Starting phenix.real_space_refine
on Tue Jul 29 00:15:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cl3_16711/07_2025/8cl3_16711.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cl3_16711/07_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_16711/07_2025/8cl3_16711.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cl3_16711/07_2025/8cl3_16711.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cl3_16711/07_2025/8cl3_16711.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cl3_16711/07_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-5711/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: 4.72, per 1000 atoms: 0.46
  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: 2.81
  Conformation dependent library (CDL) restraints added in 1.4 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: 0.88
  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: 2.82

  Time building geometry restraints manager: 3.28 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:             3.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     24.290
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.460
-------------------------------------------------------------------------------
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  : 1.037 
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: 0.2825
  time to fit residues: 85.3036
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  : 2.062 
-------------------------------------------------------------------------------
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 = 0.162533 restraints weight = 9281.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 2.82
r_work: 0.3410 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6368
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  : 1.094 
Fit side-chains
REVERT: A  128 GLU cc_start: 0.6423 (tp30) cc_final: 0.5844 (mp0)
REVERT: C  118 MET cc_start: 0.7184 (mtp) cc_final: 0.6815 (mtp)
REVERT: C  128 GLU cc_start: 0.6294 (tp30) cc_final: 0.5921 (tp30)
REVERT: C  175 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7093 (mm-30)
REVERT: C  191 VAL cc_start: 0.6221 (t) cc_final: 0.5987 (m)
REVERT: E   35 GLU cc_start: 0.6966 (pm20) cc_final: 0.6736 (pm20)
REVERT: E  128 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.6015 (mp0)
REVERT: G  128 GLU cc_start: 0.6410 (tp30) cc_final: 0.5827 (mp0)
REVERT: I  118 MET cc_start: 0.7182 (mtp) cc_final: 0.6812 (mtp)
REVERT: I  128 GLU cc_start: 0.6299 (tp30) cc_final: 0.5930 (tp30)
REVERT: I  191 VAL cc_start: 0.6218 (t) cc_final: 0.5988 (m)
REVERT: K   35 GLU cc_start: 0.6972 (pm20) cc_final: 0.6747 (pm20)
REVERT: K  128 GLU cc_start: 0.6270 (OUTLIER) cc_final: 0.6037 (mp0)
  outliers start: 21
  outliers final: 4
  residues processed: 163
  average time/residue: 0.2165
  time to fit residues: 50.0953
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  : 1.099 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 78 optimal weight:    0.7980
   chunk 126 optimal weight:    0.3980
   chunk 119 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   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:    0.7980
   overall best weight:    0.3178

-------------------------------------------------------------------------------
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 = 0.4286 r_free = 0.4286 target = 0.218974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.173870 restraints weight = 9276.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3673 rms_B_bonded: 2.62
r_work: 0.3440 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6137
moved from start:          0.2999

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= 0.115
  Angle     :  0.517   7.091  14280  Z= 0.253
  Chirality :  0.041   0.140   1608
  Planarity :  0.005   0.046   1860
  Dihedral  :  4.155  15.334   1410
  Min Nonbonded Distance : 2.644

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:  1.28 (0.22), residues: 1314
  helix:  1.08 (0.17), residues: 870
  sheet:  None (None), residues: 0
  loop :  0.64 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K 117 
 HIS   0.001   0.000   HIS I  62 
 PHE   0.009   0.001   PHE I  32 
 TYR   0.006   0.001   TYR K 169 
 ARG   0.003   0.000   ARG C 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03736 (  636)
  hydrogen bonds       : angle       3.72623 ( 1908)
  covalent geometry    : bond        0.00271 (10500)
  covalent geometry    : angle       0.51667 (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
  159 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 151
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  143 ARG cc_start: 0.5569 (ttp-110) cc_final: 0.5277 (mtp180)
REVERT: E  144 MET cc_start: 0.7333 (ttm) cc_final: 0.7057 (ttm)
REVERT: E  167 ARG cc_start: 0.7475 (mtp-110) cc_final: 0.7191 (ttp-110)
REVERT: I  144 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.7234 (ttm)
REVERT: K  128 GLU cc_start: 0.5799 (mp0) cc_final: 0.5590 (tp30)
REVERT: K  167 ARG cc_start: 0.7461 (mtp-110) cc_final: 0.7180 (ttp-110)
  outliers start: 8
  outliers final: 0
  residues processed: 153
  average time/residue: 0.2354
  time to fit residues: 50.9403
Evaluate side-chains
  147 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   chunk 96 optimal weight:    0.4980
   chunk 36 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 82 optimal weight:    0.2980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.4094 r_free = 0.4094 target = 0.202576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.154962 restraints weight = 9486.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 2.64
r_work: 0.3425 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6285
moved from start:          0.3091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10500  Z= 0.166
  Angle     :  0.545   6.843  14280  Z= 0.270
  Chirality :  0.043   0.145   1608
  Planarity :  0.005   0.051   1860
  Dihedral  :  4.149  15.300   1410
  Min Nonbonded Distance : 2.653

