mp0)
  outliers start: 21
  outliers final: 4
  residues processed: 163
  average time/residue: 0.2207
  time to fit residues: 50.7921
Evaluate side-chains
  141 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 135
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain E residue  128 GLU
Chi-restraints excluded: chain G residue   41 SER
Chi-restraints excluded: chain I residue   41 SER
Chi-restraints excluded: chain K residue  128 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    5.9990
   chunk 60 optimal weight:    0.5980
   chunk 78 optimal weight:    0.7980
   chunk 126 optimal weight:    0.3980
   chunk 119 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 87 optimal weight:    0.0970
   chunk 37 optimal weight:    0.0980
   chunk 8 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.3578

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

Flipped N/Q/H residues before XYZ refinement:
** B   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 139 ASN
** F   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 139 ASN
** L   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.212942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.165822 restraints weight = 9359.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 2.73
r_work: 0.3434 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6231
moved from start:          0.2987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10500  Z= 0.120
  Angle     :  0.520   7.119  14280  Z= 0.255
  Chirality :  0.041   0.142   1608
  Planarity :  0.005   0.046   1860
  Dihedral  :  4.174  15.318   1410
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  7.22 %
    Favored  : 92.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.22), residues: 1314
  helix:  1.06 (0.17), residues: 870
  sheet:  None (None), residues: 0
  loop :  0.63 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP K 117 
 HIS   0.001   0.000   HIS A  62 
 PHE   0.009   0.001   PHE I  32 
 TYR   0.006   0.001   TYR K 169 
 ARG   0.002   0.000   ARG C 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03769 (  636)
  hydrogen bonds       : angle       3.74617 ( 1908)
  covalent geometry    : bond        0.00284 (10500)
  covalent geometry    : angle       0.52010 (14280)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 153
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  143 ARG cc_start: 0.5636 (ttp-110) cc_final: 0.5329 (mtp180)
REVERT: E  118 MET cc_start: 0.7204 (mtp) cc_final: 0.6987 (mtm)
REVERT: E  128 GLU cc_start: 0.5914 (mp0) cc_final: 0.5698 (tp30)
REVERT: E  167 ARG cc_start: 0.7547 (mtp-110) cc_final: 0.7261 (ttp-110)
REVERT: I  144 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7282 (ttm)
REVERT: K  118 MET cc_start: 0.7223 (mtp) cc_final: 0.7007 (mtm)
REVERT: K  128 GLU cc_start: 0.5958 (mp0) cc_final: 0.5656 (tp30)
REVERT: K  167 ARG cc_start: 0.7539 (mtp-110) cc_final: 0.7257 (ttp-110)
  outliers start: 8
  outliers final: 0
  residues processed: 155
  average time/residue: 0.2298
  time to fit residues: 49.9328
Evaluate side-chains
  146 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 1.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  144 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 81 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 89 optimal weight:    3.9990
   chunk 96 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 30 optimal weight:    5.9990
   chunk 82 optimal weight:    0.0980
   chunk 13 optimal weight:    0.0770
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
B   7 GLN
D   7 GLN
F   7 GLN
H   7 GLN
J   7 GLN
L   7 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.210597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.161620 restraints weight = 9376.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 2.82
r_work: 0.3428 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6201
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10500  Z= 0.133
  Angle     :  0.512   6.696  14280  Z= 0.253
  Chirality :  0.041   0.137   1608
  Planarity :  0.005   0.050   1860
  Dihedral  :  4.002  14.731   1410
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  7.13 %
    Favored  : 91.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.23), residues: 1314
  helix:  1.31 (0.18), residues: 870
  sheet: -1.27 (0.53), residues: 54
  loop :  0.37 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP G 133 
 HIS   0.002   0.001   HIS A 120 
 PHE   0.008   0.001   PHE C  32 
 TYR   0.006   0.001   TYR I 169 
 ARG   0.002   0.000   ARG C 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03770 (  636)
  hydrogen bonds       : angle       3.72422 ( 1908)
  covalent geometry    : bond        0.00322 (10500)
  covalent geometry    : angle       0.51232 (14280)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  128 GLU cc_start: 0.6171 (tp30) cc_final: 0.5707 (mp0)
