Starting phenix.real_space_refine
on Sat May 10 10:47:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hrx_34981/05_2025/8hrx_34981.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hrx_34981/05_2025/8hrx_34981.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.89
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hrx_34981/05_2025/8hrx_34981.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hrx_34981/05_2025/8hrx_34981.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hrx_34981/05_2025/8hrx_34981.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hrx_34981/05_2025/8hrx_34981.cif"
  }
  resolution = 2.89
  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    3872      2.51       5
     N     973      2.21       5
     O    1125      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6013
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2322
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 302, 2322
          Classifications: {'peptide': 302}
          Link IDs: {'PTRANS': 16, 'TRANS': 285}
    Chain: "B"
      Number of atoms: 371
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 371
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 7, 'TRANS': 39}
    Chain: "H"
      Number of atoms: 1661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1661
          Classifications: {'peptide': 219}
          Link IDs: {'PTRANS': 14, 'TRANS': 204}
    Chain: "L"
      Number of atoms: 1659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1659
          Classifications: {'peptide': 212}
          Link IDs: {'PTRANS': 9, 'TRANS': 202}
  Time building chain proxies: 4.09, per 1000 atoms: 0.68
  Number of scatterers: 6013
  At special positions: 0
  Unit cell: (74.7, 68.06, 144.42, 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    1125      8.00
     N     973      7.00
     C    3872      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 145 " - pdb=" SG  CYS H 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " 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: 1.32
  Conformation dependent library (CDL) restraints added in 843.0 milliseconds
  

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1442

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 11 sheets defined
      34.0% alpha, 25.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 44
    Processing helix  chain 'A' and resid 47 through 57
    Processing helix  chain 'A' and resid 58 through 84
      Proline residue:  A  73  - end of helix
    Processing helix  chain 'A' and resid 86 through 99
    Processing helix  chain 'A' and resid 103 through 111
      removed outlier: 3.906A  pdb=" N   VAL A 107 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 143
      Proline residue:  A 135  - end of helix
      removed outlier: 3.891A  pdb=" N   ARG A 143 " --> pdb=" O   TYR A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 180
      removed outlier: 3.603A  pdb=" N   VAL A 160 " --> pdb=" O   TYR A 156 " (cutoff:3.500A)
      Proline residue:  A 169  - end of helix
    Processing helix  chain 'A' and resid 183 through 211
      removed outlier: 3.604A  pdb=" N   GLY A 190 " --> pdb=" O   TYR A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 218
      removed outlier: 4.150A  pdb=" N   ALA A 217 " --> pdb=" O   SER A 213 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   MET A 218 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 213 through 218'
    Processing helix  chain 'A' and resid 219 through 244
      Proline residue:  A 230  - end of helix
    Processing helix  chain 'A' and resid 247 through 259
      removed outlier: 3.638A  pdb=" N   ARG A 252 " --> pdb=" O   GLY A 248 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR A 253 " --> pdb=" O   ARG A 249 " (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 311
    Processing helix  chain 'L' and resid 121 through 128
      removed outlier: 3.618A  pdb=" N   GLY L 128 " --> pdb=" O   GLN L 124 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.601A  pdb=" N   VAL H  93 " --> pdb=" O   GLN H  39 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.590A  pdb=" N   TYR H 107 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 125 through 129
      removed outlier: 4.074A  pdb=" N   LEU H 129 " --> pdb=" O   GLY H 144 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   GLY H 144 " --> pdb=" O   LEU H 129 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   TYR H 180 " --> pdb=" O   GLY H 149 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 125 through 129
      removed outlier: 4.074A  pdb=" N   LEU H 129 " --> pdb=" O   GLY H 144 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   GLY H 144 " --> pdb=" O   LEU H 129 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   TYR H 180 " --> pdb=" O   GLY H 149 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 156 through 158
      removed outlier: 3.667A  pdb=" N   LYS H 213 " --> pdb=" O   CYS H 200 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 6
    Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.729A  pdb=" N   THR L 102 " --> pdb=" O   TYR L  86 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 5.173A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LYS L  39 " --> pdb=" O   THR L  43 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   THR L  43 " --> pdb=" O   LYS L  39 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 114 through 118
      removed outlier: 3.726A  pdb=" N   VAL L 133 " --> pdb=" O   PHE L 118 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   VAL L 132 " --> pdb=" O   LEU L 179 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   SER L 177 " --> pdb=" O   CYS L 134 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 114 through 118
      removed outlier: 3.726A  pdb=" N   VAL L 133 " --> pdb=" O   PHE L 118 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 145 through 148
      removed outlier: 3.540A  pdb=" N   TYR L 192 " --> pdb=" O   PHE L 209 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   CYS L 194 " --> pdb=" O   LYS L 207 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   LYS L 207 " --> pdb=" O   CYS L 194 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ALA L 196 " --> pdb=" O   ILE L 205 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ILE L 205 " --> pdb=" O   ALA L 196 " (cutoff:3.500A)

    304 hydrogen bonds defined for protein.
