Starting phenix.real_space_refine
on Sat Apr  4 20:39:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9man_63756/04_2026/9man_63756_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9man_63756/04_2026/9man_63756.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9man_63756/04_2026/9man_63756.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9man_63756/04_2026/9man_63756.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9man_63756/04_2026/9man_63756_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9man_63756/04_2026/9man_63756_neut.cif"
  }
  resolution = 3.78
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    1914      2.51       5
     N     559      2.21       5
     O     543      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3066
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 782
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 5, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 774
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "D"
      Number of atoms: 755
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 755
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 4, 'TRANS': 85}
    Chain: "C"
      Number of atoms: 755
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 755
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 4, 'TRANS': 85}
  Time building chain proxies: 0.85, per 1000 atoms: 0.28
  Number of scatterers: 3066
  At special positions: 0
  Unit cell: (68.224, 73.216, 122.304, 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      50     16.00
     O     543      8.00
     N     559      7.00
     C    1914      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=17, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  39 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  55 " - pdb=" SG  CYS A 110 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  65 " - pdb=" SG  CYS A 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  69 " - pdb=" SG  CYS A 128 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  93 " - pdb=" SG  CYS B  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  95 " - pdb=" SG  CYS B  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS B 131 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  39 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  55 " - pdb=" SG  CYS B 110 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  65 " - pdb=" SG  CYS B 126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  69 " - pdb=" SG  CYS B 128 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D 159 " - pdb=" SG  CYS D 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 160 " - pdb=" SG  CYS D 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 182 " - pdb=" SG  CYS D 189 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 159 " - pdb=" SG  CYS C 206 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 160 " - pdb=" SG  CYS C 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 182 " - pdb=" SG  CYS C 189 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.16
  Conformation dependent library (CDL) restraints added in 120.4 milliseconds
  

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  722

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 7 sheets defined
      33.2% alpha, 23.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'D' and resid 128 through 135
    Processing helix  chain 'D' and resid 140 through 142
      No H-bonds generated for 'chain 'D' and resid 140 through 142'
    Processing helix  chain 'D' and resid 143 through 157
      removed outlier: 3.754A  pdb=" N   ALA D 149 " --> pdb=" O   TRP D 145 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   GLN D 154 " --> pdb=" O   TRP D 150 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 165 through 172
      removed outlier: 3.994A  pdb=" N   LEU D 169 " --> pdb=" O   PHE D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 178 through 182
    Processing helix  chain 'D' and resid 188 through 196
      removed outlier: 3.514A  pdb=" N   GLN D 195 " --> pdb=" O   LYS D 191 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 206 through 215
    Processing helix  chain 'C' and resid 128 through 135
    Processing helix  chain 'C' and resid 136 through 138
      No H-bonds generated for 'chain 'C' and resid 136 through 138'
    Processing helix  chain 'C' and resid 140 through 142
      No H-bonds generated for 'chain 'C' and resid 140 through 142'
    Processing helix  chain 'C' and resid 143 through 157
      removed outlier: 3.604A  pdb=" N   THR C 147 " --> pdb=" O   TYR C 143 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   HIS C 148 " --> pdb=" O   ARG C 144 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ALA C 149 " --> pdb=" O   TRP C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 165 through 172
      removed outlier: 4.418A  pdb=" N   LEU C 169 " --> pdb=" O   PHE C 165 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 178 through 182
    Processing helix  chain 'C' and resid 188 through 196
      removed outlier: 3.616A  pdb=" N   GLN C 192 " --> pdb=" O   GLY C 188 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 201
      removed outlier: 4.054A  pdb=" N   ASP C 200 " --> pdb=" O   ASP C 197 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU C 201 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 197 through 201'
    Processing helix  chain 'C' and resid 205 through 215
      removed outlier: 4.119A  pdb=" N   LYS C 209 " --> pdb=" O   GLY C 205 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 46
      removed outlier: 3.560A  pdb=" N   GLU A  66 " --> pdb=" O   MET A  40 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 56
      removed outlier: 4.008A  pdb=" N   SER A  56 " --> pdb=" O   ARG A 109 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 92
      removed outlier: 8.461A  pdb=" N   ALA B  63 " --> pdb=" O   PRO A  77 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 94 through 98
    Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 57
    Processing sheet with id=AA6, first strand: chain 'B' and resid 74 through 77
    Processing sheet with id=AA7, first strand: chain 'B' and resid 94 through 98

    109 hydrogen bonds defined for protein.
