Starting phenix.real_space_refine
on Tue Feb 11 08:11:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ey2_28666/02_2025/8ey2_28666.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ey2_28666/02_2025/8ey2_28666.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ey2_28666/02_2025/8ey2_28666.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ey2_28666/02_2025/8ey2_28666.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ey2_28666/02_2025/8ey2_28666.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ey2_28666/02_2025/8ey2_28666.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    3108      2.51       5
     N     836      2.21       5
     O     918      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4908
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2370
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 306, 2367
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 13, 'TRANS': 292}
      Conformer: "B"
        Number of residues, atoms: 306, 2367
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 13, 'TRANS': 292}
          bond proxies already assigned to first conformer: 2416
    Chain: "C"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 84
          Classifications: {'peptide': 11}
          Link IDs: {'TRANS': 10}
    Chain: "D"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 84
          Classifications: {'peptide': 11}
          Link IDs: {'TRANS': 10}
    Chain: "B"
      Number of atoms: 2370
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 306, 2367
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 13, 'TRANS': 292}
      Conformer: "B"
        Number of residues, atoms: 306, 2367
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 13, 'TRANS': 292}
          bond proxies already assigned to first conformer: 2416
  Time building chain proxies: 5.32, per 1000 atoms: 1.08
  Number of scatterers: 4908
  At special positions: 0
  Unit cell: (72.483, 86.849, 74.442, 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      46     16.00
     O     918      8.00
     N     836      7.00
     C    3108      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: 1.08
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1164

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 7 sheets defined
      27.8% alpha, 25.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 15
    Processing helix  chain 'A' and resid 41 through 43
      No H-bonds generated for 'chain 'A' and resid 41 through 43'
    Processing helix  chain 'A' and resid 53 through 61
    Processing helix  chain 'A' and resid 200 through 215
    Processing helix  chain 'A' and resid 226 through 237
    Processing helix  chain 'A' and resid 243 through 250
    Processing helix  chain 'A' and resid 250 through 258
    Processing helix  chain 'A' and resid 260 through 275
    Processing helix  chain 'A' and resid 292 through 300
    Processing helix  chain 'B' and resid 10 through 15
    Processing helix  chain 'B' and resid 41 through 43
      No H-bonds generated for 'chain 'B' and resid 41 through 43'
    Processing helix  chain 'B' and resid 53 through 61
    Processing helix  chain 'B' and resid 200 through 215
    Processing helix  chain 'B' and resid 226 through 237
    Processing helix  chain 'B' and resid 243 through 250
    Processing helix  chain 'B' and resid 250 through 258
    Processing helix  chain 'B' and resid 260 through 275
      removed outlier: 3.549A  pdb=" N   MET B 264 " --> pdb=" O   ALA B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 300
    Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 75
      removed outlier: 3.960A  pdb=" N   VAL A  68 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   ASN A  28 " --> pdb=" O   PRO A  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 75
      removed outlier: 3.960A  pdb=" N   VAL A  68 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103
      removed outlier: 6.072A  pdb=" N   LYS A 102 " --> pdb=" O   PHE A 159 " (cutoff:3.500A)
      removed outlier: 7.723A  pdb=" N   TYR A 161 " --> pdb=" O   LYS A 102 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   GLY A 149 " --> pdb=" O   CYS A 160 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   VAL A 148 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      removed outlier: 7.922A  pdb=" N   ILE A 152 " --> pdb=" O   THR A 111 " (cutoff:3.500A)
      removed outlier: 11.604A  pdb=" N   THR A 111 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   TYR A 118 " --> pdb=" O   PRO A 122 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103
      removed outlier: 6.072A  pdb=" N   LYS A 102 " --> pdb=" O   PHE A 159 " (cutoff:3.500A)
      removed outlier: 7.723A  pdb=" N   TYR A 161 " --> pdb=" O   LYS A 102 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ALA A 173 " --> pdb=" O   HIS A 164 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 75
      removed outlier: 3.949A  pdb=" N   VAL B  68 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   ASN B  28 " --> pdb=" O   PRO B  39 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 103
      removed outlier: 6.120A  pdb=" N   LYS B 102 " --> pdb=" O   PHE B 159 " (cutoff:3.500A)
      removed outlier: 7.903A  pdb=" N   ILE B 152 " --> pdb=" O   THR B 111 " (cutoff:3.500A)
      removed outlier: 11.637A  pdb=" N   THR B 111 " --> pdb=" O   ILE B 152 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   TYR B 118 " --> pdb=" O   PRO B 122 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 162 through 166
      removed outlier: 6.904A  pdb=" N   ALA B 173 " --> pdb=" O   HIS B 164 " (cutoff:3.500A)

    206 hydrogen bonds defined for protein.