    846 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: 1.62

  Time building geometry restraints manager: 1.59 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1804
        1.34 -     1.46: 1151
        1.46 -     1.58: 3145
        1.58 -     1.70: 0
        1.70 -     1.82: 65
  Bond restraints: 6165
  Sorted by residual:
  bond pdb=" CA  SER H  21 "
       pdb=" C   SER H  21 "
    ideal  model  delta    sigma   weight residual
    1.522  1.550 -0.027 1.19e-02 7.06e+03 5.21e+00
  bond pdb=" N   SER H  21 "
       pdb=" CA  SER H  21 "
    ideal  model  delta    sigma   weight residual
    1.455  1.479 -0.024 1.21e-02 6.83e+03 3.96e+00
  bond pdb=" CA  MET H  20 "
       pdb=" C   MET H  20 "
    ideal  model  delta    sigma   weight residual
    1.522  1.545 -0.023 1.20e-02 6.94e+03 3.66e+00
  bond pdb=" CA  LYS H  19 "
       pdb=" C   LYS H  19 "
    ideal  model  delta    sigma   weight residual
    1.521  1.543 -0.022 1.24e-02 6.50e+03 3.20e+00
  bond pdb=" C   SER L 208 "
       pdb=" O   SER L 208 "
    ideal  model  delta    sigma   weight residual
    1.236  1.216  0.020 1.21e-02 6.83e+03 2.77e+00
  ... (remaining 6160 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 8244
        2.39 -     4.79: 118
        4.79 -     7.18: 18
        7.18 -     9.57: 4
        9.57 -    11.96: 2
  Bond angle restraints: 8386
  Sorted by residual:
  angle pdb=" N   VAL A 187 "
        pdb=" CA  VAL A 187 "
        pdb=" C   VAL A 187 "
      ideal   model   delta    sigma   weight residual
     110.72  116.90   -6.18 1.01e+00 9.80e-01 3.74e+01
  angle pdb=" N   LYS L 207 "
        pdb=" CA  LYS L 207 "
        pdb=" C   LYS L 207 "
      ideal   model   delta    sigma   weight residual
     108.76   99.12    9.64 1.69e+00 3.50e-01 3.25e+01
  angle pdb=" N   ILE A 188 "
        pdb=" CA  ILE A 188 "
        pdb=" C   ILE A 188 "
      ideal   model   delta    sigma   weight residual
     110.62  115.29   -4.67 1.02e+00 9.61e-01 2.10e+01
  angle pdb=" N   ALA A 217 "
        pdb=" CA  ALA A 217 "
        pdb=" C   ALA A 217 "
      ideal   model   delta    sigma   weight residual
     113.16  118.52   -5.36 1.24e+00 6.50e-01 1.87e+01
  angle pdb=" N   PHE A 216 "
        pdb=" CA  PHE A 216 "
        pdb=" C   PHE A 216 "
      ideal   model   delta    sigma   weight residual
     111.36  116.02   -4.66 1.09e+00 8.42e-01 1.83e+01
  ... (remaining 8381 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 3131
       17.51 -    35.03: 403
       35.03 -    52.54: 111
       52.54 -    70.06: 13
       70.06 -    87.57: 7
  Dihedral angle restraints: 3665
    sinusoidal: 1412
      harmonic: 2253
  Sorted by residual:
  dihedral pdb=" CB  CYS L 134 "
           pdb=" SG  CYS L 134 "
           pdb=" SG  CYS L 194 "
           pdb=" CB  CYS L 194 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -6.91  -79.09     1      1.00e+01 1.00e-02 7.78e+01
  dihedral pdb=" CB  CYS H 145 "
           pdb=" SG  CYS H 145 "
           pdb=" SG  CYS H 200 "
           pdb=" CB  CYS H 200 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   38.53   54.47     1      1.00e+01 1.00e-02 4.02e+01
  dihedral pdb=" CA  ALA H  92 "
           pdb=" C   ALA H  92 "
           pdb=" N   VAL H  93 "
           pdb=" CA  VAL H  93 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.29  -17.71     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 3662 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 805
       0.059 -    0.118: 140
       0.118 -    0.176: 12
       0.176 -    0.235: 1
       0.235 -    0.294: 1
  Chirality restraints: 959
  Sorted by residual:
  chirality pdb=" CA  LYS L 207 "
            pdb=" N   LYS L 207 "
            pdb=" C   LYS L 207 "
            pdb=" CB  LYS L 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.16e+00
  chirality pdb=" CA  ALA A 217 "
            pdb=" N   ALA A 217 "
            pdb=" C   ALA A 217 "
            pdb=" CB  ALA A 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.26    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CG  LEU A 228 "
            pdb=" CB  LEU A 228 "
            pdb=" CD1 LEU A 228 "
            pdb=" CD2 LEU A 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.05e-01
  ... (remaining 956 not shown)

  Planarity restraints: 1047
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL H 188 "    0.026 5.00e-02 4.00e+02   3.99e-02 2.55e+00
        pdb=" N   PRO H 189 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO H 189 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO H 189 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE L  94 "   -0.026 5.00e-02 4.00e+02   3.87e-02 2.40e+00
        pdb=" N   PRO L  95 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO L  95 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO L  95 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR H 127 "    0.024 5.00e-02 4.00e+02   3.58e-02 2.06e+00