    288 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: 0.36

  Time building geometry restraints manager: 0.22 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 875
        1.33 -     1.45: 576
        1.45 -     1.57: 1629
        1.57 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 3146
  Sorted by residual:
  bond pdb=" CA  PRO C 177 "
       pdb=" C   PRO C 177 "
    ideal  model  delta    sigma   weight residual
    1.517  1.546 -0.028 9.30e-03 1.16e+04 9.35e+00
  bond pdb=" C   PRO C 177 "
       pdb=" O   PRO C 177 "
    ideal  model  delta    sigma   weight residual
    1.240  1.212  0.028 1.12e-02 7.97e+03 6.45e+00
  bond pdb=" N   SER D 190 "
       pdb=" CA  SER D 190 "
    ideal  model  delta    sigma   weight residual
    1.459  1.432  0.027 1.28e-02 6.10e+03 4.38e+00
  bond pdb=" C   CYS D 189 "
       pdb=" O   CYS D 189 "
    ideal  model  delta    sigma   weight residual
    1.237  1.212  0.025 1.19e-02 7.06e+03 4.38e+00
  bond pdb=" CA  TYR C 164 "
       pdb=" C   TYR C 164 "
    ideal  model  delta    sigma   weight residual
    1.522  1.498  0.024 1.20e-02 6.94e+03 4.02e+00
  ... (remaining 3141 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.34: 4130
        2.34 -     4.67: 90
        4.67 -     7.01: 6
        7.01 -     9.34: 2
        9.34 -    11.68: 2
  Bond angle restraints: 4230
  Sorted by residual:
  angle pdb=" N   ASP C 127 "
        pdb=" CA  ASP C 127 "
        pdb=" C   ASP C 127 "
      ideal   model   delta    sigma   weight residual
     114.09  106.49    7.60 1.55e+00 4.16e-01 2.41e+01
  angle pdb=" C   PHE D 186 "
        pdb=" N   PRO D 187 "
        pdb=" CA  PRO D 187 "
      ideal   model   delta    sigma   weight residual
     119.83  115.24    4.59 1.08e+00 8.57e-01 1.81e+01
  angle pdb=" C   PRO C 177 "
        pdb=" N   PRO C 178 "
        pdb=" CA  PRO C 178 "
      ideal   model   delta    sigma   weight residual
     119.78  115.85    3.93 1.03e+00 9.43e-01 1.45e+01
  angle pdb=" N   TRP C 145 "
        pdb=" CA  TRP C 145 "
        pdb=" C   TRP C 145 "
      ideal   model   delta    sigma   weight residual
     111.82  107.46    4.36 1.16e+00 7.43e-01 1.41e+01
  angle pdb=" N   ARG C 142 "
        pdb=" CA  ARG C 142 "
        pdb=" C   ARG C 142 "
      ideal   model   delta    sigma   weight residual
     112.89  108.41    4.48 1.24e+00 6.50e-01 1.30e+01
  ... (remaining 4225 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 1593
       16.92 -    33.84: 246
       33.84 -    50.76: 88
       50.76 -    67.67: 24
       67.67 -    84.59: 9
  Dihedral angle restraints: 1960
    sinusoidal: 847
      harmonic: 1113
  Sorted by residual:
  dihedral pdb=" CB  CYS A  39 "
           pdb=" SG  CYS A  39 "
           pdb=" SG  CYS A  96 "
           pdb=" CB  CYS A  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  177.59  -84.59     1      1.00e+01 1.00e-02 8.70e+01
  dihedral pdb=" CB  CYS A 131 "
           pdb=" SG  CYS A 131 "
           pdb=" SG  CYS B 131 "
           pdb=" CB  CYS B 131 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.68  -72.68     1      1.00e+01 1.00e-02 6.74e+01
  dihedral pdb=" CB  CYS A  95 "
           pdb=" SG  CYS A  95 "
           pdb=" SG  CYS B  93 "
           pdb=" CB  CYS B  93 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   23.67   69.33     1      1.00e+01 1.00e-02 6.21e+01
  ... (remaining 1957 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 312
       0.040 -    0.081: 82
       0.081 -    0.121: 29
       0.121 -    0.162: 6
       0.162 -    0.202: 4
  Chirality restraints: 433
  Sorted by residual:
  chirality pdb=" CA  GLU D 185 "
            pdb=" N   GLU D 185 "
            pdb=" C   GLU D 185 "
            pdb=" CB  GLU D 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  LEU C 169 "
            pdb=" N   LEU C 169 "
            pdb=" C   LEU C 169 "
            pdb=" CB  LEU C 169 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  CYS C 181 "
            pdb=" N   CYS C 181 "
            pdb=" C   CYS C 181 "
            pdb=" CB  CYS C 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.85e-01
  ... (remaining 430 not shown)

  Planarity restraints: 537
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP C 168 "    0.008 2.00e-02 2.50e+03   1.57e-02 2.45e+00
        pdb=" C   TRP C 168 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   TRP C 168 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LEU C 169 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 186 "   -0.025 5.00e-02 4.00e+02   3.72e-02 2.21e+00
        pdb=" N   PRO D 187 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO D 187 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO D 187 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B  97 "    0.023 5.00e-02 4.00e+02   3.53e-02 1.99e+00
