Starting phenix.real_space_refine
on Tue Feb 11 12:33:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wsi_32759/02_2025/7wsi_32759.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wsi_32759/02_2025/7wsi_32759.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wsi_32759/02_2025/7wsi_32759.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wsi_32759/02_2025/7wsi_32759.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wsi_32759/02_2025/7wsi_32759.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wsi_32759/02_2025/7wsi_32759.cif"
  }
  resolution = 3.32
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      43      5.16       5
     C    3678      2.51       5
     N     913      2.21       5
     O    1067      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 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: 5701
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2348
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2348
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 17, 'TRANS': 288}
    Chain: "H"
      Number of atoms: 1669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1669
          Classifications: {'peptide': 221}
          Link IDs: {'PTRANS': 15, 'TRANS': 205}
    Chain: "L"
      Number of atoms: 1684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1684
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 9, 'TRANS': 206}
  Time building chain proxies: 3.76, per 1000 atoms: 0.66
  Number of scatterers: 5701
  At special positions: 0
  Unit cell: (87.15, 72.21, 141.93, 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      43     16.00
     O    1067      8.00
     N     913      7.00
     C    3678      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 148 " - pdb=" SG  CYS H 203 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.04

  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: 1.30
  Conformation dependent library (CDL) restraints added in 724.7 milliseconds
  

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1376

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 9 sheets defined
      38.0% alpha, 21.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 20
      removed outlier: 3.758A  pdb=" N   GLY A  19 " --> pdb=" O   PRO A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 44
    Processing helix  chain 'A' and resid 47 through 57
      removed outlier: 3.565A  pdb=" N   ILE A  51 " --> pdb=" O   GLU A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 70
    Processing helix  chain 'A' and resid 71 through 83
    Processing helix  chain 'A' and resid 86 through 99
    Processing helix  chain 'A' and resid 103 through 113
      removed outlier: 3.888A  pdb=" N   VAL A 107 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 142
      Proline residue:  A 135  - end of helix
    Processing helix  chain 'A' and resid 156 through 180
      Proline residue:  A 169  - end of helix
    Processing helix  chain 'A' and resid 183 through 211
      removed outlier: 3.568A  pdb=" N   ALA A 207 " --> pdb=" O   THR A 203 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ILE A 208 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLY A 211 " --> pdb=" O   ALA A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 218
    Processing helix  chain 'A' and resid 219 through 243
      Proline residue:  A 230  - end of helix
    Processing helix  chain 'A' and resid 248 through 260
      removed outlier: 3.587A  pdb=" N   ARG A 252 " --> pdb=" O   GLY A 248 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   THR A 253 " --> pdb=" O   ARG A 249 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   VAL A 254 " --> pdb=" O   CYS A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 274
    Processing helix  chain 'A' and resid 280 through 283
    Processing helix  chain 'A' and resid 284 through 309
      removed outlier: 3.675A  pdb=" N   LYS A 309 " --> pdb=" O   TRP A 305 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 62 through 66
      removed outlier: 3.520A  pdb=" N   LYS H  65 " --> pdb=" O   GLU H  62 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   GLY H  66 " --> pdb=" O   LYS H  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 62 through 66'
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 4.104A  pdb=" N   SER H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 194 through 199
      removed outlier: 4.367A  pdb=" N   SER H 198 " --> pdb=" O   SER H 194 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 126 through 132
      removed outlier: 3.547A  pdb=" N   LEU L 130 " --> pdb=" O   SER L 126 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   THR L 131 " --> pdb=" O   SER L 127 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6
      removed outlier: 3.610A  pdb=" N   THR H  71 " --> pdb=" O   TYR H  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.599A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   ILE H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   TYR H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLY H  57 " --> pdb=" O   ASN H  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.599A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   TYR H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 128 through 132
      removed outlier: 4.324A  pdb=" N   GLY H 147 " --> pdb=" O   LEU H 132 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   SER H 187 " --> pdb=" O   CYS H 148 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   MET H 185 " --> pdb=" O   VAL H 150 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   THR H 184 " --> pdb=" O   ALA H 176 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   ALA H 176 " --> pdb=" O   THR H 184 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   SER H 186 " --> pdb=" O   PHE H 174 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 159 through 161
      removed outlier: 3.868A  pdb=" N   CYS H 203 " --> pdb=" O   LYS H 216 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LYS H 216 " --> pdb=" O   CYS H 203 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12
      removed outlier: 7.009A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 110 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 69 through 73
    Processing sheet with id=AA8, first strand: chain 'L' and resid 122 through 123
      removed outlier: 4.016A  pdb=" N   ASN L 143 " --> pdb=" O   TYR L 178 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   TYR L 178 " --> pdb=" O   ASN L 143 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 158 through 159
      removed outlier: 6.077A  pdb=" N   HIS L 203 " --> pdb=" O   SER L 208 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   SER L 208 " --> pdb=" O   HIS L 203 " (cutoff:3.500A)

    275 hydrogen bonds defined for protein.