    576 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: 1.38

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1612
        1.34 -     1.46: 1160
        1.46 -     1.58: 2176
        1.58 -     1.70: 0
        1.70 -     1.81: 68
  Bond restraints: 5016
  Sorted by residual:
  bond pdb=" CG  LEU B  32 "
       pdb=" CD1 LEU B  32 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.08e+00
  bond pdb=" CB  MET A 264 "
       pdb=" CG  MET A 264 "
    ideal  model  delta    sigma   weight residual
    1.520  1.491  0.029 3.00e-02 1.11e+03 9.04e-01
  bond pdb=" CG  LEU B 272 "
       pdb=" CD1 LEU B 272 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.03e-01
  bond pdb=" CG  LEU C  -1 "
       pdb=" CD2 LEU C  -1 "
    ideal  model  delta    sigma   weight residual
    1.521  1.493  0.028 3.30e-02 9.18e+02 6.95e-01
  bond pdb=" CB  THR B 175 "
       pdb=" CG2 THR B 175 "
    ideal  model  delta    sigma   weight residual
    1.521  1.494  0.027 3.30e-02 9.18e+02 6.59e-01
  ... (remaining 5011 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 6682
        1.94 -     3.88: 119
        3.88 -     5.82: 6
        5.82 -     7.75: 1
        7.75 -     9.69: 2
  Bond angle restraints: 6810
  Sorted by residual:
  angle pdb=" N   VAL B  13 "
        pdb=" CA  VAL B  13 "
        pdb=" C   VAL B  13 "
      ideal   model   delta    sigma   weight residual
     112.96  109.13    3.83 1.00e+00 1.00e+00 1.46e+01
  angle pdb=" N   VAL A  13 "
        pdb=" CA  VAL A  13 "
        pdb=" C   VAL A  13 "
      ideal   model   delta    sigma   weight residual
     112.96  109.20    3.76 1.00e+00 1.00e+00 1.41e+01
  angle pdb=" CA  LEU C  -1 "
        pdb=" CB  LEU C  -1 "
        pdb=" CG  LEU C  -1 "
      ideal   model   delta    sigma   weight residual
     116.30  125.99   -9.69 3.50e+00 8.16e-02 7.67e+00
  angle pdb=" CA  LEU D  -1 "
        pdb=" CB  LEU D  -1 "
        pdb=" CG  LEU D  -1 "
      ideal   model   delta    sigma   weight residual
     116.30  125.27   -8.97 3.50e+00 8.16e-02 6.57e+00
  angle pdb=" C   VAL C  -2 "
        pdb=" N   LEU C  -1 "
        pdb=" CA  LEU C  -1 "
      ideal   model   delta    sigma   weight residual
     121.26  124.71   -3.45 1.59e+00 3.96e-01 4.70e+00
  ... (remaining 6805 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.12: 2616
       14.12 -    28.24: 240
       28.24 -    42.35: 88
       42.35 -    56.47: 12
       56.47 -    70.59: 6
  Dihedral angle restraints: 2962
    sinusoidal: 1142
      harmonic: 1820
  Sorted by residual:
  dihedral pdb=" CA  GLN C   0 "
           pdb=" C   GLN C   0 "
           pdb=" N   SER C   1 "
           pdb=" CA  SER C   1 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.93   23.07     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  LEU C  -1 "
           pdb=" C   LEU C  -1 "
           pdb=" N   GLN C   0 "
           pdb=" CA  GLN C   0 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.79  -21.21     0      5.00e+00 4.00e-02 1.80e+01
  dihedral pdb=" CA  THR B 175 "
           pdb=" C   THR B 175 "
           pdb=" N   ASP B 176 "
           pdb=" CA  ASP B 176 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.67   20.33     0      5.00e+00 4.00e-02 1.65e+01
  ... (remaining 2959 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 447
       0.031 -    0.062: 218
       0.062 -    0.093: 74
       0.093 -    0.123: 27
       0.123 -    0.154: 2
  Chirality restraints: 768
  Sorted by residual:
  chirality pdb=" CG  LEU D  -1 "
            pdb=" CB  LEU D  -1 "
            pdb=" CD1 LEU D  -1 "
            pdb=" CD2 LEU D  -1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.95e-01
  chirality pdb=" CA  VAL C  -2 "
            pdb=" N   VAL C  -2 "
            pdb=" C   VAL C  -2 "
            pdb=" CB  VAL C  -2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.18e-01
  chirality pdb=" CA  ILE B 281 "
            pdb=" N   ILE B 281 "
            pdb=" C   ILE B 281 "
            pdb=" CB  ILE B 281 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.24e-01
  ... (remaining 765 not shown)

  Planarity restraints: 884
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A  51 "    0.036 5.00e-02 4.00e+02   5.47e-02 4.78e+00
        pdb=" N   PRO A  52 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A  52 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A  52 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B  51 "   -0.036 5.00e-02 4.00e+02   5.47e-02 4.78e+00
        pdb=" N   PRO B  52 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO B  52 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B  52 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D   3 "    0.011 2.00e-02 2.50e+03   1.11e-02 2.15e+00