        pdb=" N   PRO B  98 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B  98 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B  98 "    0.020 5.00e-02 4.00e+02
  ... (remaining 534 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 1079
        2.86 -     3.37: 2766
        3.37 -     3.88: 4938
        3.88 -     4.39: 5618
        4.39 -     4.90: 9321
  Nonbonded interactions: 23722
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D 197 "
            pdb=" N   SER D 199 "
     model   vdw
     2.347 3.120
  nonbonded pdb=" O   LEU D 201 "
            pdb=" NE2 GLN D 203 "
     model   vdw
     2.350 3.120
  nonbonded pdb=" OG  SER A  80 "
            pdb=" OG1 THR A  83 "
     model   vdw
     2.376 3.040
  nonbonded pdb=" NH2 ARG A  64 "
            pdb=" OE2 GLU B  76 "
     model   vdw
     2.405 3.120
  nonbonded pdb=" O   GLY C 161 "
            pdb=" N   CYS C 206 "
     model   vdw
     2.424 3.120
  ... (remaining 23717 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 36 through 133)
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             14.650
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.460
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
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   0.032   3163  Z= 0.297
  Angle     :  0.774  11.677   4264  Z= 0.451
  Chirality :  0.048   0.202    433
  Planarity :  0.004   0.037    537
  Dihedral  : 18.337  76.692   1187
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 30.26 %
    Favored  : 64.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.60 (0.43), residues: 369
  helix: -1.29 (0.52), residues: 86
  sheet: -1.04 (0.51), residues: 90
  loop : -0.83 (0.47), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 184 
 TYR   0.009   0.001   TYR C 138 
 PHE   0.021   0.001   PHE D 186 
 TRP   0.014   0.002   TRP C 168 
 HIS   0.003   0.001   HIS B  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 3146)
  covalent geometry    : angle       0.77381 ( 4230)
  SS BOND              : bond        0.00317 (   17)
  SS BOND              : angle       0.78109 (   34)
  hydrogen bonds       : bond        0.17675 (  109)
  hydrogen bonds       : angle       7.38480 (  288)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   58 LYS cc_start: 0.9224 (pttt) cc_final: 0.8130 (tptt)
REVERT: D  134 ARG cc_start: 0.8695 (mmm-85) cc_final: 0.7736 (mtt180)
REVERT: C  134 ARG cc_start: 0.8486 (mmt180) cc_final: 0.8091 (mtt180)
REVERT: C  137 ASN cc_start: 0.9333 (t0) cc_final: 0.8472 (t0)
REVERT: C  143 TYR cc_start: 0.8234 (m-80) cc_final: 0.7983 (m-80)
  outliers start: 18
  outliers final: 5
  residues processed: 117
  average time/residue: 0.1170
  time to fit residues: 15.1266
Evaluate side-chains
  100 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 SER
Chi-restraints excluded: chain C residue  130 THR
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  169 LEU
Chi-restraints excluded: chain C residue  176 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 19 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
B  87 GLN
** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.090541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.077399 restraints weight = 7816.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.079693 restraints weight = 3939.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.081234 restraints weight = 2498.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.082307 restraints weight = 1818.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.082957 restraints weight = 1454.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3163  Z= 0.167
  Angle     :  0.553   7.898   4264  Z= 0.283
  Chirality :  0.037   0.118    433
  Planarity :  0.004   0.033    537
  Dihedral  :  5.907  53.236    433
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 31.12 %
    Favored  : 67.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.45), residues: 369
  helix: -1.11 (0.50), residues: 102
  sheet: -1.15 (0.51), residues: 86
  loop : -0.25 (0.52), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 134 
 TYR   0.009   0.001   TYR A  44 
 PHE   0.016   0.001   PHE C 153 
 TRP   0.010   0.001   TRP D 176 
 HIS   0.003   0.001   HIS B  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 3146)
  covalent geometry    : angle       0.55150 ( 4230)
  SS BOND              : bond        0.00344 (   17)
  SS BOND              : angle       0.66791 (   34)
  hydrogen bonds       : bond        0.03060 (  109)
  hydrogen bonds       : angle       5.20666 (  288)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.122 
Fit side-chains
REVERT: B   58 LYS cc_start: 0.9256 (pttt) cc_final: 0.8026 (tptt)
REVERT: D  134 ARG cc_start: 0.8629 (mmm-85) cc_final: 0.7579 (mtt180)
REVERT: C  134 ARG cc_start: 0.8549 (mmt180) cc_final: 0.7653 (mtt180)
REVERT: C  137 ASN cc_start: 0.9293 (t0) cc_final: 0.9003 (t0)