REVERT: E  118 MET cc_start: 0.7058 (mtp) cc_final: 0.6685 (mtp)
REVERT: E  144 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.7037 (ttm)
REVERT: E  167 ARG cc_start: 0.7467 (mtp-110) cc_final: 0.7203 (ttp-110)
REVERT: I  128 GLU cc_start: 0.6188 (tp30) cc_final: 0.5730 (mp0)
REVERT: I  144 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7229 (ttm)
REVERT: K  118 MET cc_start: 0.7065 (mtp) cc_final: 0.6691 (mtp)
REVERT: K  167 ARG cc_start: 0.7455 (mtp-110) cc_final: 0.7194 (ttp-110)
  outliers start: 14
  outliers final: 6
  residues processed: 145
  average time/residue: 0.2272
  time to fit residues: 46.2341
Evaluate side-chains
  146 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 138
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue  144 MET
Chi-restraints excluded: chain C residue   15 ILE
Chi-restraints excluded: chain E residue  144 MET
Chi-restraints excluded: chain G residue   15 ILE
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain I residue   15 ILE
Chi-restraints excluded: chain I residue  144 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 123 optimal weight:    0.8980
   chunk 101 optimal weight:    0.5980
   chunk 57 optimal weight:    0.5980
   chunk 71 optimal weight:    0.1980
   chunk 12 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 102 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 70 optimal weight:    0.2980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.4110 r_free = 0.4110 target = 0.204487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.156877 restraints weight = 9480.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 2.68
r_work: 0.3502 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6316
moved from start:          0.3320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10500  Z= 0.128
  Angle     :  0.499   6.691  14280  Z= 0.246
  Chirality :  0.041   0.140   1608
  Planarity :  0.005   0.053   1860
  Dihedral  :  3.900  14.324   1410
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  6.20 %
    Favored  : 92.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.23), residues: 1314
  helix:  1.46 (0.18), residues: 870
  sheet: -1.20 (0.50), residues: 54
  loop :  0.41 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP G  23 
 HIS   0.001   0.000   HIS C  62 
 PHE   0.008   0.001   PHE I  32 
 TYR   0.006   0.001   TYR E 169 
 ARG   0.002   0.000   ARG G 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03666 (  636)
  hydrogen bonds       : angle       3.66408 ( 1908)
  covalent geometry    : bond        0.00309 (10500)
  covalent geometry    : angle       0.49905 (14280)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  212 GLU cc_start: 0.7746 (tp30) cc_final: 0.7502 (tp30)
REVERT: C  128 GLU cc_start: 0.6223 (tp30) cc_final: 0.5802 (mp0)
REVERT: E   35 GLU cc_start: 0.6845 (pm20) cc_final: 0.6616 (pm20)
REVERT: E  118 MET cc_start: 0.7260 (mtp) cc_final: 0.7055 (mtp)
REVERT: E  128 GLU cc_start: 0.5754 (mp0) cc_final: 0.5494 (mp0)
REVERT: E  144 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.7105 (ttm)
REVERT: E  167 ARG cc_start: 0.7578 (mtp-110) cc_final: 0.7316 (ttp-110)
REVERT: I  128 GLU cc_start: 0.6227 (tp30) cc_final: 0.5803 (mp0)
REVERT: I  144 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7318 (ttm)
REVERT: K  118 MET cc_start: 0.7282 (mtp) cc_final: 0.7074 (mtp)
REVERT: K  128 GLU cc_start: 0.5739 (mp0) cc_final: 0.5492 (mp0)
REVERT: K  167 ARG cc_start: 0.7574 (mtp-110) cc_final: 0.7313 (ttp-110)
  outliers start: 19
  outliers final: 11
  residues processed: 149
  average time/residue: 0.2283
  time to fit residues: 48.1818
Evaluate side-chains
  158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue  144 MET
Chi-restraints excluded: chain C residue   15 ILE
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain E residue   15 ILE
Chi-restraints excluded: chain E residue  144 MET
Chi-restraints excluded: chain G residue   15 ILE
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain I residue   15 ILE
Chi-restraints excluded: chain I residue   41 SER
Chi-restraints excluded: chain I residue  144 MET
Chi-restraints excluded: chain K residue   15 ILE
Chi-restraints excluded: chain K residue  146 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 111 optimal weight:    1.9990
   chunk 15 optimal weight:    0.2980
   chunk 56 optimal weight:    0.9980
   chunk 94 optimal weight:    1.9990
   chunk 43 optimal weight:    0.3980
   chunk 89 optimal weight:    1.9990
   chunk 127 optimal weight:    0.2980
   chunk 12 optimal weight:    0.9980
   chunk 121 optimal weight:    0.0040
   chunk 114 optimal weight:    0.9980
   overall best weight:    0.3592