    753 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: 1.42

  Time building geometry restraints manager: 1.52 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1736
        1.35 -     1.46: 1445
        1.46 -     1.58: 2593
        1.58 -     1.70: 0
        1.70 -     1.82: 65
  Bond restraints: 5839
  Sorted by residual:
  bond pdb=" CA  GLY L  70 "
       pdb=" C   GLY L  70 "
    ideal  model  delta    sigma   weight residual
    1.520  1.513  0.008 7.30e-03 1.88e+04 1.06e+00
  bond pdb=" N   SER L  25 "
       pdb=" CA  SER L  25 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.013 1.29e-02 6.01e+03 1.06e+00
  bond pdb=" CA  THR L  20 "
       pdb=" CB  THR L  20 "
    ideal  model  delta    sigma   weight residual
    1.527  1.541 -0.014 1.61e-02 3.86e+03 7.89e-01
  bond pdb=" CA  ALA H  16 "
       pdb=" CB  ALA H  16 "
    ideal  model  delta    sigma   weight residual
    1.530  1.515  0.015 1.69e-02 3.50e+03 7.72e-01
  bond pdb=" SD  MET A 122 "
       pdb=" CE  MET A 122 "
    ideal  model  delta    sigma   weight residual
    1.791  1.770  0.021 2.50e-02 1.60e+03 7.33e-01
  ... (remaining 5834 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 7474
        1.21 -     2.43: 343
        2.43 -     3.64: 78
        3.64 -     4.85: 26
        4.85 -     6.07: 13
  Bond angle restraints: 7934
  Sorted by residual:
  angle pdb=" N   ILE A 214 "
        pdb=" CA  ILE A 214 "
        pdb=" C   ILE A 214 "
      ideal   model   delta    sigma   weight residual
     111.77  108.04    3.73 1.04e+00 9.25e-01 1.29e+01
  angle pdb=" C   PRO L   8 "
        pdb=" N   SER L   9 "
        pdb=" CA  SER L   9 "
      ideal   model   delta    sigma   weight residual
     121.54  126.59   -5.05 1.91e+00 2.74e-01 6.98e+00
  angle pdb=" CA  CYS L  94 "
        pdb=" CB  CYS L  94 "
        pdb=" SG  CYS L  94 "
      ideal   model   delta    sigma   weight residual
     114.40  120.23   -5.83 2.30e+00 1.89e-01 6.43e+00
  angle pdb=" C   ASP A 149 "
        pdb=" N   LEU A 150 "
        pdb=" CA  LEU A 150 "
      ideal   model   delta    sigma   weight residual
     121.54  126.15   -4.61 1.91e+00 2.74e-01 5.82e+00
  angle pdb=" N   THR L 169 "
        pdb=" CA  THR L 169 "
        pdb=" C   THR L 169 "
      ideal   model   delta    sigma   weight residual
     110.53  107.76    2.77 1.29e+00 6.01e-01 4.61e+00
  ... (remaining 7929 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.97: 3061
       13.97 -    27.94: 325
       27.94 -    41.91: 84
       41.91 -    55.87: 12
       55.87 -    69.84: 2
  Dihedral angle restraints: 3484
    sinusoidal: 1332
      harmonic: 2152
  Sorted by residual:
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  94 "
           pdb=" CB  CYS L  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  158.44  -65.44     1      1.00e+01 1.00e-02 5.61e+01
  dihedral pdb=" CB  CYS H 148 "
           pdb=" SG  CYS H 148 "
           pdb=" SG  CYS H 203 "
           pdb=" CB  CYS H 203 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -118.30   32.30     1      1.00e+01 1.00e-02 1.49e+01
  dihedral pdb=" CA  TYR L  92 "
           pdb=" C   TYR L  92 "
           pdb=" N   TYR L  93 "
           pdb=" CA  TYR L  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.69  -18.31     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 3481 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 559
       0.032 -    0.064: 241
       0.064 -    0.096: 77
       0.096 -    0.127: 37
       0.127 -    0.159: 4
  Chirality restraints: 918
  Sorted by residual:
  chirality pdb=" CA  ILE L  54 "
            pdb=" N   ILE L  54 "
            pdb=" C   ILE L  54 "
            pdb=" CB  ILE L  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.34e-01
  chirality pdb=" CA  ILE H 104 "
            pdb=" N   ILE H 104 "
            pdb=" C   ILE H 104 "
            pdb=" CB  ILE H 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  chirality pdb=" CA  ILE A 145 "
            pdb=" N   ILE A 145 "
            pdb=" C   ILE A 145 "
            pdb=" CB  ILE A 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.58e-01
  ... (remaining 915 not shown)

  Planarity restraints: 981
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL L  64 "    0.041 5.00e-02 4.00e+02   6.35e-02 6.45e+00
        pdb=" N   PRO L  65 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO L  65 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO L  65 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 180 "   -0.036 5.00e-02 4.00e+02   5.40e-02 4.67e+00
        pdb=" N   PRO A 181 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 181 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 181 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L  49 "   -0.024 5.00e-02 4.00e+02   3.57e-02 2.04e+00
        pdb=" N   PRO L  50 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO L  50 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO L  50 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 978 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 82
        2.68 -     3.23: 5605
        3.23 -     3.79: 8449
        3.79 -     4.34: 11132
        4.34 -     4.90: 18947
  Nonbonded interactions: 44215
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP H 102 "
            pdb=" N   GLY H 103 "