REVERT: C  143 TYR cc_start: 0.8307 (m-80) cc_final: 0.8035 (m-80)
REVERT: C  196 GLU cc_start: 0.8223 (mp0) cc_final: 0.7985 (mp0)
  outliers start: 6
  outliers final: 3
  residues processed: 99
  average time/residue: 0.0873
  time to fit residues: 9.9031
Evaluate side-chains
  96 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  176 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B  87 GLN
** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.091558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.078308 restraints weight = 7795.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.080602 restraints weight = 3848.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.082112 restraints weight = 2406.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.082938 restraints weight = 1755.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.083772 restraints weight = 1451.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3163  Z= 0.114
  Angle     :  0.528   8.458   4264  Z= 0.263
  Chirality :  0.035   0.110    433
  Planarity :  0.003   0.030    537
  Dihedral  :  4.240  47.972    427
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 32.56 %
    Favored  : 64.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.45), residues: 369
  helix: -0.61 (0.54), residues: 102
  sheet: -1.27 (0.50), residues: 88
  loop : -0.23 (0.51), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 184 
 TYR   0.014   0.001   TYR C 164 
 PHE   0.014   0.001   PHE C 165 
 TRP   0.008   0.001   TRP C 168 
 HIS   0.002   0.000   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 3146)
  covalent geometry    : angle       0.52870 ( 4230)
  SS BOND              : bond        0.00246 (   17)
  SS BOND              : angle       0.49352 (   34)
  hydrogen bonds       : bond        0.02619 (  109)
  hydrogen bonds       : angle       4.89269 (  288)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 ASP cc_start: 0.7813 (t0) cc_final: 0.7455 (t0)
REVERT: A   38 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7323 (ttp-110)
REVERT: B   58 LYS cc_start: 0.9249 (pttt) cc_final: 0.8000 (tptt)
REVERT: B  127 HIS cc_start: 0.7442 (OUTLIER) cc_final: 0.7071 (p-80)
REVERT: D  134 ARG cc_start: 0.8523 (mmm-85) cc_final: 0.7516 (mtt180)
REVERT: C  134 ARG cc_start: 0.8692 (mmt180) cc_final: 0.7595 (mtt180)
REVERT: C  137 ASN cc_start: 0.9307 (m-40) cc_final: 0.8960 (t0)
REVERT: C  143 TYR cc_start: 0.8288 (m-80) cc_final: 0.7984 (m-80)
  outliers start: 10
  outliers final: 4
  residues processed: 108
  average time/residue: 0.0917
  time to fit residues: 11.2501
Evaluate side-chains
  99 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  127 HIS
Chi-restraints excluded: chain C residue  159 CYS
Chi-restraints excluded: chain C residue  173 GLU
Chi-restraints excluded: chain C residue  176 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 12 optimal weight:    9.9990
   chunk 0 optimal weight:    8.9990
   chunk 33 optimal weight:    0.2980
   chunk 17 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0030
   overall best weight:    1.6596

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

Flipped N/Q/H residues before XYZ refinement:
B  87 GLN
** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.089520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.076329 restraints weight = 7817.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.078603 restraints weight = 3876.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.080106 restraints weight = 2429.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.081126 restraints weight = 1769.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.081816 restraints weight = 1425.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3163  Z= 0.177
  Angle     :  0.569   8.774   4264  Z= 0.286
  Chirality :  0.037   0.119    433
  Planarity :  0.004   0.032    537
  Dihedral  :  4.279  45.899    427
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 32.28 %
    Favored  : 64.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.44), residues: 369
  helix: -0.62 (0.54), residues: 102
  sheet: -1.24 (0.50), residues: 86
  loop : -0.28 (0.50), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 184 
 TYR   0.014   0.002   TYR C 164 
 PHE   0.017   0.002   PHE C 165 
 TRP   0.009   0.001   TRP C 168 
 HIS   0.003   0.001   HIS B  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 3146)
  covalent geometry    : angle       0.56826 ( 4230)
  SS BOND              : bond        0.00348 (   17)
  SS BOND              : angle       0.64206 (   34)
  hydrogen bonds       : bond        0.02693 (  109)
  hydrogen bonds       : angle       4.87971 (  288)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A   35 ASP cc_start: 0.7809 (t0) cc_final: 0.7500 (t0)
REVERT: A   38 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7288 (ttp-110)