        pdb=" CG  PHE D   3 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 PHE D   3 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE D   3 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE D   3 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE D   3 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE D   3 "    0.002 2.00e-02 2.50e+03
  ... (remaining 881 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 134
        2.70 -     3.25: 4949
        3.25 -     3.80: 8026
        3.80 -     4.35: 10191
        4.35 -     4.90: 17041
  Nonbonded interactions: 40341
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 292 "
            pdb=" OD2 ASP A 295 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" OG1 THR B 292 "
            pdb=" OD2 ASP B 295 "
     model   vdw
     2.152 3.040
  nonbonded pdb=" OH  TYR A 209 "
            pdb=" OG  SER A 254 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" O   THR A  26 "
            pdb=" OG  SER C   1 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" OG1 THR B  45 "
            pdb=" OD1 ASP B  48 "
     model   vdw
     2.217 3.040
  ... (remaining 40336 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 116 or resid 118 through 306))
  selection = (chain 'B' and (resid 1 through 116 or resid 118 through 306))
}
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=0.17 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:             0.550
  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:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     18.720
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
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      :  0.003   0.034   5016  Z= 0.189
  Angle     :  0.600   9.693   6810  Z= 0.315
  Chirality :  0.042   0.154    768
  Planarity :  0.005   0.055    884
  Dihedral  : 13.039  70.588   1798
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.29 (0.35), residues: 628
  helix:  1.88 (0.44), residues: 150
  sheet: -1.02 (0.54), residues: 102
  loop : -0.82 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 218 
 HIS   0.007   0.001   HIS A  41 
 PHE   0.026   0.001   PHE D   3 
 TYR   0.024   0.002   TYR A 239 
 ARG   0.002   0.000   ARG D   4 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ASP cc_start: 0.8298 (p0) cc_final: 0.7777 (p0)
REVERT: A   49 MET cc_start: 0.5976 (mmt) cc_final: 0.5328 (tpp)
REVERT: A  100 LYS cc_start: 0.8860 (mtpt) cc_final: 0.8622 (mtpp)
REVERT: A  121 SER cc_start: 0.8685 (m) cc_final: 0.8476 (p)
REVERT: A  214 ASN cc_start: 0.8538 (t0) cc_final: 0.8086 (t0)
REVERT: A  232 LEU cc_start: 0.7767 (mt) cc_final: 0.7127 (mp)
REVERT: A  286 LEU cc_start: 0.8563 (mt) cc_final: 0.8051 (pt)
REVERT: C    4 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7848 (ttp80)
REVERT: B   34 ASP cc_start: 0.8166 (p0) cc_final: 0.7786 (p0)
REVERT: B  121 SER cc_start: 0.8664 (m) cc_final: 0.8438 (p)
REVERT: B  214 ASN cc_start: 0.8604 (t0) cc_final: 0.8103 (t0)
REVERT: B  232 LEU cc_start: 0.7754 (mt) cc_final: 0.7142 (mp)
REVERT: B  286 LEU cc_start: 0.8542 (mt) cc_final: 0.8058 (pt)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.1786
  time to fit residues: 38.8273
Evaluate side-chains
  136 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 46 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0070
   chunk 29 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.8800

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

Flipped N/Q/H residues before XYZ refinement:
A  80 HIS
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 HIS ** 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 = 0.3901 r_free = 0.3901 target = 0.138276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.117994 restraints weight = 13395.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.123380 restraints weight = 5362.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.126825 restraints weight = 2939.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3726
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3726 r_free = 0.3726    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3726 r_free = 0.3726    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3726
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.1936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5016  Z= 0.200
  Angle     :  0.662   9.415   6810  Z= 0.337
  Chirality :  0.043   0.200    768
  Planarity :  0.005   0.045    884
  Dihedral  :  5.121  20.673    680
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 11.90 %
    Favored  : 86.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.33), residues: 628
  helix:  0.71 (0.38), residues: 168