     model   vdw
     2.122 3.120
  nonbonded pdb=" OG  SER A 105 "
            pdb=" OE1 GLU A 257 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" NE2 GLN L  96 "
            pdb=" OG1 THR L 102 "
     model   vdw
     2.328 3.120
  nonbonded pdb=" NH1 ARG L 160 "
            pdb=" O   ASN L 162 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" O   TYR L  55 "
            pdb=" OG1 THR L  59 "
     model   vdw
     2.354 3.040
  ... (remaining 44210 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  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:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     16.590
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
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   0.027   5839  Z= 0.199
  Angle     :  0.668   6.068   7934  Z= 0.349
  Chirality :  0.043   0.159    918
  Planarity :  0.005   0.063    981
  Dihedral  : 12.247  69.843   2099
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  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: -0.23 (0.32), residues: 737
  helix:  0.97 (0.34), residues: 241
  sheet:  0.43 (0.39), residues: 195
  loop : -1.50 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L  41 
 HIS   0.002   0.001   HIS H 106 
 PHE   0.018   0.001   PHE A 292 
 TYR   0.017   0.002   TYR A  69 
 ARG   0.004   0.000   ARG A 180 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 298
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 TRP cc_start: 0.5403 (m-10) cc_final: 0.5077 (m-10)
REVERT: H    3 GLN cc_start: 0.7813 (pp30) cc_final: 0.7395 (pp30)
REVERT: H  117 LEU cc_start: 0.8462 (tt) cc_final: 0.8099 (tp)
REVERT: L   42 TYR cc_start: 0.8120 (m-80) cc_final: 0.7786 (m-80)
REVERT: L   44 GLN cc_start: 0.8043 (tt0) cc_final: 0.7616 (tt0)
REVERT: L  128 GLU cc_start: 0.7847 (pm20) cc_final: 0.7550 (pm20)
REVERT: L  143 ASN cc_start: 0.8175 (m-40) cc_final: 0.7957 (m-40)
REVERT: L  160 ARG cc_start: 0.8007 (ptm-80) cc_final: 0.7635 (ptp90)
REVERT: L  168 TRP cc_start: 0.8956 (m-90) cc_final: 0.8650 (m-90)
  outliers start: 0
  outliers final: 0
  residues processed: 298
  average time/residue: 0.1736
  time to fit residues: 66.5033
Evaluate side-chains
  234 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN
H  39 GLN
L   6 GLN
L 215 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.142505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.113589 restraints weight = 10584.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 3.63
r_work: 0.3251 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5839  Z= 0.238
  Angle     :  0.733   7.630   7934  Z= 0.367
  Chirality :  0.045   0.155    918
  Planarity :  0.005   0.077    981
  Dihedral  :  4.642  16.416    794
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.19 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 16.38 %
    Favored  : 78.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.42 (0.31), residues: 737
  helix:  0.87 (0.34), residues: 252
  sheet:  0.44 (0.40), residues: 182
  loop : -1.75 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP L 168 
 HIS   0.002   0.001   HIS L 203 
 PHE   0.015   0.001   PHE A 292 
 TYR   0.021   0.002   TYR L  98 
 ARG   0.006   0.001   ARG L  60 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 226
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.8726 (t80) cc_final: 0.8439 (t80)
REVERT: A  176 LEU cc_start: 0.8401 (tt) cc_final: 0.7713 (tt)
REVERT: A  180 ARG cc_start: 0.7826 (tmt170) cc_final: 0.7311 (ttp80)
REVERT: A  246 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7558 (mm)
REVERT: A  256 MET cc_start: 0.8050 (ttm) cc_final: 0.7777 (ttm)
REVERT: H    3 GLN cc_start: 0.8936 (pp30) cc_final: 0.7959 (pp30)
REVERT: H  130 TYR cc_start: 0.9053 (m-10) cc_final: 0.8364 (m-80)
REVERT: L   27 GLN cc_start: 0.8440 (pm20) cc_final: 0.8152 (pm20)
REVERT: L   29 LEU cc_start: 0.9586 (pp) cc_final: 0.9348 (pp)
REVERT: L   85 GLN cc_start: 0.7026 (tm-30) cc_final: 0.6780 (tm-30)
REVERT: L   87 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8547 (pp20)
REVERT: L  160 ARG cc_start: 0.8320 (ptm-80) cc_final: 0.7937 (ptp90)
REVERT: L  198 THR cc_start: 0.8728 (m) cc_final: 0.8461 (p)
REVERT: L  200 GLU cc_start: 0.7312 (tt0) cc_final: 0.7102 (tt0)
  outliers start: 30
  outliers final: 19
  residues processed: 236
  average time/residue: 0.1483
  time to fit residues: 46.9779
Evaluate side-chains
  234 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 213
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  161 ILE
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain H residue  128 SER
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  122 ILE
Chi-restraints excluded: chain L residue  136 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 69 optimal weight:    0.5980
   chunk 55 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 71 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 42 optimal weight:    7.9990
   chunk 70 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
A 247 ASN
L 215 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.134218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.104611 restraints weight = 10682.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 3.67
r_work: 0.3103 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.3120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   5839  Z= 0.394