REVERT: B   58 LYS cc_start: 0.9222 (pttt) cc_final: 0.7936 (tptt)
REVERT: B  127 HIS cc_start: 0.7488 (OUTLIER) cc_final: 0.7193 (p-80)
REVERT: D  134 ARG cc_start: 0.8604 (mmm-85) cc_final: 0.7600 (mtt180)
REVERT: C  134 ARG cc_start: 0.8764 (mmt180) cc_final: 0.7608 (mtt180)
REVERT: C  156 GLU cc_start: 0.7827 (tp30) cc_final: 0.7386 (mm-30)
REVERT: C  191 LYS cc_start: 0.8526 (mmmm) cc_final: 0.8088 (mmmm)
REVERT: C  195 GLN cc_start: 0.8827 (mt0) cc_final: 0.8531 (mt0)
  outliers start: 12
  outliers final: 7
  residues processed: 106
  average time/residue: 0.0883
  time to fit residues: 10.6818
Evaluate side-chains
  104 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  127 HIS
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  176 TRP
Chi-restraints excluded: chain C residue  183 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 30 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 18 optimal weight:    6.9990
   chunk 4 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
B  87 GLN
** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.090887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.077544 restraints weight = 7676.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.079818 restraints weight = 3799.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.081354 restraints weight = 2375.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.082367 restraints weight = 1724.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.083066 restraints weight = 1392.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3163  Z= 0.128
  Angle     :  0.564   9.231   4264  Z= 0.277
  Chirality :  0.036   0.112    433
  Planarity :  0.003   0.030    537
  Dihedral  :  4.155  43.436    427
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 32.56 %
    Favored  : 64.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.44), residues: 369
  helix: -0.55 (0.53), residues: 102
  sheet: -1.46 (0.46), residues: 93
  loop : -0.35 (0.50), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 115 
 TYR   0.012   0.001   TYR C 164 
 PHE   0.016   0.001   PHE C 165 
 TRP   0.007   0.001   TRP C 168 
 HIS   0.003   0.000   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 3146)
  covalent geometry    : angle       0.56454 ( 4230)
  SS BOND              : bond        0.00283 (   17)
  SS BOND              : angle       0.51207 (   34)
  hydrogen bonds       : bond        0.02557 (  109)
  hydrogen bonds       : angle       4.79845 (  288)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 ASP cc_start: 0.7823 (t0) cc_final: 0.7609 (t0)
REVERT: A   38 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7310 (ttp-110)
REVERT: B   58 LYS cc_start: 0.9224 (pttt) cc_final: 0.7944 (tptt)
REVERT: B  127 HIS cc_start: 0.7385 (OUTLIER) cc_final: 0.7092 (p-80)
REVERT: D  134 ARG cc_start: 0.8531 (mmm-85) cc_final: 0.7411 (mtt180)
REVERT: D  175 ASP cc_start: 0.8840 (p0) cc_final: 0.8489 (p0)
REVERT: C  134 ARG cc_start: 0.8755 (mmt180) cc_final: 0.7659 (mtt180)
REVERT: C  156 GLU cc_start: 0.7874 (tp30) cc_final: 0.7474 (mm-30)
REVERT: C  196 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8158 (mp0)
  outliers start: 10
  outliers final: 8
  residues processed: 107
  average time/residue: 0.0931
  time to fit residues: 11.4562
Evaluate side-chains
  105 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  127 HIS
Chi-restraints excluded: chain D residue  159 CYS
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  159 CYS
Chi-restraints excluded: chain C residue  176 TRP
Chi-restraints excluded: chain C residue  183 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 23 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
B  87 GLN
** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.092289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.079051 restraints weight = 7498.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.081342 restraints weight = 3685.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.082887 restraints weight = 2301.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.083931 restraints weight = 1669.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.084584 restraints weight = 1335.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.3061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3163  Z= 0.128
  Angle     :  0.581  10.285   4264  Z= 0.280
  Chirality :  0.036   0.112    433
  Planarity :  0.003   0.028    537
  Dihedral  :  4.113  41.652    427
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 31.99 %
    Favored  : 63.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.44), residues: 369
  helix: -0.41 (0.54), residues: 102
  sheet: -1.45 (0.45), residues: 93
  loop : -0.33 (0.50), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 115 
 TYR   0.013   0.001   TYR C 143 
 PHE   0.013   0.001   PHE C 165 