  sheet: -0.98 (0.53), residues: 102
  loop : -0.92 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 218 
 HIS   0.009   0.001   HIS B  41 
 PHE   0.015   0.001   PHE D   3 
 TYR   0.010   0.002   TYR A 239 
 ARG   0.002   0.000   ARG A  40 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 134
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ASP cc_start: 0.8314 (p0) cc_final: 0.7759 (p0)
REVERT: A   49 MET cc_start: 0.5924 (mmt) cc_final: 0.4372 (mmm)
REVERT: A  214 ASN cc_start: 0.8596 (t0) cc_final: 0.8205 (t0)
REVERT: A  286 LEU cc_start: 0.8537 (mt) cc_final: 0.8068 (pt)
REVERT: C    4 ARG cc_start: 0.8336 (ttt90) cc_final: 0.7902 (ttp80)
REVERT: B   34 ASP cc_start: 0.8194 (p0) cc_final: 0.7761 (p0)
REVERT: B  214 ASN cc_start: 0.8748 (t0) cc_final: 0.8451 (t0)
REVERT: B  286 LEU cc_start: 0.8530 (mt) cc_final: 0.8053 (pt)
  outliers start: 9
  outliers final: 6
  residues processed: 134
  average time/residue: 0.1536
  time to fit residues: 26.7931
Evaluate side-chains
  128 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 122
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain C residue    1 SER
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  166 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   chunk 38 optimal weight:    9.9990
   chunk 51 optimal weight:   10.0000
   chunk 18 optimal weight:    7.9990
   chunk 11 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 27 optimal weight:   10.0000
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.138528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.118681 restraints weight = 12426.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.124004 restraints weight = 5071.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.127356 restraints weight = 2811.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3740
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3740 r_free = 0.3740    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3740 r_free = 0.3740    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3740
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5016  Z= 0.191
  Angle     :  0.623   7.508   6810  Z= 0.318
  Chirality :  0.042   0.138    768
  Planarity :  0.004   0.040    884
  Dihedral  :  5.073  20.776    680
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 14.65 %
    Favored  : 83.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.98 (0.32), residues: 628
  helix:  0.46 (0.37), residues: 172
  sheet: -2.16 (0.65), residues: 56
  loop : -0.92 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 218 
 HIS   0.008   0.001   HIS B  41 
 PHE   0.011   0.001   PHE B 181 
 TYR   0.022   0.002   TYR B 161 
 ARG   0.002   0.000   ARG B  40 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ASP cc_start: 0.8285 (p0) cc_final: 0.7722 (p0)
REVERT: A   49 MET cc_start: 0.6092 (mmt) cc_final: 0.5696 (tpp)
REVERT: A  214 ASN cc_start: 0.8591 (t0) cc_final: 0.8174 (t0)
REVERT: A  286 LEU cc_start: 0.8527 (mt) cc_final: 0.8019 (pt)
REVERT: C    4 ARG cc_start: 0.8409 (ttt90) cc_final: 0.7963 (ttp80)
REVERT: B   34 ASP cc_start: 0.8203 (p0) cc_final: 0.7771 (p0)
REVERT: B  286 LEU cc_start: 0.8437 (mt) cc_final: 0.7955 (pt)
  outliers start: 12
  outliers final: 9
  residues processed: 116
  average time/residue: 0.1734
  time to fit residues: 25.8374
Evaluate side-chains
  121 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain C residue    1 SER
Chi-restraints excluded: chain D residue    1 SER
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  166 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 2 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 45 optimal weight:    0.8980
   chunk 56 optimal weight:   10.0000
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.136924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.114789 restraints weight = 17574.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.120694 restraints weight = 6299.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.124539 restraints weight = 3300.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3715
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3715 r_free = 0.3715    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3715 r_free = 0.3715    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3715
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.2668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5016  Z= 0.207
  Angle     :  0.601   8.045   6810  Z= 0.310
  Chirality :  0.042   0.130    768
  Planarity :  0.004   0.037    884
  Dihedral  :  5.004  22.185    680
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.02 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.33), residues: 628