  Angle     :  0.766   8.745   7934  Z= 0.385
  Chirality :  0.047   0.145    918
  Planarity :  0.005   0.046    981
  Dihedral  :  4.980  19.120    794
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  6.80 %
    Allowed  : 20.87 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.31), residues: 737
  helix:  0.70 (0.33), residues: 255
  sheet:  0.29 (0.41), residues: 172
  loop : -1.82 (0.33), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 305 
 HIS   0.004   0.001   HIS L 203 
 PHE   0.023   0.002   PHE H 154 
 TYR   0.030   0.002   TYR H 183 
 ARG   0.005   0.001   ARG L  60 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 219
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8273 (mttp)
REVERT: A  133 MET cc_start: 0.8795 (ppp) cc_final: 0.8581 (ppp)
REVERT: A  143 ARG cc_start: 0.8588 (ttt180) cc_final: 0.7710 (mmt90)
REVERT: A  223 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8198 (mt)
REVERT: H    3 GLN cc_start: 0.9043 (pp30) cc_final: 0.8008 (pp30)
REVERT: H   48 ILE cc_start: 0.9353 (mt) cc_final: 0.9057 (mm)
REVERT: H  130 TYR cc_start: 0.9038 (m-10) cc_final: 0.8280 (m-80)
REVERT: L   27 GLN cc_start: 0.8683 (pm20) cc_final: 0.8348 (pm20)
REVERT: L   48 GLN cc_start: 0.8721 (mp10) cc_final: 0.7987 (mp10)
REVERT: L   85 GLN cc_start: 0.7268 (tm-30) cc_final: 0.6999 (tm-30)
REVERT: L   87 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8627 (pp20)
REVERT: L  110 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8263 (mp0)
REVERT: L  123 PHE cc_start: 0.9305 (m-80) cc_final: 0.8858 (m-80)
REVERT: L  161 GLN cc_start: 0.8996 (tm-30) cc_final: 0.8698 (tm-30)
REVERT: L  180 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7330 (tpt)
  outliers start: 44
  outliers final: 30
  residues processed: 234
  average time/residue: 0.1548
  time to fit residues: 47.8693
Evaluate side-chains
  242 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 209
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   56 TRP
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain A residue  287 LEU
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   90 ASP
Chi-restraints excluded: chain H residue  128 SER
Chi-restraints excluded: chain H residue  149 LEU
Chi-restraints excluded: chain H residue  205 VAL
Chi-restraints excluded: chain L residue   32 SER
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  136 SER
Chi-restraints excluded: chain L residue  180 MET
Chi-restraints excluded: chain L residue  181 SER
Chi-restraints excluded: chain L residue  211 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 71 optimal weight:   10.0000
   chunk 67 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
L 166 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.138170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.108759 restraints weight = 10859.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 3.65
r_work: 0.3177 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.3268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5839  Z= 0.214
  Angle     :  0.699   8.593   7934  Z= 0.346
  Chirality :  0.046   0.160    918
  Planarity :  0.004   0.041    981
  Dihedral  :  4.671  18.154    794
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 24.42 %
    Favored  : 70.17 %
  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: -0.46 (0.31), residues: 737
  helix:  0.80 (0.33), residues: 259
  sheet:  0.60 (0.42), residues: 166
  loop : -1.80 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.020   0.001   PHE A 292 
 TYR   0.032   0.002   TYR H 183 
 ARG   0.003   0.000   ARG A 180 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 220
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.8111 (m-30) cc_final: 0.7885 (m-30)
REVERT: A   50 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8135 (mttp)
REVERT: A  143 ARG cc_start: 0.8466 (ttt180) cc_final: 0.7532 (mmt90)
REVERT: A  223 ILE cc_start: 0.8462 (mt) cc_final: 0.8197 (mt)
REVERT: H    3 GLN cc_start: 0.9048 (pp30) cc_final: 0.8004 (pp30)
REVERT: H   98 ARG cc_start: 0.8803 (tmm-80) cc_final: 0.8505 (tmm-80)
REVERT: H  130 TYR cc_start: 0.9041 (m-10) cc_final: 0.8346 (m-80)
REVERT: L   27 GLN cc_start: 0.8639 (pm20) cc_final: 0.8183 (pm20)
REVERT: L   29 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9212 (pp)
REVERT: L   48 GLN cc_start: 0.8740 (mp10) cc_final: 0.7980 (mp10)
REVERT: L   87 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8680 (pp20)
REVERT: L  161 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8510 (tm-30)
REVERT: L  168 TRP cc_start: 0.9460 (m-90) cc_final: 0.8860 (m-90)
REVERT: L  180 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7541 (tpt)
  outliers start: 35
  outliers final: 23
  residues processed: 233
  average time/residue: 0.1489
  time to fit residues: 46.1962
Evaluate side-chains
  235 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 209
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   56 TRP
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain H residue  149 LEU
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  187 SER
Chi-restraints excluded: chain L residue   29 LEU
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  122 ILE
Chi-restraints excluded: chain L residue  136 SER