 TRP   0.005   0.001   TRP D 145 
 HIS   0.002   0.000   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 3146)
  covalent geometry    : angle       0.58148 ( 4230)
  SS BOND              : bond        0.00260 (   17)
  SS BOND              : angle       0.49718 (   34)
  hydrogen bonds       : bond        0.02454 (  109)
  hydrogen bonds       : angle       4.75447 (  288)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7301 (ttp-110)
REVERT: B   58 LYS cc_start: 0.9216 (pttt) cc_final: 0.7940 (tptt)
REVERT: B  127 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.7141 (p-80)
REVERT: D  134 ARG cc_start: 0.8521 (mmm-85) cc_final: 0.7503 (mtt180)
REVERT: D  175 ASP cc_start: 0.8857 (p0) cc_final: 0.8501 (p0)
REVERT: D  197 ASP cc_start: 0.8461 (t0) cc_final: 0.8177 (t0)
REVERT: C  134 ARG cc_start: 0.8807 (mmt180) cc_final: 0.7690 (mtt180)
REVERT: C  137 ASN cc_start: 0.9434 (OUTLIER) cc_final: 0.8631 (t0)
REVERT: C  156 GLU cc_start: 0.7891 (tp30) cc_final: 0.7538 (mm-30)
REVERT: C  196 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8133 (mp0)
  outliers start: 14
  outliers final: 9
  residues processed: 108
  average time/residue: 0.0890
  time to fit residues: 10.9740
Evaluate side-chains
  107 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ARG
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  127 HIS
Chi-restraints excluded: chain D residue  159 CYS
Chi-restraints excluded: chain C residue  137 ASN
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  159 CYS
Chi-restraints excluded: chain C residue  176 TRP
Chi-restraints excluded: chain C residue  183 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 26 optimal weight:   10.0000
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
B  87 GLN
** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.087970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.074930 restraints weight = 7773.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.077134 restraints weight = 3817.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.078612 restraints weight = 2401.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.079550 restraints weight = 1754.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.080212 restraints weight = 1428.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.3229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3163  Z= 0.220
  Angle     :  0.673   9.618   4264  Z= 0.331
  Chirality :  0.038   0.125    433
  Planarity :  0.004   0.031    537
  Dihedral  :  4.264  37.646    427
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 32.85 %
    Favored  : 62.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.44), residues: 369
  helix: -0.58 (0.53), residues: 102
  sheet: -1.33 (0.48), residues: 88
  loop : -0.36 (0.50), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 184 
 TYR   0.018   0.002   TYR C 164 
 PHE   0.012   0.002   PHE C 186 
 TRP   0.008   0.002   TRP C 168 
 HIS   0.003   0.001   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 3146)
  covalent geometry    : angle       0.67259 ( 4230)
  SS BOND              : bond        0.00396 (   17)
  SS BOND              : angle       0.75069 (   34)
  hydrogen bonds       : bond        0.02830 (  109)
  hydrogen bonds       : angle       4.89671 (  288)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: B   58 LYS cc_start: 0.9211 (pttt) cc_final: 0.8001 (tptt)
REVERT: B  127 HIS cc_start: 0.7519 (OUTLIER) cc_final: 0.7233 (p-80)
REVERT: D  134 ARG cc_start: 0.8640 (mmm-85) cc_final: 0.7554 (mtt180)
REVERT: D  175 ASP cc_start: 0.8879 (p0) cc_final: 0.8557 (p0)
REVERT: D  197 ASP cc_start: 0.8512 (t0) cc_final: 0.8291 (t0)
REVERT: C  137 ASN cc_start: 0.9395 (OUTLIER) cc_final: 0.8805 (t0)
REVERT: C  156 GLU cc_start: 0.7950 (tp30) cc_final: 0.7594 (mm-30)
  outliers start: 15
  outliers final: 9
  residues processed: 109
  average time/residue: 0.0881
  time to fit residues: 11.0249
Evaluate side-chains
  109 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  127 HIS
Chi-restraints excluded: chain D residue  159 CYS
Chi-restraints excluded: chain C residue  137 ASN
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  176 TRP
Chi-restraints excluded: chain C residue  183 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 1 optimal weight:    0.1980
   chunk 19 optimal weight:    0.0060
   chunk 8 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
B  87 GLN
** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.091674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.078684 restraints weight = 7761.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.080950 restraints weight = 3781.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.082456 restraints weight = 2344.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.083483 restraints weight = 1699.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.084179 restraints weight = 1355.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.3355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3163  Z= 0.114
  Angle     :  0.636   9.953   4264  Z= 0.304