        pdb=" N   PRO H 128 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO H 128 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO H 128 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1044 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.35: 12
        2.35 -     2.99: 3144
        2.99 -     3.62: 8889
        3.62 -     4.26: 13333
        4.26 -     4.90: 23120
  Nonbonded interactions: 48498
  Sorted by model distance:
  nonbonded pdb=" O   MET A 218 "
            pdb=" O   THR A 219 "
     model   vdw
     1.709 3.040
  nonbonded pdb=" CE  MET H  20 "
            pdb=" CE  MET H  81 "
     model   vdw
     1.734 3.880
  nonbonded pdb=" N   GLU L 187 "
            pdb=" OE1 GLU L 187 "
     model   vdw
     2.177 3.120
  nonbonded pdb=" O   GLY H  42 "
            pdb=" CG  LYS H  43 "
     model   vdw
     2.212 3.440
  nonbonded pdb=" OD1 ASN L  31 "
            pdb=" OG1 THR L  51 "
     model   vdw
     2.269 3.040
  ... (remaining 48493 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:             1.340
  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:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     16.940
  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:12.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
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   0.043   6169  Z= 0.158
  Angle     :  0.702  11.963   8394  Z= 0.377
  Chirality :  0.045   0.294    959
  Planarity :  0.004   0.040   1047
  Dihedral  : 16.539  87.569   2211
  Min Nonbonded Distance : 1.709

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.61 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 31.57 %
    Favored  : 64.90 %
  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:  0.01 (0.31), residues: 772
  helix:  1.63 (0.33), residues: 251
  sheet: -0.23 (0.41), residues: 188
  loop : -1.11 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H 159 
 HIS   0.001   0.000   HIS L 198 
 PHE   0.007   0.001   PHE A 285 
 TYR   0.014   0.001   TYR L 173 
 ARG   0.004   0.000   ARG L  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17545 (  279)
  hydrogen bonds       : angle       7.49067 (  846)
  SS BOND              : bond        0.00357 (    4)
  SS BOND              : angle       1.49375 (    8)
  covalent geometry    : bond        0.00297 ( 6165)
  covalent geometry    : angle       0.70035 ( 8386)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 150
  time to evaluate  : 0.651 
Fit side-chains
REVERT: L  207 LYS cc_start: 0.7120 (mmmm) cc_final: 0.6888 (mmmm)
  outliers start: 24
  outliers final: 21
  residues processed: 170
  average time/residue: 0.7003
  time to fit residues: 127.8968
Evaluate side-chains
  166 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 145
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  152 ASP
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  184 SER
Chi-restraints excluded: chain H residue  202 VAL
Chi-restraints excluded: chain H residue  218 SER
Chi-restraints excluded: chain L residue   65 SER
Chi-restraints excluded: chain L residue  131 SER
Chi-restraints excluded: chain L residue  197 THR
Chi-restraints excluded: chain L residue  200 THR
Chi-restraints excluded: chain L residue  205 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    0.2980
   chunk 57 optimal weight:    0.0980
   chunk 31 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 30 optimal weight:    0.2980
   chunk 59 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0870
   chunk 36 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   overall best weight:    0.2758

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
A 209 ASN
A 262 ASN
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  59 ASN
L 210 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.129141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.101373 restraints weight = 9171.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 2.65
r_work: 0.3078 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.0926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6169  Z= 0.118
  Angle     :  0.622   8.800   8394  Z= 0.309
  Chirality :  0.042   0.131    959
  Planarity :  0.004   0.041   1047
  Dihedral  :  5.672  46.254    858
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.74 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 28.49 %
    Favored  : 67.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.05 (0.31), residues: 772
  helix:  1.64 (0.32), residues: 260
  sheet: -0.22 (0.40), residues: 203
  loop : -1.15 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H  47 
 HIS   0.001   0.000   HIS H  41 
 PHE   0.007   0.001   PHE A  77 
 TYR   0.009   0.001   TYR A 307 
 ARG   0.002   0.000   ARG L  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04146 (  279)
  hydrogen bonds       : angle       5.20323 (  846)
  SS BOND              : bond        0.00433 (    4)
  SS BOND              : angle       1.85518 (    8)
  covalent geometry    : bond        0.00244 ( 6165)