Chi-restraints excluded: chain L residue  180 MET
Chi-restraints excluded: chain L residue  181 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    0.0670
   chunk 60 optimal weight:    4.9990
   chunk 21 optimal weight:    0.0000
   chunk 48 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 50 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0770
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.6284

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

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN
L   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.138377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.109613 restraints weight = 10584.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 3.66
r_work: 0.3198 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5839  Z= 0.201
  Angle     :  0.691   8.952   7934  Z= 0.337
  Chirality :  0.045   0.161    918
  Planarity :  0.004   0.036    981
  Dihedral  :  4.559  16.986    794
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 24.42 %
    Favored  : 70.17 %
  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: -0.35 (0.32), residues: 737
  helix:  0.83 (0.33), residues: 260
  sheet:  0.68 (0.42), residues: 166
  loop : -1.72 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.019   0.001   PHE A 292 
 TYR   0.025   0.002   TYR H 183 
 ARG   0.003   0.000   ARG A 180 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 213
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.8879 (t80) cc_final: 0.8656 (t80)
REVERT: A   24 ASP cc_start: 0.8117 (m-30) cc_final: 0.7880 (m-30)
REVERT: A   50 LYS cc_start: 0.8555 (mmmt) cc_final: 0.8096 (mttp)
REVERT: A  141 TYR cc_start: 0.9030 (m-80) cc_final: 0.8294 (m-80)
REVERT: A  223 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8174 (mt)
REVERT: H    3 GLN cc_start: 0.9054 (pp30) cc_final: 0.8023 (pp30)
REVERT: H   98 ARG cc_start: 0.8808 (tmm-80) cc_final: 0.8499 (tmm-80)
REVERT: H  130 TYR cc_start: 0.9057 (m-10) cc_final: 0.8301 (m-80)
REVERT: H  215 ASP cc_start: 0.8690 (t0) cc_final: 0.7911 (p0)
REVERT: L   27 GLN cc_start: 0.8615 (pm20) cc_final: 0.8162 (pm20)
REVERT: L   29 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9214 (pp)
REVERT: L   48 GLN cc_start: 0.8700 (mp10) cc_final: 0.7933 (mp10)
REVERT: L   87 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8618 (pp20)
REVERT: L  110 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8204 (mp0)
REVERT: L  161 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8451 (tm-30)
REVERT: L  168 TRP cc_start: 0.9461 (m-90) cc_final: 0.8855 (m-90)
REVERT: L  180 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7606 (tpt)
  outliers start: 35
  outliers final: 23
  residues processed: 223
  average time/residue: 0.1452
  time to fit residues: 43.7651
Evaluate side-chains
  234 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 207
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue   56 TRP
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  149 LEU
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain L residue   29 LEU
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  122 ILE
Chi-restraints excluded: chain L residue  136 SER
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  169 THR
Chi-restraints excluded: chain L residue  180 MET
Chi-restraints excluded: chain L residue  181 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 5 optimal weight:    0.2980
   chunk 49 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0670
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN
L   6 GLN
L 166 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.140629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.111852 restraints weight = 10673.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 3.49
r_work: 0.3250 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5839  Z= 0.184
  Angle     :  0.675   9.483   7934  Z= 0.330
  Chirality :  0.044   0.172    918
  Planarity :  0.004   0.036    981
  Dihedral  :  4.410  16.033    794
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 27.05 %
    Favored  : 68.01 %
  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: -0.21 (0.32), residues: 737
  helix:  1.08 (0.34), residues: 253
  sheet:  0.77 (0.42), residues: 165
  loop : -1.70 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.018   0.001   PHE A 292 
 TYR   0.024   0.002   TYR H 183 
 ARG   0.003   0.000   ARG L 160 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 224
  time to evaluate  : 0.666 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.8907 (t80) cc_final: 0.8685 (t80)
REVERT: A   24 ASP cc_start: 0.8071 (m-30) cc_final: 0.7854 (m-30)
REVERT: A   46 MET cc_start: 0.9029 (mtt) cc_final: 0.8726 (mtp)
REVERT: A   50 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8067 (mttp)
REVERT: A  141 TYR cc_start: 0.8972 (m-80) cc_final: 0.8210 (m-80)
REVERT: A  167 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8414 (tt)
REVERT: A  176 LEU cc_start: 0.8728 (tt) cc_final: 0.8358 (tt)
REVERT: A  223 ILE cc_start: 0.8389 (mt) cc_final: 0.8125 (mt)
REVERT: H    3 GLN cc_start: 0.9030 (pp30) cc_final: 0.7976 (pp30)
REVERT: H   81 MET cc_start: 0.9135 (ttt) cc_final: 0.8813 (ttm)
REVERT: H   98 ARG cc_start: 0.8821 (tmm-80) cc_final: 0.8491 (tmm-80)