-------------------------------------------------------------------------------
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 = 0.4210 r_free = 0.4210 target = 0.211239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.164539 restraints weight = 9367.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 2.74
r_work: 0.3445 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6052
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10500  Z= 0.112
  Angle     :  0.476   6.416  14280  Z= 0.234
  Chirality :  0.040   0.133   1608
  Planarity :  0.005   0.053   1860
  Dihedral  :  3.747  14.158   1410
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  :  8.80 %
    Favored  : 90.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.23), residues: 1314
  helix:  1.60 (0.18), residues: 870
  sheet: -1.15 (0.49), residues: 54
  loop :  0.42 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E  23 
 HIS   0.002   0.000   HIS K  62 
 PHE   0.009   0.001   PHE I  32 
 TYR   0.006   0.001   TYR K 169 
 ARG   0.002   0.000   ARG G 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03492 (  636)
  hydrogen bonds       : angle       3.60637 ( 1908)
  covalent geometry    : bond        0.00265 (10500)
  covalent geometry    : angle       0.47561 (14280)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.6684 (pm20) cc_final: 0.6474 (pm20)
REVERT: E  118 MET cc_start: 0.7065 (mtp) cc_final: 0.6836 (mtp)
REVERT: E  128 GLU cc_start: 0.5532 (mp0) cc_final: 0.5133 (mp0)
REVERT: E  144 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6994 (ttm)
REVERT: E  167 ARG cc_start: 0.7350 (mtp-110) cc_final: 0.7126 (ttp-110)
REVERT: G   35 GLU cc_start: 0.6684 (pm20) cc_final: 0.6470 (pm20)
REVERT: I  144 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.7055 (ttm)
REVERT: K  118 MET cc_start: 0.7069 (mtp) cc_final: 0.6836 (mtp)
REVERT: K  128 GLU cc_start: 0.5518 (mp0) cc_final: 0.5121 (mp0)
REVERT: K  167 ARG cc_start: 0.7346 (mtp-110) cc_final: 0.7122 (ttp-110)
  outliers start: 11
  outliers final: 8
  residues processed: 148
  average time/residue: 0.2139
  time to fit residues: 44.8906
Evaluate side-chains
  149 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 139
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLN
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue  144 MET
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain E residue   13 GLN
Chi-restraints excluded: chain E residue  144 MET
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain I residue   41 SER
Chi-restraints excluded: chain I residue  144 MET
Chi-restraints excluded: chain K residue   13 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 121 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 122 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 127 optimal weight:    0.3980
   chunk 103 optimal weight:    0.7980
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.203350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.155713 restraints weight = 9651.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 2.67
r_work: 0.3464 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6212
moved from start:          0.3465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10500  Z= 0.142
  Angle     :  0.507   6.375  14280  Z= 0.250
  Chirality :  0.041   0.136   1608
  Planarity :  0.005   0.053   1860
  Dihedral  :  3.843  14.368   1410
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  8.98 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.23), residues: 1314
  helix:  1.52 (0.18), residues: 870
  sheet: -1.06 (0.47), residues: 54
  loop :  0.47 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  80 
 HIS   0.002   0.001   HIS K  62 
 PHE   0.008   0.001   PHE I  32 
 TYR   0.007   0.001   TYR K 169 
 ARG   0.002   0.000   ARG G 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03701 (  636)
  hydrogen bonds       : angle       3.66491 ( 1908)
  covalent geometry    : bond        0.00346 (10500)
  covalent geometry    : angle       0.50653 (14280)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.6814 (pm20) cc_final: 0.6586 (pm20)
REVERT: C  128 GLU cc_start: 0.6178 (tp30) cc_final: 0.5474 (mm-30)
REVERT: E  118 MET cc_start: 0.7173 (mtp) cc_final: 0.6916 (mtp)
REVERT: E  128 GLU cc_start: 0.5711 (mp0) cc_final: 0.5468 (mp0)
REVERT: E  144 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7067 (ttm)
REVERT: E  167 ARG cc_start: 0.7431 (mtp-110) cc_final: 0.7193 (ttp-110)
REVERT: G   35 GLU cc_start: 0.6829 (pm20) cc_final: 0.6597 (pm20)
REVERT: I  128 GLU cc_start: 0.6181 (tp30) cc_final: 0.5473 (mm-30)
REVERT: I  144 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7172 (ttm)
REVERT: I  212 GLU cc_start: 0.6954 (tt0) cc_final: 0.6726 (tp30)
REVERT: K  118 MET cc_start: 0.7163 (mtp) cc_final: 0.6904 (mtp)