  covalent geometry    : angle       0.61939 ( 8386)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 155
  time to evaluate  : 0.651 
Fit side-chains
REVERT: A   55 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8447 (mp)
REVERT: A  218 MET cc_start: 0.5999 (mmm) cc_final: 0.5696 (mmt)
REVERT: H   73 ASP cc_start: 0.8298 (t0) cc_final: 0.8080 (t0)
REVERT: L   61 ARG cc_start: 0.8704 (ptt-90) cc_final: 0.8345 (ptt-90)
REVERT: L   79 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8272 (mp0)
REVERT: L  207 LYS cc_start: 0.7753 (mmmm) cc_final: 0.7467 (mmmm)
  outliers start: 30
  outliers final: 10
  residues processed: 178
  average time/residue: 0.7380
  time to fit residues: 141.0228
Evaluate side-chains
  153 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 142
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  202 VAL
Chi-restraints excluded: chain L residue   50 TYR
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  180 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0050
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0870
   overall best weight:    0.8174

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

Flipped N/Q/H residues before XYZ refinement:
A 103 ASN
A 106 ASN
A 209 ASN
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 196 GLN
L   6 GLN
L  34 ASN
L 161 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.126925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.099550 restraints weight = 9232.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 2.66
r_work: 0.3045 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.1199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6169  Z= 0.142
  Angle     :  0.648  10.591   8394  Z= 0.317
  Chirality :  0.043   0.136    959
  Planarity :  0.004   0.041   1047
  Dihedral  :  4.492  25.802    836
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.61 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 27.46 %
    Favored  : 67.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.02 (0.31), residues: 772
  helix:  1.65 (0.32), residues: 259
  sheet: -0.37 (0.39), residues: 206
  loop : -1.17 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H  47 
 HIS   0.002   0.000   HIS H 204 
 PHE   0.007   0.001   PHE L  98 
 TYR   0.009   0.001   TYR L  91 
 ARG   0.002   0.000   ARG L  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04129 (  279)
  hydrogen bonds       : angle       4.78757 (  846)
  SS BOND              : bond        0.00517 (    4)
  SS BOND              : angle       2.27214 (    8)
  covalent geometry    : bond        0.00324 ( 6165)
  covalent geometry    : angle       0.64418 ( 8386)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 146
  time to evaluate  : 0.711 
Fit side-chains
REVERT: A   55 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8551 (mp)
REVERT: A  184 MET cc_start: 0.3883 (OUTLIER) cc_final: 0.3652 (ttt)
REVERT: H   73 ASP cc_start: 0.8505 (t0) cc_final: 0.8244 (t0)
REVERT: L   61 ARG cc_start: 0.8752 (ptt-90) cc_final: 0.8443 (ptt-90)
REVERT: L   79 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8376 (mp0)
REVERT: L  207 LYS cc_start: 0.8000 (mmmm) cc_final: 0.7654 (mmmm)
  outliers start: 34
  outliers final: 20
  residues processed: 170
  average time/residue: 0.7986
  time to fit residues: 145.0025
Evaluate side-chains
  161 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  113 LYS
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  266 CYS
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  182 MET
Chi-restraints excluded: chain H residue  202 VAL
Chi-restraints excluded: chain L residue   50 TYR
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  176 SER
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  205 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 18 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
A 293 GLN
B  18 GLN
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 161 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.125383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.097893 restraints weight = 9370.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 2.66
r_work: 0.3023 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.1334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6169  Z= 0.152
  Angle     :  0.638   9.129   8394  Z= 0.317
  Chirality :  0.043   0.135    959
  Planarity :  0.004   0.040   1047
  Dihedral  :  4.548  29.266    835
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.99 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 28.19 %
    Favored  : 66.96 %
  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 (0.31), residues: 772
  helix:  1.60 (0.32), residues: 259
  sheet: -0.44 (0.38), residues: 206
  loop : -1.21 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP L 163 
 HIS   0.002   0.000   HIS H 204 
 PHE   0.009   0.001   PHE H 102 
 TYR   0.011   0.001   TYR A 183 