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  6.30 %
    Favored  : 91.85 %
  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:  1.15 (0.23), residues: 1314
  helix:  1.18 (0.18), residues: 870
  sheet: -1.35 (0.52), residues: 54
  loop :  0.38 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K  80 
 HIS   0.002   0.001   HIS G 120 
 PHE   0.008   0.001   PHE I  32 
 TYR   0.007   0.001   TYR K 169 
 ARG   0.002   0.000   ARG C 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04011 (  636)
  hydrogen bonds       : angle       3.81499 ( 1908)
  covalent geometry    : bond        0.00409 (10500)
  covalent geometry    : angle       0.54502 (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
  158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  128 GLU cc_start: 0.6268 (tp30) cc_final: 0.5582 (tp30)
REVERT: E  144 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.7096 (ttm)
REVERT: E  167 ARG cc_start: 0.7511 (mtp-110) cc_final: 0.7231 (ttp-110)
REVERT: I  128 GLU cc_start: 0.6248 (tp30) cc_final: 0.5939 (tp30)
REVERT: I  144 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.7267 (ttm)
REVERT: K  167 ARG cc_start: 0.7509 (mtp-110) cc_final: 0.7226 (ttp-110)
  outliers start: 20
  outliers final: 10
  residues processed: 144
  average time/residue: 0.2472
  time to fit residues: 50.4229
Evaluate side-chains
  147 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 135
  time to evaluate  : 1.533 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 123 optimal weight:    0.0020
   chunk 101 optimal weight:    0.5980
   chunk 57 optimal weight:    0.5980
   chunk 71 optimal weight:    0.0970
   chunk 12 optimal weight:    0.7980
   chunk 60 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   chunk 107 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0670
   overall best weight:    0.2724

-------------------------------------------------------------------------------
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 = 0.4224 r_free = 0.4224 target = 0.212519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.164497 restraints weight = 9367.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 2.80
r_work: 0.3464 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6210
moved from start:          0.3365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10500  Z= 0.105
  Angle     :  0.478   6.722  14280  Z= 0.235
  Chirality :  0.040   0.137   1608
  Planarity :  0.005   0.053   1860
  Dihedral  :  3.834  14.478   1410
  Min Nonbonded Distance : 2.674

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  7.96 %
    Favored  : 91.48 %
  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:  1.56 (0.23), residues: 1314
  helix:  1.53 (0.18), residues: 870
  sheet: -1.07 (0.52), residues: 54
  loop :  0.43 (0.32), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP G 133 
 HIS   0.001   0.000   HIS A  62 
 PHE   0.009   0.001   PHE I  32 
 TYR   0.005   0.001   TYR K 169 
 ARG   0.002   0.000   ARG G 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03498 (  636)
  hydrogen bonds       : angle       3.61011 ( 1908)
  covalent geometry    : bond        0.00243 (10500)
  covalent geometry    : angle       0.47840 (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
  158 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 152
  time to evaluate  : 1.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  201 ILE cc_start: 0.5107 (mt) cc_final: 0.4880 (tp)
REVERT: E   35 GLU cc_start: 0.6765 (pm20) cc_final: 0.6543 (pm20)
REVERT: E  118 MET cc_start: 0.7027 (mtm) cc_final: 0.6787 (mtp)
REVERT: E  128 GLU cc_start: 0.6161 (tp30) cc_final: 0.5725 (tp30)
REVERT: E  144 MET cc_start: 0.7325 (ttm) cc_final: 0.7050 (ttm)
REVERT: E  167 ARG cc_start: 0.7500 (mtp-110) cc_final: 0.7240 (ttp-110)
REVERT: I  144 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7241 (ttm)
REVERT: I  201 ILE cc_start: 0.5095 (mt) cc_final: 0.4871 (tp)
REVERT: K  118 MET cc_start: 0.7074 (mtm) cc_final: 0.6829 (mtp)
REVERT: K  128 GLU cc_start: 0.5713 (mp0) cc_final: 0.5443 (mp0)
REVERT: K  167 ARG cc_start: 0.7506 (mtp-110) cc_final: 0.7249 (ttp-110)
  outliers start: 6
  outliers final: 3
  residues processed: 153
  average time/residue: 0.2756
  time to fit residues: 61.2673
Evaluate side-chains
  143 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 139
  time to evaluate  : 1.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 MET
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain I residue  144 MET
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:    0.8980
   chunk 111 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9990
   chunk 43 optimal weight:    0.4980
   chunk 89 optimal weight:    0.8980
   chunk 127 optimal weight:    0.0370
   chunk 12 optimal weight:    0.9980
   chunk 121 optimal weight:    0.1980
   chunk 114 optimal weight:    0.6980
   overall best weight:    0.4458