REVERT: H  130 TYR cc_start: 0.8813 (m-10) cc_final: 0.8401 (m-80)
REVERT: H  189 VAL cc_start: 0.9014 (p) cc_final: 0.8776 (m)
REVERT: H  215 ASP cc_start: 0.8651 (t0) cc_final: 0.7930 (p0)
REVERT: L   29 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9211 (pp)
REVERT: L   48 GLN cc_start: 0.8684 (mp10) cc_final: 0.7955 (mp10)
REVERT: L   85 GLN cc_start: 0.7369 (tm-30) cc_final: 0.6652 (tm-30)
REVERT: L  110 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8207 (mp0)
REVERT: L  160 ARG cc_start: 0.8476 (ptm-80) cc_final: 0.7523 (ptm-80)
REVERT: L  161 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8367 (tm-30)
REVERT: L  168 TRP cc_start: 0.9417 (m-90) cc_final: 0.8836 (m-90)
REVERT: L  180 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7579 (tpt)
  outliers start: 32
  outliers final: 22
  residues processed: 235
  average time/residue: 0.1410
  time to fit residues: 45.1226
Evaluate side-chains
  234 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 209
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   56 TRP
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  149 LEU
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain L residue   29 LEU
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue  122 ILE
Chi-restraints excluded: chain L residue  136 SER
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain L residue  169 THR
Chi-restraints excluded: chain L residue  180 MET
Chi-restraints excluded: chain L residue  181 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 66 optimal weight:    0.0270
   chunk 69 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 59 optimal weight:    0.2980
   chunk 56 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 14 optimal weight:    0.1980
   chunk 27 optimal weight:    0.5980
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.4038

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

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN
L   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.141401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.111506 restraints weight = 10705.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.3350 rms_B_bonded: 3.71
r_work: 0.3231 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.3735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5839  Z= 0.178
  Angle     :  0.683  12.068   7934  Z= 0.329
  Chirality :  0.044   0.182    918
  Planarity :  0.004   0.034    981
  Dihedral  :  4.329  15.247    794
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 28.44 %
    Favored  : 67.08 %
  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: -0.07 (0.32), residues: 737
  helix:  1.29 (0.34), residues: 246
  sheet:  0.80 (0.43), residues: 165
  loop : -1.60 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.020   0.001   PHE A 292 
 TYR   0.023   0.001   TYR H 183 
 ARG   0.002   0.000   ARG A 180 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 224
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 PHE cc_start: 0.8930 (t80) cc_final: 0.8721 (t80)
REVERT: A   24 ASP cc_start: 0.8029 (m-30) cc_final: 0.7805 (m-30)
REVERT: A   46 MET cc_start: 0.9118 (mtt) cc_final: 0.8765 (mtp)
REVERT: A   50 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8127 (mttp)
REVERT: A  141 TYR cc_start: 0.8974 (m-80) cc_final: 0.8207 (m-80)
REVERT: A  176 LEU cc_start: 0.8768 (tt) cc_final: 0.8367 (tt)
REVERT: A  223 ILE cc_start: 0.8313 (mt) cc_final: 0.8051 (mt)
REVERT: A  256 MET cc_start: 0.8325 (ttm) cc_final: 0.8124 (ttm)
REVERT: H    3 GLN cc_start: 0.9024 (pp30) cc_final: 0.7997 (pp30)
REVERT: H   81 MET cc_start: 0.9161 (ttt) cc_final: 0.8867 (ttm)
REVERT: H  130 TYR cc_start: 0.8821 (m-10) cc_final: 0.8447 (m-80)
REVERT: H  189 VAL cc_start: 0.9039 (p) cc_final: 0.8795 (m)
REVERT: H  215 ASP cc_start: 0.8554 (t70) cc_final: 0.7851 (p0)
REVERT: L   29 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9222 (pp)
REVERT: L   48 GLN cc_start: 0.8574 (mp10) cc_final: 0.7829 (mp10)
REVERT: L   85 GLN cc_start: 0.7309 (tm-30) cc_final: 0.7082 (tm-30)
REVERT: L   87 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8694 (pp20)
REVERT: L  160 ARG cc_start: 0.8519 (ptm-80) cc_final: 0.7650 (ptm-80)
REVERT: L  161 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8309 (tm-30)
REVERT: L  168 TRP cc_start: 0.9430 (m-90) cc_final: 0.8901 (m-90)
REVERT: L  180 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7584 (tpt)
  outliers start: 29
  outliers final: 22
  residues processed: 235
  average time/residue: 0.1433
  time to fit residues: 45.4166
Evaluate side-chains
  229 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 204
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   56 TRP
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  149 LEU
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain L residue   29 LEU
Chi-restraints excluded: chain L residue   81 ILE
Chi-restraints excluded: chain L residue   87 GLU
Chi-restraints excluded: chain L residue  122 ILE
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain L residue  169 THR
Chi-restraints excluded: chain L residue  180 MET
Chi-restraints excluded: chain L residue  181 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 41 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0570
   chunk 65 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.9502