 ARG   0.001   0.000   ARG L  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04076 (  279)
  hydrogen bonds       : angle       4.54916 (  846)
  SS BOND              : bond        0.00401 (    4)
  SS BOND              : angle       1.97532 (    8)
  covalent geometry    : bond        0.00352 ( 6165)
  covalent geometry    : angle       0.63511 ( 8386)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 150
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A   55 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8486 (mp)
REVERT: A   96 CYS cc_start: 0.8635 (m) cc_final: 0.8342 (m)
REVERT: A  180 ARG cc_start: 0.7070 (mtt90) cc_final: 0.6661 (mtt-85)
REVERT: A  182 GLN cc_start: 0.7205 (pm20) cc_final: 0.6232 (pt0)
REVERT: A  183 TYR cc_start: 0.6713 (m-80) cc_final: 0.6267 (m-80)
REVERT: H   73 ASP cc_start: 0.8569 (t0) cc_final: 0.8299 (t0)
REVERT: L   79 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8326 (mp0)
REVERT: L  207 LYS cc_start: 0.8052 (mmmm) cc_final: 0.7779 (mmmm)
  outliers start: 33
  outliers final: 17
  residues processed: 174
  average time/residue: 0.7702
  time to fit residues: 143.2328
Evaluate side-chains
  162 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  152 ASP
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  245 CYS
Chi-restraints excluded: chain A residue  266 CYS
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  182 MET
Chi-restraints excluded: chain H residue  202 VAL
Chi-restraints excluded: chain L residue   50 TYR
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  176 SER
Chi-restraints excluded: chain L residue  180 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 23 optimal weight:    0.2980
   chunk 58 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 161 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.126167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.098081 restraints weight = 9209.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 2.71
r_work: 0.3029 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2909 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6169  Z= 0.135
  Angle     :  0.645  11.594   8394  Z= 0.317
  Chirality :  0.043   0.134    959
  Planarity :  0.004   0.041   1047
  Dihedral  :  4.588  30.377    835
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 29.07 %
    Favored  : 66.08 %
  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: -0.12 (0.31), residues: 772
  helix:  1.57 (0.32), residues: 259
  sheet: -0.43 (0.38), residues: 207
  loop : -1.23 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP L 163 
 HIS   0.001   0.000   HIS B  17 
 PHE   0.008   0.001   PHE L  98 
 TYR   0.012   0.001   TYR A 183 
 ARG   0.001   0.000   ARG L  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03979 (  279)
  hydrogen bonds       : angle       4.46513 (  846)
  SS BOND              : bond        0.00384 (    4)
  SS BOND              : angle       1.87099 (    8)
  covalent geometry    : bond        0.00311 ( 6165)
  covalent geometry    : angle       0.64297 ( 8386)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 156
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A   55 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8478 (mp)
REVERT: A   96 CYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8320 (m)
REVERT: A  219 THR cc_start: 0.7204 (m) cc_final: 0.6796 (p)
REVERT: H   73 ASP cc_start: 0.8594 (t0) cc_final: 0.8309 (t0)
REVERT: L   79 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8418 (mp0)
  outliers start: 33
  outliers final: 16
  residues processed: 175
  average time/residue: 0.7304
  time to fit residues: 136.8308
Evaluate side-chains
  156 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  245 CYS
Chi-restraints excluded: chain A residue  266 CYS
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  182 MET
Chi-restraints excluded: chain H residue  202 VAL
Chi-restraints excluded: chain L residue   50 TYR
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  176 SER
Chi-restraints excluded: chain L residue  180 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 51 optimal weight:    0.0010
   chunk 43 optimal weight:    2.9990
   chunk 3 optimal weight:    0.4980
   chunk 58 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 61 optimal weight:    6.9990
   chunk 60 optimal weight:    4.9990
   overall best weight:    1.0388

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
A 262 ASN
A 293 GLN
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 161 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.124068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.096061 restraints weight = 9182.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 2.68
r_work: 0.3004 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6169  Z= 0.166
  Angle     :  0.655   8.923   8394  Z= 0.327
  Chirality :  0.044   0.142    959
  Planarity :  0.004   0.040   1047
  Dihedral  :  4.732  33.650    835
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 29.07 %