REVERT: K  128 GLU cc_start: 0.5707 (mp0) cc_final: 0.5462 (mp0)
REVERT: K  167 ARG cc_start: 0.7441 (mtp-110) cc_final: 0.7203 (ttp-110)
  outliers start: 21
  outliers final: 15
  residues processed: 139
  average time/residue: 0.2266
  time to fit residues: 44.5984
Evaluate side-chains
  148 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 131
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLN
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue  144 MET
Chi-restraints excluded: chain C residue   15 ILE
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain E residue   13 GLN
Chi-restraints excluded: chain E residue   15 ILE
Chi-restraints excluded: chain E residue  144 MET
Chi-restraints excluded: chain G residue   13 GLN
Chi-restraints excluded: chain G residue   15 ILE
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain I residue   15 ILE
Chi-restraints excluded: chain I residue   41 SER
Chi-restraints excluded: chain I residue  144 MET
Chi-restraints excluded: chain K residue   13 GLN
Chi-restraints excluded: chain K residue   15 ILE
Chi-restraints excluded: chain K residue  146 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 112 optimal weight:    1.9990
   chunk 85 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0040
   chunk 128 optimal weight:    0.8980
   chunk 106 optimal weight:    0.5980
   chunk 34 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 121 optimal weight:    0.9980
   chunk 99 optimal weight:    0.8980
   chunk 82 optimal weight:    0.5980
   overall best weight:    0.5592

-------------------------------------------------------------------------------
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 = 0.4101 r_free = 0.4101 target = 0.203217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.156009 restraints weight = 9569.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 2.65
r_work: 0.3427 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6070
moved from start:          0.3511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10500  Z= 0.139
  Angle     :  0.508   6.558  14280  Z= 0.251
  Chirality :  0.041   0.135   1608
  Planarity :  0.005   0.054   1860
  Dihedral  :  3.838  14.514   1410
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  9.63 %
    Favored  : 88.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.23), residues: 1314
  helix:  1.51 (0.18), residues: 870
  sheet: -0.98 (0.45), residues: 54
  loop :  0.55 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP G  80 
 HIS   0.002   0.001   HIS K  62 
 PHE   0.008   0.001   PHE K  32 
 TYR   0.007   0.001   TYR K 169 
 ARG   0.002   0.000   ARG A 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03696 (  636)
  hydrogen bonds       : angle       3.69617 ( 1908)
  covalent geometry    : bond        0.00338 (10500)
  covalent geometry    : angle       0.50833 (14280)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.6693 (pm20) cc_final: 0.6449 (pm20)
REVERT: C   29 GLU cc_start: 0.8243 (mt-10) cc_final: 0.8035 (mt-10)
REVERT: C  128 GLU cc_start: 0.6061 (tp30) cc_final: 0.5306 (mm-30)
REVERT: E  118 MET cc_start: 0.7013 (mtp) cc_final: 0.6757 (mtp)
REVERT: E  128 GLU cc_start: 0.5574 (mp0) cc_final: 0.5134 (mp0)
REVERT: E  144 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6994 (ttm)
REVERT: E  167 ARG cc_start: 0.7285 (mtp-110) cc_final: 0.7071 (ttp-110)
REVERT: G   35 GLU cc_start: 0.6700 (pm20) cc_final: 0.6457 (pm20)
REVERT: I   29 GLU cc_start: 0.8233 (mt-10) cc_final: 0.8031 (mt-10)
REVERT: I  128 GLU cc_start: 0.6063 (tp30) cc_final: 0.5306 (mm-30)
REVERT: I  144 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.7174 (ttm)
REVERT: K  118 MET cc_start: 0.7021 (mtp) cc_final: 0.6764 (mtp)
REVERT: K  128 GLU cc_start: 0.5675 (mp0) cc_final: 0.5210 (mp0)
REVERT: K  167 ARG cc_start: 0.7289 (mtp-110) cc_final: 0.7074 (ttp-110)
  outliers start: 18
  outliers final: 14
  residues processed: 136
  average time/residue: 0.2699
  time to fit residues: 52.9708
Evaluate side-chains
  148 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 1.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLN
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue  144 MET
Chi-restraints excluded: chain C residue   15 ILE
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain E residue   13 GLN
Chi-restraints excluded: chain E residue   15 ILE
Chi-restraints excluded: chain E residue  144 MET
Chi-restraints excluded: chain G residue   15 ILE
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain I residue   15 ILE
Chi-restraints excluded: chain I residue   41 SER
Chi-restraints excluded: chain I residue  144 MET
Chi-restraints excluded: chain K residue   13 GLN
Chi-restraints excluded: chain K residue   15 ILE
Chi-restraints excluded: chain K residue  146 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 122 optimal weight:    0.6980