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

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN
L   6 GLN
L 166 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.139239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.109649 restraints weight = 10740.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 3.66
r_work: 0.3196 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.3836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   5839  Z= 0.231
  Angle     :  0.691   9.939   7934  Z= 0.336
  Chirality :  0.045   0.189    918
  Planarity :  0.004   0.034    981
  Dihedral  :  4.435  15.870    794
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 28.59 %
    Favored  : 66.77 %
  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: -0.03 (0.32), residues: 737
  helix:  1.19 (0.34), residues: 252
  sheet:  0.81 (0.43), residues: 165
  loop : -1.51 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP L 168 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.023   0.001   PHE A 292 
 TYR   0.023   0.002   TYR H 183 
 ARG   0.003   0.000   ARG L  60 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 210
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.8027 (m-30) cc_final: 0.7810 (m-30)
REVERT: A   50 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8202 (mttp)
REVERT: A  106 ASN cc_start: 0.8743 (m110) cc_final: 0.8099 (m-40)
REVERT: A  141 TYR cc_start: 0.9024 (m-80) cc_final: 0.8248 (m-80)
REVERT: A  223 ILE cc_start: 0.8324 (mt) cc_final: 0.8059 (mt)
REVERT: A  246 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7335 (mt)
REVERT: H    3 GLN cc_start: 0.9047 (pp30) cc_final: 0.8085 (pp30)
REVERT: H   81 MET cc_start: 0.9142 (ttt) cc_final: 0.8316 (ttm)
REVERT: H  100 TYR cc_start: 0.8950 (t80) cc_final: 0.8491 (t80)
REVERT: H  117 LEU cc_start: 0.9390 (tp) cc_final: 0.9165 (tt)
REVERT: H  130 TYR cc_start: 0.8831 (m-10) cc_final: 0.8446 (m-80)
REVERT: H  189 VAL cc_start: 0.9037 (p) cc_final: 0.8776 (m)
REVERT: L   29 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9227 (pp)
REVERT: L   48 GLN cc_start: 0.8604 (mp10) cc_final: 0.7885 (mp10)
REVERT: L   85 GLN cc_start: 0.7391 (tm-30) cc_final: 0.7128 (tm-30)
REVERT: L  110 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8372 (mp0)
REVERT: L  161 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8298 (tm-30)
REVERT: L  168 TRP cc_start: 0.9447 (m-90) cc_final: 0.9015 (m-90)
REVERT: L  180 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7646 (tpt)
  outliers start: 30
  outliers final: 21
  residues processed: 223
  average time/residue: 0.1424
  time to fit residues: 42.9832
Evaluate side-chains
  229 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 205
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   56 TRP
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  149 LEU
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  218 LEU
Chi-restraints excluded: chain L residue   29 LEU
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain L residue  169 THR
Chi-restraints excluded: chain L residue  180 MET
Chi-restraints excluded: chain L residue  181 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 64 optimal weight:    0.2980
   chunk 4 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0980
   chunk 17 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN
L   6 GLN
L 215 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.140743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.111981 restraints weight = 10709.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 3.67
r_work: 0.3231 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.3974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5839  Z= 0.187
  Angle     :  0.691  10.110   7934  Z= 0.335
  Chirality :  0.044   0.198    918
  Planarity :  0.004   0.033    981
  Dihedral  :  4.356  15.480    794
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 29.83 %
    Favored  : 66.15 %
  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: -0.00 (0.32), residues: 737
  helix:  1.21 (0.34), residues: 252
  sheet:  0.84 (0.43), residues: 165
  loop : -1.50 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.020   0.001   PHE A 292 
 TYR   0.021   0.001   TYR L  98 
 ARG   0.005   0.001   ARG A 251 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 212
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.7979 (m-30) cc_final: 0.7766 (m-30)
REVERT: A   46 MET cc_start: 0.9015 (mtt) cc_final: 0.8677 (mtp)
REVERT: A   50 LYS cc_start: 0.8552 (mmmt) cc_final: 0.8131 (mttp)
REVERT: A  106 ASN cc_start: 0.8783 (m110) cc_final: 0.8141 (m-40)
REVERT: A  141 TYR cc_start: 0.8989 (m-80) cc_final: 0.8232 (m-80)
REVERT: A  223 ILE cc_start: 0.8263 (mt) cc_final: 0.8009 (mt)
REVERT: H    3 GLN cc_start: 0.9040 (pp30) cc_final: 0.8072 (pp30)
REVERT: H  130 TYR cc_start: 0.8821 (m-10) cc_final: 0.8559 (m-80)
REVERT: H  189 VAL cc_start: 0.9070 (p) cc_final: 0.8818 (m)
REVERT: H  215 ASP cc_start: 0.8725 (t0) cc_final: 0.7819 (p0)
REVERT: L   29 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9216 (pp)
REVERT: L   48 GLN cc_start: 0.8554 (mp10) cc_final: 0.7827 (mp10)
REVERT: L   85 GLN cc_start: 0.7830 (tm-30) cc_final: 0.7320 (tm-30)
REVERT: L  160 ARG cc_start: 0.8190 (ptm-80) cc_final: 0.7166 (ptm-80)