  helix:  0.94 (0.39), residues: 172
  sheet: -1.18 (0.54), residues: 90
  loop : -0.85 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 218 
 HIS   0.008   0.001   HIS B  41 
 PHE   0.012   0.001   PHE B 181 
 TYR   0.030   0.002   TYR B 161 
 ARG   0.001   0.000   ARG B 298 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ASP cc_start: 0.8260 (p0) cc_final: 0.7668 (p0)
REVERT: A  214 ASN cc_start: 0.8633 (t0) cc_final: 0.8229 (t0)
REVERT: A  286 LEU cc_start: 0.8508 (mt) cc_final: 0.8044 (pt)
REVERT: C    4 ARG cc_start: 0.8536 (ttt90) cc_final: 0.8028 (ttp80)
REVERT: D   -1 LEU cc_start: 0.8281 (tt) cc_final: 0.7895 (tt)
REVERT: B   34 ASP cc_start: 0.8243 (p0) cc_final: 0.7861 (p0)
REVERT: B  286 LEU cc_start: 0.8469 (mt) cc_final: 0.7996 (pt)
  outliers start: 13
  outliers final: 11
  residues processed: 118
  average time/residue: 0.1576
  time to fit residues: 24.3914
Evaluate side-chains
  121 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain C residue    1 SER
Chi-restraints excluded: chain D residue    1 SER
Chi-restraints excluded: chain B residue   28 ASN
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  166 GLU
Chi-restraints excluded: chain B residue  263 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 60 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9990
   chunk 34 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.137893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.116979 restraints weight = 14479.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.122578 restraints weight = 5574.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.126199 restraints weight = 3011.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3732
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3732 r_free = 0.3732    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3732 r_free = 0.3732    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3732
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.2874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5016  Z= 0.183
  Angle     :  0.605   8.501   6810  Z= 0.314
  Chirality :  0.042   0.215    768
  Planarity :  0.004   0.037    884
  Dihedral  :  4.983  23.141    680
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.12 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.33), residues: 628
  helix:  0.93 (0.39), residues: 172
  sheet: -1.66 (0.54), residues: 78
  loop : -0.92 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 218 
 HIS   0.005   0.001   HIS A  41 
 PHE   0.010   0.001   PHE B 181 
 TYR   0.030   0.002   TYR B 161 
 ARG   0.001   0.000   ARG B 298 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.578 
Fit side-chains
REVERT: A   34 ASP cc_start: 0.8262 (p0) cc_final: 0.7688 (p0)
REVERT: A   49 MET cc_start: 0.6497 (mmt) cc_final: 0.5701 (mmm)
REVERT: A  119 ASN cc_start: 0.7930 (t0) cc_final: 0.7653 (t0)
REVERT: A  214 ASN cc_start: 0.8658 (t0) cc_final: 0.8275 (t0)
REVERT: A  232 LEU cc_start: 0.7884 (mt) cc_final: 0.7148 (mp)
REVERT: A  286 LEU cc_start: 0.8498 (mt) cc_final: 0.8015 (pt)
REVERT: C    4 ARG cc_start: 0.8553 (ttt90) cc_final: 0.8028 (ttp80)
REVERT: B   34 ASP cc_start: 0.8242 (p0) cc_final: 0.7882 (p0)
REVERT: B  119 ASN cc_start: 0.7921 (t0) cc_final: 0.7632 (t0)
REVERT: B  286 LEU cc_start: 0.8485 (mt) cc_final: 0.7960 (pt)
  outliers start: 13
  outliers final: 11
  residues processed: 118
  average time/residue: 0.1448
  time to fit residues: 22.7173
Evaluate side-chains
  115 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ASN
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain C residue    1 SER
Chi-restraints excluded: chain D residue    1 SER
Chi-restraints excluded: chain B residue   28 ASN
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  181 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 35 optimal weight:    0.4980
   chunk 51 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 30 optimal weight:    7.9990
   chunk 23 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 16 optimal weight:    0.0010
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.8788

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

Flipped N/Q/H residues before XYZ refinement:
** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.136994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.116137 restraints weight = 13982.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.121493 restraints weight = 5485.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.125012 restraints weight = 3030.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3724
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3724 r_free = 0.3724    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3724 r_free = 0.3724    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3724