  Chirality :  0.036   0.108    433
  Planarity :  0.003   0.029    537
  Dihedral  :  4.070  35.296    427
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 33.43 %
    Favored  : 63.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.44), residues: 369
  helix: -0.48 (0.53), residues: 102
  sheet: -1.41 (0.46), residues: 95
  loop : -0.20 (0.51), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 184 
 TYR   0.013   0.001   TYR C 143 
 PHE   0.023   0.002   PHE C 165 
 TRP   0.006   0.001   TRP C 168 
 HIS   0.002   0.000   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3146)
  covalent geometry    : angle       0.63736 ( 4230)
  SS BOND              : bond        0.00219 (   17)
  SS BOND              : angle       0.44383 (   34)
  hydrogen bonds       : bond        0.02420 (  109)
  hydrogen bonds       : angle       4.72787 (  288)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
REVERT: B   58 LYS cc_start: 0.9199 (pttt) cc_final: 0.7917 (tptt)
REVERT: B  127 HIS cc_start: 0.7332 (OUTLIER) cc_final: 0.6970 (p-80)
REVERT: D  134 ARG cc_start: 0.8544 (mmm-85) cc_final: 0.7501 (mtt180)
REVERT: D  175 ASP cc_start: 0.8873 (p0) cc_final: 0.8514 (p0)
REVERT: C  137 ASN cc_start: 0.9307 (OUTLIER) cc_final: 0.8779 (t0)
REVERT: C  156 GLU cc_start: 0.7868 (tp30) cc_final: 0.7565 (mm-30)
  outliers start: 12
  outliers final: 10
  residues processed: 107
  average time/residue: 0.0819
  time to fit residues: 10.2039
Evaluate side-chains
  109 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  127 HIS
Chi-restraints excluded: chain D residue  159 CYS
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain C residue  137 ASN
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  176 TRP
Chi-restraints excluded: chain C residue  183 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 9 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
B  87 GLN
** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.091375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.078109 restraints weight = 7860.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.080407 restraints weight = 3914.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.081903 restraints weight = 2454.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.082940 restraints weight = 1795.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.083590 restraints weight = 1440.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3163  Z= 0.135
  Angle     :  0.640  10.210   4264  Z= 0.310
  Chirality :  0.036   0.112    433
  Planarity :  0.004   0.030    537
  Dihedral  :  4.076  32.803    427
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 33.43 %
    Favored  : 63.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.44), residues: 369
  helix: -0.49 (0.53), residues: 102
  sheet: -1.48 (0.45), residues: 97
  loop : -0.23 (0.51), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 184 
 TYR   0.012   0.001   TYR C 143 
 PHE   0.031   0.002   PHE C 153 
 TRP   0.007   0.001   TRP C 168 
 HIS   0.003   0.001   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 3146)
  covalent geometry    : angle       0.64067 ( 4230)
  SS BOND              : bond        0.00258 (   17)
  SS BOND              : angle       0.48223 (   34)
  hydrogen bonds       : bond        0.02364 (  109)
  hydrogen bonds       : angle       4.71384 (  288)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
REVERT: B   58 LYS cc_start: 0.9206 (pttt) cc_final: 0.7984 (tptt)
REVERT: B  127 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.7035 (p-80)
REVERT: D  134 ARG cc_start: 0.8570 (mmm-85) cc_final: 0.7522 (mtt180)
REVERT: D  154 GLN cc_start: 0.8591 (mt0) cc_final: 0.8341 (mt0)
REVERT: D  175 ASP cc_start: 0.8849 (p0) cc_final: 0.8479 (p0)
REVERT: D  197 ASP cc_start: 0.8286 (t0) cc_final: 0.7728 (t0)
REVERT: C  137 ASN cc_start: 0.9291 (OUTLIER) cc_final: 0.8762 (t0)
REVERT: C  156 GLU cc_start: 0.7899 (tp30) cc_final: 0.7619 (mm-30)
REVERT: C  175 ASP cc_start: 0.8343 (m-30) cc_final: 0.8131 (m-30)
  outliers start: 12
  outliers final: 10
  residues processed: 107
  average time/residue: 0.0782
  time to fit residues: 9.6906
Evaluate side-chains
  111 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  106 LEU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  127 HIS
Chi-restraints excluded: chain D residue  159 CYS
Chi-restraints excluded: chain D residue  180 SER
Chi-restraints excluded: chain C residue  137 ASN
Chi-restraints excluded: chain C residue  147 THR
Chi-restraints excluded: chain C residue  183 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 33 optimal weight:    0.4980
   chunk 1 optimal weight:    0.3980