REVERT: L  161 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8156 (tm-30)
REVERT: L  168 TRP cc_start: 0.9444 (m-90) cc_final: 0.8932 (m-90)
REVERT: L  180 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7698 (tpt)
  outliers start: 26
  outliers final: 21
  residues processed: 223
  average time/residue: 0.1420
  time to fit residues: 42.8990
Evaluate side-chains
  227 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 204
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   56 TRP
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  149 LEU
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  218 LEU
Chi-restraints excluded: chain L residue   29 LEU
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain L residue  169 THR
Chi-restraints excluded: chain L residue  180 MET
Chi-restraints excluded: chain L residue  181 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 13 optimal weight:    0.4980
   chunk 58 optimal weight:    0.7980
   chunk 59 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 12 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN
L 166 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.140711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.111019 restraints weight = 10886.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 3.72
r_work: 0.3219 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.4057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5839  Z= 0.215
  Angle     :  0.724  10.088   7934  Z= 0.349
  Chirality :  0.045   0.210    918
  Planarity :  0.004   0.035    981
  Dihedral  :  4.427  15.267    794
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 30.45 %
    Favored  : 66.00 %
  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:  0.06 (0.32), residues: 737
  helix:  1.30 (0.34), residues: 251
  sheet:  0.71 (0.42), residues: 175
  loop : -1.44 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.021   0.001   PHE A 292 
 TYR   0.022   0.002   TYR H 183 
 ARG   0.003   0.000   ARG L  60 

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 209
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 MET cc_start: 0.8987 (mtt) cc_final: 0.8656 (mtp)
REVERT: A   50 LYS cc_start: 0.8587 (mmmt) cc_final: 0.8175 (mttp)
REVERT: A  106 ASN cc_start: 0.8782 (m110) cc_final: 0.8079 (m-40)
REVERT: A  141 TYR cc_start: 0.9003 (m-80) cc_final: 0.8358 (m-80)
REVERT: A  223 ILE cc_start: 0.8263 (mt) cc_final: 0.8008 (mt)
REVERT: H    3 GLN cc_start: 0.9045 (pp30) cc_final: 0.8025 (pp30)
REVERT: H  100 TYR cc_start: 0.8923 (t80) cc_final: 0.8452 (t80)
REVERT: H  117 LEU cc_start: 0.9413 (tp) cc_final: 0.9180 (tt)
REVERT: H  130 TYR cc_start: 0.8876 (m-10) cc_final: 0.8632 (m-80)
REVERT: H  189 VAL cc_start: 0.9063 (p) cc_final: 0.8792 (m)
REVERT: H  215 ASP cc_start: 0.8737 (t0) cc_final: 0.7842 (p0)
REVERT: L   17 GLU cc_start: 0.8951 (pm20) cc_final: 0.8648 (pm20)
REVERT: L   29 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9223 (pp)
REVERT: L   48 GLN cc_start: 0.8563 (mp10) cc_final: 0.7845 (mp10)
REVERT: L   85 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7340 (tm-30)
REVERT: L  110 GLU cc_start: 0.8162 (mp0) cc_final: 0.7687 (mp0)
REVERT: L  161 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8059 (tm-30)
REVERT: L  168 TRP cc_start: 0.9454 (m-90) cc_final: 0.8921 (m-90)
REVERT: L  180 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7590 (tpt)
  outliers start: 23
  outliers final: 19
  residues processed: 220
  average time/residue: 0.1368
  time to fit residues: 41.0048
Evaluate side-chains
  224 residues out of total 647 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 203
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   56 TRP
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  253 THR
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue  149 LEU
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain H residue  218 LEU
Chi-restraints excluded: chain L residue   29 LEU
Chi-restraints excluded: chain L residue  169 THR
Chi-restraints excluded: chain L residue  180 MET
Chi-restraints excluded: chain L residue  181 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 67 optimal weight:    0.2980
   chunk 17 optimal weight:    0.7980
   chunk 31 optimal weight:    0.4980
   chunk 6 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.140778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.111779 restraints weight = 10843.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 3.68
r_work: 0.3231 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.4122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5839  Z= 0.201
  Angle     :  0.716  10.126   7934  Z= 0.345
  Chirality :  0.045   0.208    918
  Planarity :  0.004   0.033    981
  Dihedral  :  4.377  15.683    794
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 30.29 %
    Favored  : 66.00 %
  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:  0.10 (0.32), residues: 737
  helix:  1.31 (0.34), residues: 252
  sheet:  0.75 (0.42), residues: 175
  loop : -1.44 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.021   0.001   PHE A 292 
 TYR   0.021   0.001   TYR L  98 
 ARG   0.003   0.000   ARG L  60 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2884.79 seconds
wall clock time: 52 minutes 1.01 seconds (3121.01 seconds total)