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5016  Z= 0.174
  Angle     :  0.620   8.209   6810  Z= 0.319
  Chirality :  0.042   0.150    768
  Planarity :  0.004   0.037    884
  Dihedral  :  4.926  22.475    680
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.58 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.32), residues: 628
  helix:  0.71 (0.38), residues: 172
  sheet: -1.67 (0.54), residues: 78
  loop : -0.94 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 218 
 HIS   0.008   0.001   HIS B  41 
 PHE   0.009   0.001   PHE A 181 
 TYR   0.031   0.002   TYR B 161 
 ARG   0.001   0.000   ARG B   4 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 0.577 
Fit side-chains
REVERT: A   34 ASP cc_start: 0.8277 (p0) cc_final: 0.7700 (p0)
REVERT: A   49 MET cc_start: 0.6559 (mmt) cc_final: 0.5827 (mmm)
REVERT: A  119 ASN cc_start: 0.7930 (t0) cc_final: 0.7645 (t0)
REVERT: A  214 ASN cc_start: 0.8648 (t0) cc_final: 0.8266 (t0)
REVERT: A  286 LEU cc_start: 0.8484 (mt) cc_final: 0.8035 (pt)
REVERT: C    4 ARG cc_start: 0.8576 (ttt90) cc_final: 0.8059 (ttp80)
REVERT: B   34 ASP cc_start: 0.8251 (p0) cc_final: 0.7900 (p0)
REVERT: B  119 ASN cc_start: 0.7904 (t0) cc_final: 0.7605 (t0)
REVERT: B  286 LEU cc_start: 0.8465 (mt) cc_final: 0.7953 (pt)
  outliers start: 14
  outliers final: 12
  residues processed: 113
  average time/residue: 0.1347
  time to fit residues: 20.4264
Evaluate side-chains
  116 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ASN
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain C residue    1 SER
Chi-restraints excluded: chain D residue    1 SER
Chi-restraints excluded: chain B residue   28 ASN
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  181 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.133262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.111004 restraints weight = 17911.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.116908 restraints weight = 6331.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.120708 restraints weight = 3307.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3659
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3659 r_free = 0.3659    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3659 r_free = 0.3659    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3659
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.3098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5016  Z= 0.271
  Angle     :  0.643   8.748   6810  Z= 0.331
  Chirality :  0.043   0.175    768
  Planarity :  0.004   0.037    884
  Dihedral  :  5.122  24.099    680
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.77 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.69 (0.33), residues: 628
  helix:  1.04 (0.39), residues: 170
  sheet: -2.21 (0.64), residues: 56
  loop : -0.87 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 218 
 HIS   0.010   0.002   HIS B  41 
 PHE   0.012   0.001   PHE B 181 
 TYR   0.031   0.002   TYR B 161 
 ARG   0.002   0.000   ARG B  40 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 ASP cc_start: 0.8300 (p0) cc_final: 0.7847 (p0)
REVERT: A   49 MET cc_start: 0.6889 (mmt) cc_final: 0.6634 (mmm)
REVERT: A  119 ASN cc_start: 0.8076 (t0) cc_final: 0.7820 (t0)
REVERT: A  214 ASN cc_start: 0.8710 (t0) cc_final: 0.8300 (t0)
REVERT: A  286 LEU cc_start: 0.8497 (mt) cc_final: 0.8066 (pt)
REVERT: C    4 ARG cc_start: 0.8641 (ttt90) cc_final: 0.8049 (ttp80)
REVERT: B  119 ASN cc_start: 0.8039 (t0) cc_final: 0.7781 (t0)
REVERT: B  286 LEU cc_start: 0.8508 (mt) cc_final: 0.8000 (pt)
  outliers start: 15
  outliers final: 11
  residues processed: 118
  average time/residue: 0.1391
  time to fit residues: 22.0353
Evaluate side-chains
  113 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ASN
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain C residue    1 SER
Chi-restraints excluded: chain B residue   28 ASN
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  181 PHE
Chi-restraints excluded: chain B residue  263 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 38 optimal weight:    7.9990
   chunk 0 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 8 optimal weight:    8.9990
   chunk 50 optimal weight:    7.9990
   chunk 49 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 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 = 0.3816 r_free = 0.3816 target = 0.132513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.112628 restraints weight = 11540.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.117731 restraints weight = 4867.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.120961 restraints weight = 2768.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3690