-------------------------------------------------------------------------------
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 = 0.4156 r_free = 0.4156 target = 0.207463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.159666 restraints weight = 9422.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 2.70
r_work: 0.3444 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6124
moved from start:          0.3422

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= 0.124
  Angle     :  0.490   6.215  14280  Z= 0.242
  Chirality :  0.041   0.136   1608
  Planarity :  0.005   0.054   1860
  Dihedral  :  3.811  14.260   1410
  Min Nonbonded Distance : 2.672

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  8.80 %
    Favored  : 89.91 %
  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: 876
  sheet: -1.05 (0.48), residues: 54
  loop :  0.47 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  23 
 HIS   0.002   0.001   HIS K  62 
 PHE   0.009   0.001   PHE I  32 
 TYR   0.006   0.001   TYR A 169 
 ARG   0.002   0.000   ARG C 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03601 (  636)
  hydrogen bonds       : angle       3.65883 ( 1908)
  covalent geometry    : bond        0.00298 (10500)
  covalent geometry    : angle       0.49044 (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
  154 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 1.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  128 GLU cc_start: 0.6076 (tp30) cc_final: 0.5404 (mm-30)
REVERT: C  201 ILE cc_start: 0.5138 (mt) cc_final: 0.4936 (tp)
REVERT: E  128 GLU cc_start: 0.6090 (tp30) cc_final: 0.5660 (tp30)
REVERT: E  144 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6981 (ttm)
REVERT: E  167 ARG cc_start: 0.7367 (mtp-110) cc_final: 0.7130 (ttp-110)
REVERT: G   35 GLU cc_start: 0.6763 (pm20) cc_final: 0.6561 (pm20)
REVERT: I  128 GLU cc_start: 0.6091 (tp30) cc_final: 0.5414 (mm-30)
REVERT: I  144 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7194 (ttm)
REVERT: I  201 ILE cc_start: 0.5137 (mt) cc_final: 0.4931 (tp)
REVERT: K  128 GLU cc_start: 0.5537 (mp0) cc_final: 0.5284 (mp0)
REVERT: K  167 ARG cc_start: 0.7372 (mtp-110) cc_final: 0.7136 (ttp-110)
  outliers start: 14
  outliers final: 9
  residues processed: 143
  average time/residue: 0.2958
  time to fit residues: 59.2345
Evaluate side-chains
  149 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 GLN
Chi-restraints excluded: chain A residue  144 MET
Chi-restraints excluded: chain C residue   15 ILE
Chi-restraints excluded: chain E residue   13 GLN
Chi-restraints excluded: chain E residue  144 MET
Chi-restraints excluded: chain G residue   13 GLN
Chi-restraints excluded: chain G residue  144 MET
Chi-restraints excluded: chain I residue   15 ILE
Chi-restraints excluded: chain I residue  144 MET
Chi-restraints excluded: chain K residue   13 GLN
Chi-restraints excluded: chain K residue  146 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 121 optimal weight:    0.0020
   chunk 32 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 122 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 127 optimal weight:    0.5980
   chunk 103 optimal weight:    0.3980
   overall best weight:    0.4788

-------------------------------------------------------------------------------
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 = 0.4137 r_free = 0.4137 target = 0.205727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.158201 restraints weight = 9618.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 2.71
r_work: 0.3454 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6134
moved from start:          0.3466

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= 0.127
  Angle     :  0.492   6.610  14280  Z= 0.242
  Chirality :  0.041   0.136   1608
  Planarity :  0.005   0.054   1860
  Dihedral  :  3.791  14.056   1410
  Min Nonbonded Distance : 2.665