   chunk 88 optimal weight:    6.9990
   chunk 20 optimal weight:    0.5980
   chunk 119 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 89 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4142 r_free = 0.4142 target = 0.204790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.154487 restraints weight = 9622.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 2.92
r_work: 0.3345 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6211
moved from start:          0.3474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10500  Z= 0.173
  Angle     :  0.544   7.921  14280  Z= 0.269
  Chirality :  0.043   0.136   1608
  Planarity :  0.005   0.053   1860
  Dihedral  :  3.996  15.494   1410
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  9.26 %
    Favored  : 88.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.24), residues: 1314
  helix:  1.39 (0.18), residues: 870
  sheet: -1.01 (0.45), residues: 54
  loop :  0.58 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP G  80 
 HIS   0.002   0.001   HIS K  62 
 PHE   0.007   0.001   PHE K  32 
 TYR   0.008   0.001   TYR K 169 
 ARG   0.002   0.000   ARG A 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03972 (  636)
  hydrogen bonds       : angle       3.79513 ( 1908)
  covalent geometry    : bond        0.00429 (10500)
  covalent geometry    : angle       0.54416 (14280)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 1.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLU cc_start: 0.6755 (pm20) cc_final: 0.6509 (pm20)
REVERT: E  128 GLU cc_start: 0.5797 (mp0) cc_final: 0.5336 (mp0)
REVERT: E  144 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6992 (ttm)
REVERT: I  144 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7149 (ttm)
REVERT: K   29 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8097 (pt0)
REVERT: K  128 GLU cc_start: 0.5955 (mp0) cc_final: 0.5448 (mp0)
  outliers start: 22
  outliers final: 17
  residues processed: 136
  average time/residue: 0.2343
  time to fit residues: 44.6971
Evaluate side-chains
  147 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLN
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue  144 MET
Chi-restraints excluded: chain C residue   15 ILE
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain C residue  131 LYS
Chi-restraints excluded: chain E residue   13 GLN
Chi-restraints excluded: chain E residue   15 ILE
Chi-restraints excluded: chain E residue  144 MET
Chi-restraints excluded: chain G residue   15 ILE
Chi-restraints excluded: chain G residue   41 SER
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain I residue   15 ILE
Chi-restraints excluded: chain I residue   41 SER
Chi-restraints excluded: chain I residue  144 MET
Chi-restraints excluded: chain K residue   13 GLN
Chi-restraints excluded: chain K residue   15 ILE
Chi-restraints excluded: chain K residue  146 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 129 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0980
   chunk 58 optimal weight:    0.9980
   chunk 96 optimal weight:    0.9980
   chunk 110 optimal weight:    4.9990
   chunk 105 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0670
   chunk 86 optimal weight:    0.0980
   overall best weight:    0.3718

-------------------------------------------------------------------------------
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 = 0.4140 r_free = 0.4140 target = 0.206003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.158981 restraints weight = 9542.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3673 rms_B_bonded: 2.67
r_work: 0.3460 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6161
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10500  Z= 0.117
  Angle     :  0.490   6.749  14280  Z= 0.242
  Chirality :  0.040   0.133   1608
  Planarity :  0.005   0.053   1860
  Dihedral  :  3.753  14.486   1410
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  9.44 %
    Favored  : 88.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.24), residues: 1314
  helix:  1.55 (0.18), residues: 870
  sheet: -0.95 (0.46), residues: 54
  loop :  0.60 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP G  23 
 HIS   0.001   0.000   HIS K  62 
 PHE   0.009   0.001   PHE K  32 
 TYR   0.006   0.001   TYR E 169 
 ARG   0.003   0.000   ARG C 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03558 (  636)
  hydrogen bonds       : angle       3.68061 ( 1908)
  covalent geometry    : bond        0.00278 (10500)
  covalent geometry    : angle       0.48961 (14280)

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

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

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2628 Ramachandran restraints generated.