    Favored  : 65.64 %
  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: -0.17 (0.31), residues: 772
  helix:  1.48 (0.32), residues: 260
  sheet: -0.43 (0.37), residues: 207
  loop : -1.25 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L 163 
 HIS   0.002   0.001   HIS H  84 
 PHE   0.011   0.001   PHE L 118 
 TYR   0.011   0.001   TYR L  91 
 ARG   0.002   0.000   ARG L  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04197 (  279)
  hydrogen bonds       : angle       4.38738 (  846)
  SS BOND              : bond        0.00498 (    4)
  SS BOND              : angle       1.83264 (    8)
  covalent geometry    : bond        0.00389 ( 6165)
  covalent geometry    : angle       0.65319 ( 8386)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 145
  time to evaluate  : 0.691 
Fit side-chains
REVERT: A   55 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8532 (mp)
REVERT: A   96 CYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8387 (m)
REVERT: A  182 GLN cc_start: 0.7289 (pm20) cc_final: 0.6392 (pt0)
REVERT: A  183 TYR cc_start: 0.6831 (m-80) cc_final: 0.6359 (m-80)
REVERT: H   73 ASP cc_start: 0.8685 (t0) cc_final: 0.8421 (t0)
REVERT: L   79 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8449 (mp0)
REVERT: L  144 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8491 (pt)
REVERT: L  209 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7514 (t80)
  outliers start: 36
  outliers final: 19
  residues processed: 166
  average time/residue: 0.7127
  time to fit residues: 126.7528
Evaluate side-chains
  160 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 137
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  245 CYS
Chi-restraints excluded: chain A residue  266 CYS
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   31 ASP
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  147 VAL
Chi-restraints excluded: chain H residue  182 MET
Chi-restraints excluded: chain H residue  202 VAL
Chi-restraints excluded: chain L residue   50 TYR
Chi-restraints excluded: chain L residue  144 ILE
Chi-restraints excluded: chain L residue  176 SER
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  209 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 3 optimal weight:    0.3980
   chunk 74 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
A 262 ASN
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  40 ASN
H 196 GLN
L 161 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.125353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.097134 restraints weight = 9150.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 2.74
r_work: 0.3011 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6169  Z= 0.149
  Angle     :  0.669  11.636   8394  Z= 0.327
  Chirality :  0.044   0.139    959
  Planarity :  0.004   0.039   1047
  Dihedral  :  4.761  34.935    835
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 30.25 %
    Favored  : 65.05 %
  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: -0.20 (0.31), residues: 772
  helix:  1.47 (0.32), residues: 260
  sheet: -0.46 (0.37), residues: 207
  loop : -1.26 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 159 
 HIS   0.001   0.000   HIS B  17 
 PHE   0.010   0.001   PHE L 118 
 TYR   0.010   0.001   TYR H  95 
 ARG   0.001   0.000   ARG L  61 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04070 (  279)
  hydrogen bonds       : angle       4.31499 (  846)
  SS BOND              : bond        0.00453 (    4)
  SS BOND              : angle       2.08032 (    8)
  covalent geometry    : bond        0.00348 ( 6165)
  covalent geometry    : angle       0.66602 ( 8386)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 149
  time to evaluate  : 0.727 
Fit side-chains
REVERT: A   55 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8456 (mp)
REVERT: A   96 CYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8286 (m)
REVERT: A  182 GLN cc_start: 0.7309 (pm20) cc_final: 0.6468 (pt0)
REVERT: A  183 TYR cc_start: 0.6769 (m-80) cc_final: 0.6313 (m-80)
REVERT: A  221 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7799 (mm)
REVERT: B   18 GLN cc_start: 0.9439 (OUTLIER) cc_final: 0.9214 (mp10)
REVERT: H   73 ASP cc_start: 0.8651 (t0) cc_final: 0.8360 (t0)
REVERT: L   17 ASP cc_start: 0.8432 (t0) cc_final: 0.7818 (t0)
REVERT: L   79 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8419 (mp0)
REVERT: L  209 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7482 (t80)
  outliers start: 32
  outliers final: 18
  residues processed: 169
  average time/residue: 0.7790
  time to fit residues: 140.9743
Evaluate side-chains
  157 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 0.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  245 CYS
Chi-restraints excluded: chain A residue  266 CYS
Chi-restraints excluded: chain B residue   18 GLN
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  147 VAL
Chi-restraints excluded: chain H residue  182 MET