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3690 r_free = 0.3690    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3689 r_free = 0.3689    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3689
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.3280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5016  Z= 0.279
  Angle     :  0.646   9.261   6810  Z= 0.333
  Chirality :  0.043   0.187    768
  Planarity :  0.004   0.037    884
  Dihedral  :  5.246  24.937    680
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 19.23 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.33), residues: 628
  helix:  0.99 (0.39), residues: 170
  sheet: -2.35 (0.63), residues: 56
  loop : -0.89 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 218 
 HIS   0.009   0.002   HIS B  41 
 PHE   0.011   0.001   PHE B 181 
 TYR   0.029   0.002   TYR B 161 
 ARG   0.002   0.000   ARG B  40 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LEU cc_start: 0.8762 (tp) cc_final: 0.8468 (tt)
REVERT: A   95 ASN cc_start: 0.8772 (t0) cc_final: 0.8568 (t0)
REVERT: A  119 ASN cc_start: 0.8067 (t0) cc_final: 0.7857 (t0)
REVERT: A  214 ASN cc_start: 0.8699 (t0) cc_final: 0.8269 (t0)
REVERT: A  286 LEU cc_start: 0.8490 (mt) cc_final: 0.8091 (pt)
REVERT: C    4 ARG cc_start: 0.8671 (ttt90) cc_final: 0.8100 (ttp80)
REVERT: B   34 ASP cc_start: 0.8272 (p0) cc_final: 0.7931 (p0)
REVERT: B  119 ASN cc_start: 0.8097 (t0) cc_final: 0.7843 (t0)
REVERT: B  286 LEU cc_start: 0.8507 (mt) cc_final: 0.8078 (pt)
  outliers start: 11
  outliers final: 10
  residues processed: 120
  average time/residue: 0.1371
  time to fit residues: 22.2280
Evaluate side-chains
  116 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ASN
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain B residue   28 ASN
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  181 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 23 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   chunk 35 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 56 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 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 = 0.3838 r_free = 0.3838 target = 0.134090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.112644 restraints weight = 16942.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.118357 restraints weight = 6162.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.122114 restraints weight = 3253.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3672
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3672 r_free = 0.3672    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3671 r_free = 0.3671    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3671
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5016  Z= 0.228
  Angle     :  0.634   9.002   6810  Z= 0.326
  Chirality :  0.043   0.165    768
  Planarity :  0.004   0.037    884
  Dihedral  :  5.220  25.536    680
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 19.41 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.33), residues: 628
  helix:  1.04 (0.39), residues: 170
  sheet: -2.40 (0.63), residues: 56
  loop : -0.93 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 218 
 HIS   0.007   0.001   HIS B  41 
 PHE   0.011   0.001   PHE B 181 
 TYR   0.030   0.002   TYR B 161 
 ARG   0.001   0.000   ARG B  40 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.446 
Fit side-chains
REVERT: A   34 ASP cc_start: 0.8246 (p0) cc_final: 0.7923 (p0)
REVERT: A   58 LEU cc_start: 0.8773 (tp) cc_final: 0.8505 (tt)
REVERT: A   95 ASN cc_start: 0.8778 (t0) cc_final: 0.8563 (t0)
REVERT: A  214 ASN cc_start: 0.8677 (t0) cc_final: 0.8265 (t0)
REVERT: A  286 LEU cc_start: 0.8471 (mt) cc_final: 0.8078 (pt)
REVERT: C    0 GLN cc_start: 0.6985 (mp10) cc_final: 0.6429 (mp10)
REVERT: C    4 ARG cc_start: 0.8681 (ttt90) cc_final: 0.8210 (ttp80)
REVERT: B   34 ASP cc_start: 0.8246 (p0) cc_final: 0.7840 (p0)
REVERT: B  119 ASN cc_start: 0.8092 (t0) cc_final: 0.7832 (t0)
REVERT: B  286 LEU cc_start: 0.8506 (mt) cc_final: 0.8079 (pt)
  outliers start: 13
  outliers final: 11
  residues processed: 119
  average time/residue: 0.1364
  time to fit residues: 22.0318
Evaluate side-chains
  122 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ASN
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue   81 SER
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain C residue    1 SER
Chi-restraints excluded: chain B residue   28 ASN
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  181 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 42 optimal weight:    0.6980