    1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 136
  time to evaluate  : 1.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 GLU cc_start: 0.6939 (pm20) cc_final: 0.6315 (pm20)
REVERT: C  128 GLU cc_start: 0.6196 (tp30) cc_final: 0.5725 (tp30)
REVERT: E  128 GLU cc_start: 0.5678 (mp0) cc_final: 0.5241 (mp0)
REVERT: E  144 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7082 (ttm)
REVERT: G   35 GLU cc_start: 0.6778 (pm20) cc_final: 0.6536 (pm20)
REVERT: I   35 GLU cc_start: 0.6927 (pm20) cc_final: 0.6268 (pm20)
REVERT: I  128 GLU cc_start: 0.6209 (tp30) cc_final: 0.5742 (tp30)
REVERT: I  144 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7244 (ttm)
REVERT: K  128 GLU cc_start: 0.5664 (mp0) cc_final: 0.5217 (mp0)
  outliers start: 18
  outliers final: 15
  residues processed: 140
  average time/residue: 0.2260
  time to fit residues: 44.7129
Evaluate side-chains
  152 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 135
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ILE
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue  144 MET
Chi-restraints excluded: chain C residue   15 ILE
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain E residue   13 GLN
Chi-restraints excluded: chain E residue   15 ILE
Chi-restraints excluded: chain E residue  144 MET
Chi-restraints excluded: chain G residue   15 ILE
Chi-restraints excluded: chain G residue   41 SER
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain I residue   15 ILE
Chi-restraints excluded: chain I residue   41 SER
Chi-restraints excluded: chain I residue  144 MET
Chi-restraints excluded: chain K residue   13 GLN
Chi-restraints excluded: chain K residue   15 ILE
Chi-restraints excluded: chain K residue  146 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 128 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 126 optimal weight:    0.4980
   chunk 18 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4121 r_free = 0.4121 target = 0.203900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.156320 restraints weight = 9524.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 2.68
r_work: 0.3412 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6136
moved from start:          0.3612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10500  Z= 0.153
  Angle     :  0.529   7.708  14280  Z= 0.263
  Chirality :  0.042   0.135   1608
  Planarity :  0.005   0.054   1860
  Dihedral  :  3.861  14.610   1410
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  9.63 %
    Favored  : 88.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.24), residues: 1314
  helix:  1.42 (0.18), residues: 876
  sheet: -1.03 (0.45), residues: 54
  loop :  0.68 (0.34), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP G  80 
 HIS   0.002   0.001   HIS K  62 
 PHE   0.008   0.001   PHE I  32 
 TYR   0.007   0.001   TYR E 169 
 ARG   0.003   0.000   ARG G 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03824 (  636)
  hydrogen bonds       : angle       3.76937 ( 1908)
  covalent geometry    : bond        0.00376 (10500)
  covalent geometry    : angle       0.52895 (14280)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4461.94 seconds
wall clock time: 78 minutes 48.86 seconds (4728.86 seconds total)