   chunk 26 optimal weight:    8.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  87 GLN
** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.092683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.079543 restraints weight = 7699.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.081820 restraints weight = 3793.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.083330 restraints weight = 2382.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.084354 restraints weight = 1729.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.085042 restraints weight = 1391.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3163  Z= 0.121
  Angle     :  0.684  10.783   4264  Z= 0.327
  Chirality :  0.036   0.136    433
  Planarity :  0.003   0.030    537
  Dihedral  :  3.710  15.815    425
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 34.29 %
    Favored  : 63.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.11 (0.44), residues: 369
  helix: -0.53 (0.53), residues: 102
  sheet: -1.41 (0.45), residues: 97
  loop : -0.21 (0.51), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 184 
 TYR   0.015   0.001   TYR C 143 
 PHE   0.033   0.002   PHE C 153 
 TRP   0.007   0.001   TRP C 145 
 HIS   0.002   0.000   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 3146)
  covalent geometry    : angle       0.68550 ( 4230)
  SS BOND              : bond        0.00217 (   17)
  SS BOND              : angle       0.43358 (   34)
  hydrogen bonds       : bond        0.02300 (  109)
  hydrogen bonds       : angle       4.77342 (  288)

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

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

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  738 Ramachandran restraints generated.
    369 Oldfield, 0 Emsley, 369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
REVERT: B   58 LYS cc_start: 0.9200 (pttt) cc_final: 0.7983 (tptt)
REVERT: B  127 HIS cc_start: 0.7317 (OUTLIER) cc_final: 0.7017 (p-80)
REVERT: D  134 ARG cc_start: 0.8534 (mmm-85) cc_final: 0.7459 (mtt180)
REVERT: D  154 GLN cc_start: 0.8565 (mt0) cc_final: 0.8324 (mt0)
REVERT: D  175 ASP cc_start: 0.8837 (p0) cc_final: 0.8463 (p0)
REVERT: D  197 ASP cc_start: 0.8329 (t0) cc_final: 0.7796 (t0)
REVERT: C  137 ASN cc_start: 0.9248 (OUTLIER) cc_final: 0.8785 (t0)
REVERT: C  153 PHE cc_start: 0.8470 (m-80) cc_final: 0.8265 (m-80)
REVERT: C  156 GLU cc_start: 0.7894 (tp30) cc_final: 0.7682 (mm-30)
  outliers start: 9
  outliers final: 7
  residues processed: 100
  average time/residue: 0.0777
  time to fit residues: 8.9413
Evaluate side-chains
  105 residues out of total 347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain B residue   78 LEU
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  124 LEU
Chi-restraints excluded: chain B residue  127 HIS
Chi-restraints excluded: chain D residue  159 CYS
Chi-restraints excluded: chain C residue  137 ASN
Chi-restraints excluded: chain C residue  183 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0030
   chunk 3 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 5 optimal weight:    0.1980
   chunk 26 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
B  87 GLN
** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.094587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.081225 restraints weight = 7673.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.083573 restraints weight = 3744.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.085113 restraints weight = 2340.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.086158 restraints weight = 1694.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.086837 restraints weight = 1356.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.3567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3163  Z= 0.113
  Angle     :  0.665  11.054   4264  Z= 0.315
  Chirality :  0.036   0.120    433
  Planarity :  0.003   0.030    537
  Dihedral  :  3.618  14.112    425
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 33.72 %
    Favored  : 63.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.44), residues: 369
  helix: -0.52 (0.53), residues: 102
  sheet: -1.35 (0.46), residues: 97
  loop : -0.13 (0.52), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 184 
 TYR   0.016   0.001   TYR C 143 
 PHE   0.033   0.002   PHE C 153 
 TRP   0.008   0.001   TRP C 145 
 HIS   0.002   0.000   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 3146)
  covalent geometry    : angle       0.66669 ( 4230)
  SS BOND              : bond        0.00210 (   17)
  SS BOND              : angle       0.40196 (   34)
  hydrogen bonds       : bond        0.02260 (  109)
  hydrogen bonds       : angle       4.69456 (  288)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 961.07 seconds
wall clock time: 17 minutes 16.72 seconds (1036.72 seconds total)