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  9.17 %
    Favored  : 89.26 %
  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:  1.55 (0.18), residues: 876
  sheet: -1.01 (0.46), residues: 54
  loop :  0.53 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP G  23 
 HIS   0.002   0.000   HIS K  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        0.03590 (  636)
  hydrogen bonds       : angle       3.65007 ( 1908)
  covalent geometry    : bond        0.00307 (10500)
  covalent geometry    : angle       0.49162 (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
  157 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 1.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  212 GLU cc_start: 0.7694 (tp30) cc_final: 0.7485 (tp30)
REVERT: C  128 GLU cc_start: 0.6151 (tp30) cc_final: 0.5693 (tp30)
REVERT: E  144 MET cc_start: 0.7281 (OUTLIER) cc_final: 0.7010 (ttm)
REVERT: E  167 ARG cc_start: 0.7371 (mtp-110) cc_final: 0.7150 (ttp-110)
REVERT: G   35 GLU cc_start: 0.6759 (pm20) cc_final: 0.6532 (pm20)
REVERT: I  128 GLU cc_start: 0.6156 (tp30) cc_final: 0.5704 (tp30)
REVERT: I  144 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.7142 (ttm)
REVERT: K  167 ARG cc_start: 0.7386 (mtp-110) cc_final: 0.7162 (ttp-110)
  outliers start: 17
  outliers final: 9
  residues processed: 145
  average time/residue: 0.3155
  time to fit residues: 65.2129
Evaluate side-chains
  144 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 133
  time to evaluate  : 1.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  144 MET
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  146 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 112 optimal weight:    2.9990
   chunk 85 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0980
   chunk 128 optimal weight:    0.9990
   chunk 106 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 64 optimal weight:    0.4980
   chunk 121 optimal weight:    0.7980
   chunk 99 optimal weight:    0.8980
   chunk 82 optimal weight:    0.5980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.4148 r_free = 0.4148 target = 0.206148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.158420 restraints weight = 9523.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 2.71
r_work: 0.3413 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6158
moved from start:          0.3499

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= 0.136
  Angle     :  0.505   6.451  14280  Z= 0.249
  Chirality :  0.041   0.135   1608
  Planarity :  0.005   0.054   1860
  Dihedral  :  3.816  15.080   1410
  Min Nonbonded Distance : 2.661

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  9.26 %
    Favored  : 88.98 %
  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:  1.64 (0.24), residues: 1314
  helix:  1.52 (0.18), residues: 876
  sheet: -0.95 (0.45), residues: 54
  loop :  0.60 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K  23 
 HIS   0.002   0.000   HIS K  62 
 PHE   0.008   0.001   PHE K  32 
 TYR   0.007   0.001   TYR E 169 
 ARG   0.002   0.000   ARG A 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03669 (  636)
  hydrogen bonds       : angle       3.68009 ( 1908)
  covalent geometry    : bond        0.00330 (10500)
  covalent geometry    : angle       0.50452 (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
  156 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  128 GLU cc_start: 0.6226 (tp30) cc_final: 0.5791 (tp30)
REVERT: C  212 GLU cc_start: 0.6904 (tt0) cc_final: 0.6698 (tp30)
REVERT: E  144 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.7011 (ttm)
REVERT: E  167 ARG cc_start: 0.7368 (mtp-110) cc_final: 0.7155 (ttp-110)
REVERT: G   35 GLU cc_start: 0.6771 (pm20) cc_final: 0.6531 (pm20)
REVERT: I  128 GLU cc_start: 0.6223 (tp30) cc_final: 0.5772 (tp30)
REVERT: I  144 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7227 (ttm)
REVERT: I  212 GLU cc_start: 0.6924 (tt0) cc_final: 0.6704 (tp30)
REVERT: K  167 ARG cc_start: 0.7373 (mtp-110) cc_final: 0.7154 (ttp-110)
  outliers start: 19
  outliers final: 14
  residues processed: 143
  average time/residue: 0.2296
  time to fit residues: 47.4589
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  : 2.433 
-------------------------------------------------------------------------------
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  146 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0060
   chunk 122 optimal weight:    0.6980
   chunk 88 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 119 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.5596