   chunk 31 optimal weight:    0.4980
   chunk 36 optimal weight:    0.5980
   chunk 41 optimal weight:    4.9990
   chunk 11 optimal weight:    0.4980
   chunk 7 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 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 = 0.3881 r_free = 0.3881 target = 0.137376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.117545 restraints weight = 12413.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.122749 restraints weight = 5085.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.126111 restraints weight = 2836.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3725 r_free = 0.3725    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3725 r_free = 0.3725    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3725
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.3502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5016  Z= 0.180
  Angle     :  0.661   8.555   6810  Z= 0.342
  Chirality :  0.042   0.150    768
  Planarity :  0.004   0.038    884
  Dihedral  :  5.206  26.850    680
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 20.33 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.33), residues: 628
  helix:  0.59 (0.38), residues: 172
  sheet: -2.29 (0.63), residues: 56
  loop : -0.98 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 218 
 HIS   0.007   0.001   HIS B  41 
 PHE   0.010   0.001   PHE A 223 
 TYR   0.031   0.002   TYR A 161 
 ARG   0.001   0.000   ARG B 105 

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.592 
Fit side-chains
REVERT: A   34 ASP cc_start: 0.8280 (p0) cc_final: 0.7953 (p0)
REVERT: A   49 MET cc_start: 0.6450 (mmt) cc_final: 0.4746 (mmm)
REVERT: A   58 LEU cc_start: 0.8756 (tp) cc_final: 0.8494 (tt)
REVERT: A  214 ASN cc_start: 0.8670 (t0) cc_final: 0.8293 (t0)
REVERT: A  286 LEU cc_start: 0.8453 (mt) cc_final: 0.8066 (pt)
REVERT: C    0 GLN cc_start: 0.6629 (mp10) cc_final: 0.6087 (mp10)
REVERT: C    4 ARG cc_start: 0.8662 (ttt90) cc_final: 0.8199 (ttp80)
REVERT: D    4 ARG cc_start: 0.8559 (ptm160) cc_final: 0.8322 (ttt90)
REVERT: B   34 ASP cc_start: 0.8238 (p0) cc_final: 0.7848 (p0)
REVERT: B  119 ASN cc_start: 0.8021 (t0) cc_final: 0.7767 (t0)
REVERT: B  155 ASP cc_start: 0.7397 (m-30) cc_final: 0.6628 (t0)
REVERT: B  286 LEU cc_start: 0.8494 (mt) cc_final: 0.8051 (pt)
  outliers start: 11
  outliers final: 9
  residues processed: 118
  average time/residue: 0.1409
  time to fit residues: 22.5579
Evaluate side-chains
  116 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ASN
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain C residue    1 SER
Chi-restraints excluded: chain B residue   28 ASN
Chi-restraints excluded: chain B residue   81 SER
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  181 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 47 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 59 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0970
   chunk 25 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   overall best weight:    3.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  19 GLN
B  65 ASN
** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 299 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 = 0.3791 r_free = 0.3791 target = 0.130497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.110302 restraints weight = 11532.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.115338 restraints weight = 4958.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.118501 restraints weight = 2873.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3629
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3629 r_free = 0.3629    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3628 r_free = 0.3628    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3628
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
moved from start:          0.3581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   5016  Z= 0.377
  Angle     :  0.763   9.063   6810  Z= 0.394
  Chirality :  0.047   0.192    768
  Planarity :  0.005   0.037    884
  Dihedral  :  5.524  28.199    680
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 20.51 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.32), residues: 628
  helix:  0.51 (0.38), residues: 170
  sheet: -2.40 (0.64), residues: 56
  loop : -1.21 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 218 
 HIS   0.008   0.002   HIS B  41 
 PHE   0.012   0.002   PHE B 181 
 TYR   0.030   0.003   TYR A 161 
 ARG   0.005   0.001   ARG B  40 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1930.53 seconds
wall clock time: 35 minutes 19.69 seconds (2119.69 seconds total)