Chi-restraints excluded: chain H residue  202 VAL
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  176 SER
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  209 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 26 optimal weight:    0.2980
   chunk 8 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0060
   chunk 57 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 70 optimal weight:    3.9990
   chunk 25 optimal weight:    0.4980
   chunk 61 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
A 262 ASN
A 293 GLN
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  40 ASN
L 161 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.126770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.098951 restraints weight = 9098.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 2.70
r_work: 0.3049 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.1647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6169  Z= 0.121
  Angle     :  0.643   8.498   8394  Z= 0.316
  Chirality :  0.043   0.132    959
  Planarity :  0.004   0.039   1047
  Dihedral  :  4.649  34.087    835
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 31.86 %
    Favored  : 64.61 %
  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: -0.17 (0.31), residues: 772
  helix:  1.50 (0.32), residues: 260
  sheet: -0.49 (0.37), residues: 207
  loop : -1.22 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 159 
 HIS   0.001   0.000   HIS B  17 
 PHE   0.011   0.001   PHE L 118 
 TYR   0.009   0.001   TYR A 146 
 ARG   0.002   0.000   ARG L  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03768 (  279)
  hydrogen bonds       : angle       4.22316 (  846)
  SS BOND              : bond        0.00310 (    4)
  SS BOND              : angle       1.42990 (    8)
  covalent geometry    : bond        0.00273 ( 6165)
  covalent geometry    : angle       0.64186 ( 8386)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 146
  time to evaluate  : 0.721 
Fit side-chains
REVERT: A   55 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8462 (mp)
REVERT: A   96 CYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8326 (m)
REVERT: A  221 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7701 (mm)
REVERT: H   73 ASP cc_start: 0.8665 (t0) cc_final: 0.8358 (t0)
REVERT: L   79 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8433 (mp0)
REVERT: L  199 LYS cc_start: 0.7677 (mmmt) cc_final: 0.7312 (mtmm)
  outliers start: 24
  outliers final: 16
  residues processed: 161
  average time/residue: 0.7940
  time to fit residues: 137.0681
Evaluate side-chains
  153 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  266 CYS
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   31 ASP
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  147 VAL
Chi-restraints excluded: chain H residue  182 MET
Chi-restraints excluded: chain H residue  202 VAL
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  176 SER
Chi-restraints excluded: chain L residue  180 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 0 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 50 optimal weight:    9.9990
   chunk 11 optimal weight:    0.5980
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 196 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.124212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.096577 restraints weight = 9231.667|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 2.69
r_work: 0.2995 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6169  Z= 0.185
  Angle     :  0.702  12.180   8394  Z= 0.343
  Chirality :  0.045   0.152    959
  Planarity :  0.004   0.038   1047
  Dihedral  :  4.860  35.994    835
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 31.86 %
    Favored  : 64.32 %
  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: -0.25 (0.31), residues: 772
  helix:  1.44 (0.32), residues: 260
  sheet: -0.52 (0.37), residues: 207
  loop : -1.28 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H 159 
 HIS   0.001   0.000   HIS H 204 
 PHE   0.012   0.001   PHE H 102 
 TYR   0.013   0.001   TYR A 183 
 ARG   0.004   0.000   ARG L  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04176 (  279)
  hydrogen bonds       : angle       4.25120 (  846)
  SS BOND              : bond        0.00522 (    4)
  SS BOND              : angle       2.12290 (    8)
  covalent geometry    : bond        0.00440 ( 6165)
  covalent geometry    : angle       0.69878 ( 8386)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 140
  time to evaluate  : 0.667 
Fit side-chains
REVERT: A   55 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8473 (mp)
REVERT: A   96 CYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8278 (m)
REVERT: A  221 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7795 (mm)
REVERT: B   29 ASN cc_start: 0.8302 (p0) cc_final: 0.8081 (p0)
REVERT: H   73 ASP cc_start: 0.8685 (t0) cc_final: 0.8395 (t0)
REVERT: L   79 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8455 (mp0)