-------------------------------------------------------------------------------
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 = 0.4165 r_free = 0.4165 target = 0.207182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.157244 restraints weight = 9540.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 2.89
r_work: 0.3388 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6125
moved from start:          0.3518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10500  Z= 0.140
  Angle     :  0.516   8.338  14280  Z= 0.255
  Chirality :  0.041   0.135   1608
  Planarity :  0.005   0.054   1860
  Dihedral  :  3.826  14.412   1410
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  9.35 %
    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:  1.67 (0.24), residues: 1314
  helix:  1.56 (0.18), residues: 870
  sheet: -1.04 (0.44), residues: 54
  loop :  0.59 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 117 
 HIS   0.002   0.001   HIS K  62 
 PHE   0.009   0.001   PHE K  32 
 TYR   0.007   0.001   TYR E 169 
 ARG   0.002   0.000   ARG A 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03700 (  636)
  hydrogen bonds       : angle       3.70462 ( 1908)
  covalent geometry    : bond        0.00343 (10500)
  covalent geometry    : angle       0.51620 (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: 19
    poor density    : 133
  time to evaluate  : 3.680 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 GLU cc_start: 0.6914 (pm20) cc_final: 0.6279 (pm20)
REVERT: E  118 MET cc_start: 0.6870 (mtm) cc_final: 0.6616 (mtp)
REVERT: E  144 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6989 (ttm)
REVERT: G   35 GLU cc_start: 0.6649 (pm20) cc_final: 0.6406 (pm20)
REVERT: I   35 GLU cc_start: 0.6921 (pm20) cc_final: 0.6284 (pm20)
REVERT: I  128 GLU cc_start: 0.6167 (tp30) cc_final: 0.5688 (tp30)
REVERT: I  144 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7194 (ttm)
  outliers start: 19
  outliers final: 15
  residues processed: 136
  average time/residue: 0.3319
  time to fit residues: 65.6290
Evaluate side-chains
  149 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 1.881 
-------------------------------------------------------------------------------
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 129 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0870
   chunk 58 optimal weight:    0.8980
   chunk 96 optimal weight:    4.9990
   chunk 110 optimal weight:    0.4980
   chunk 105 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   overall best weight:    0.6358

-------------------------------------------------------------------------------
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 = 0.4103 r_free = 0.4103 target = 0.202876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.154199 restraints weight = 9539.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3604 rms_B_bonded: 2.74
r_work: 0.3389 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6152
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  10500  Z= 0.151
  Angle     :  0.525   7.400  14280  Z= 0.260
  Chirality :  0.042   0.135   1608
  Planarity :  0.005   0.055   1860
  Dihedral  :  3.867  14.567   1410
  Min Nonbonded Distance : 2.654

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  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 (0.24), residues: 1314
  helix:  1.49 (0.18), residues: 870
  sheet: -1.08 (0.44), residues: 54
  loop :  0.62 (0.33), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP K 117 
 HIS   0.002   0.001   HIS I  62 
 PHE   0.008   0.001   PHE I  32 
 TYR   0.007   0.001   TYR E 169 
 ARG   0.002   0.000   ARG A 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03800 (  636)
  hydrogen bonds       : angle       3.75067 ( 1908)
  covalent geometry    : bond        0.00372 (10500)
  covalent geometry    : angle       0.52529 (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
  150 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   35 GLU cc_start: 0.6884 (pm20) cc_final: 0.6298 (pm20)
REVERT: E  128 GLU cc_start: 0.6150 (tp30) cc_final: 0.5697 (tp30)
REVERT: E  144 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.7026 (ttm)
REVERT: G   35 GLU cc_start: 0.6707 (pm20) cc_final: 0.6462 (pm20)
REVERT: I   35 GLU cc_start: 0.6899 (pm20) cc_final: 0.6252 (pm20)
REVERT: I  128 GLU cc_start: 0.6204 (tp30) cc_final: 0.5714 (tp30)
REVERT: I  144 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7219 (ttm)
REVERT: K  118 MET cc_start: 0.6962 (mtm) cc_final: 0.6675 (mtp)
  outliers start: 18
  outliers final: 15
  residues processed: 136
  average time/residue: 0.2255
  time to fit residues: 43.5184
Evaluate side-chains
  149 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 33 optimal weight:    0.2980
   chunk 126 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 40 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4114 r_free = 0.4114 target = 0.203819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.156796 restraints weight = 9504.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3678 rms_B_bonded: 2.64
r_work: 0.3467 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6223
moved from start:          0.3579

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= 0.140
  Angle     :  0.512   6.680  14280  Z= 0.254
  Chirality :  0.041   0.135   1608
  Planarity :  0.005   0.055   1860
  Dihedral  :  3.838  14.483   1410
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  9.35 %
    Favored  : 88.80 %
  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:  1.59 (0.24), residues: 1314
  helix:  1.46 (0.18), residues: 876
  sheet: -1.08 (0.44), residues: 54
  loop :  0.68 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP K 117 
 HIS   0.001   0.001   HIS I  62 
 PHE   0.009   0.001   PHE K  32 
 TYR   0.006   0.001   TYR A 169 
 ARG   0.002   0.000   ARG A 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03717 (  636)
  hydrogen bonds       : angle       3.73309 ( 1908)
  covalent geometry    : bond        0.00342 (10500)
  covalent geometry    : angle       0.51211 (14280)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6464.50 seconds
wall clock time: 119 minutes 22.00 seconds (7162.00 seconds total)