REVERT: L  209 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7411 (t80)
  outliers start: 26
  outliers final: 18
  residues processed: 156
  average time/residue: 0.8135
  time to fit residues: 135.5730
Evaluate side-chains
  152 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  215 MET
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  266 CYS
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   31 ASP
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  147 VAL
Chi-restraints excluded: chain H residue  182 MET
Chi-restraints excluded: chain H residue  202 VAL
Chi-restraints excluded: chain L residue   50 TYR
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  176 SER
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  209 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0030
   chunk 46 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 71 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
A 262 ASN
A 293 GLN
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 196 GLN
L 161 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.126107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.097817 restraints weight = 9235.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.77
r_work: 0.3018 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6169  Z= 0.138
  Angle     :  0.675  10.028   8394  Z= 0.332
  Chirality :  0.044   0.139    959
  Planarity :  0.004   0.039   1047
  Dihedral  :  4.837  36.593    835
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 32.45 %
    Favored  : 64.02 %
  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 (0.31), residues: 772
  helix:  1.44 (0.32), residues: 261
  sheet: -0.56 (0.38), residues: 203
  loop : -1.20 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H 159 
 HIS   0.002   0.000   HIS B  17 
 PHE   0.010   0.001   PHE L 118 
 TYR   0.012   0.001   TYR A 146 
 ARG   0.004   0.000   ARG L  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03981 (  279)
  hydrogen bonds       : angle       4.23171 (  846)
  SS BOND              : bond        0.00438 (    4)
  SS BOND              : angle       1.21288 (    8)
  covalent geometry    : bond        0.00321 ( 6165)
  covalent geometry    : angle       0.67453 ( 8386)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 0.697 
Fit side-chains
REVERT: A   55 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8431 (mp)
REVERT: A   96 CYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8167 (m)
REVERT: A  221 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7736 (mm)
REVERT: H   73 ASP cc_start: 0.8660 (t0) cc_final: 0.8370 (t0)
REVERT: L   79 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8380 (mp0)
REVERT: L  209 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7275 (t80)
  outliers start: 24
  outliers final: 15
  residues processed: 151
  average time/residue: 0.8227
  time to fit residues: 132.3204
Evaluate side-chains
  148 residues out of total 681 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  266 CYS
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  147 VAL
Chi-restraints excluded: chain H residue  182 MET
Chi-restraints excluded: chain H residue  202 VAL
Chi-restraints excluded: chain L residue   50 TYR
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  176 SER
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  209 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
** B  40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  40 ASN
H 196 GLN
L 161 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.124193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.096510 restraints weight = 9374.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3109 rms_B_bonded: 2.71
r_work: 0.2995 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6169  Z= 0.181
  Angle     :  0.714  13.814   8394  Z= 0.352
  Chirality :  0.045   0.156    959
  Planarity :  0.004   0.038   1047
  Dihedral  :  5.001  39.694    835
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.25 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 32.60 %
    Favored  : 63.88 %
  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: -0.28 (0.31), residues: 772
  helix:  1.43 (0.32), residues: 260
  sheet: -0.57 (0.37), residues: 207
  loop : -1.27 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H 159 
 HIS   0.002   0.001   HIS L 198 
 PHE   0.019   0.001   PHE H  29 
 TYR   0.012   0.001   TYR A 183 
 ARG   0.004   0.000   ARG L  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04232 (  279)
  hydrogen bonds       : angle       4.28601 (  846)
  SS BOND              : bond        0.00517 (    4)
  SS BOND              : angle       1.61922 (    8)
  covalent geometry    : bond        0.00430 ( 6165)
  covalent geometry    : angle       0.71289 ( 8386)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4879.16 seconds
wall clock time: 84 minutes 56.23 seconds (5096.23 seconds total)