Starting phenix.real_space_refine
on Tue Feb 11 12:18:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vae_31838/02_2025/7vae_31838.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vae_31838/02_2025/7vae_31838.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vae_31838/02_2025/7vae_31838.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vae_31838/02_2025/7vae_31838.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vae_31838/02_2025/7vae_31838.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vae_31838/02_2025/7vae_31838.cif"
  }
  resolution = 3.55
  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=   0.002
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      39      5.16       5
     C    3638      2.51       5
     N     909      2.21       5
     O    1057      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 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: 5643
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2290
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2290
          Classifications: {'peptide': 299}
          Link IDs: {'PTRANS': 15, 'TRANS': 283}
    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: 3.73, per 1000 atoms: 0.66
  Number of scatterers: 5643
  At special positions: 0
  Unit cell: (90.885, 73.455, 140.685, 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      39     16.00
     O    1057      8.00
     N     909      7.00
     C    3638      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  96 " - pdb=" SG  CYS A 266 " distance=2.04
    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: 1.35
  Conformation dependent library (CDL) restraints added in 707.0 milliseconds
  

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1358

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 10 sheets defined
      38.3% alpha, 22.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 46
    Processing helix  chain 'A' and resid 47 through 57
      removed outlier: 3.659A  pdb=" N   ILE A  51 " --> pdb=" O   GLU A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 84
      Proline residue:  A  73  - end of helix
    Processing helix  chain 'A' and resid 86 through 98
    Processing helix  chain 'A' and resid 102 through 113
      removed outlier: 3.833A  pdb=" N   ASN A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 142
      removed outlier: 4.127A  pdb=" N   GLY A 132 " --> pdb=" O   PHE A 128 " (cutoff:3.500A)
      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 209
      removed outlier: 3.588A  pdb=" N   VAL A 187 " --> pdb=" O   TYR A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 217
      removed outlier: 3.846A  pdb=" N   PHE A 216 " --> pdb=" O   LYS A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 244
      Proline residue:  A 230  - end of helix
    Processing helix  chain 'A' and resid 247 through 260
    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 310
      removed outlier: 3.925A  pdb=" N   GLY A 295 " --> pdb=" O   ILE A 291 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   LEU A 299 " --> pdb=" O   GLY A 295 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   CYS A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 30
      No H-bonds generated for 'chain 'H' and resid 28 through 30'
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 4.274A  pdb=" N   SER H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 85 through 89
      removed outlier: 3.841A  pdb=" N   LEU L  89 " --> pdb=" O   ALA L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 126 through 131
    Processing helix  chain 'L' and resid 190 through 195
      removed outlier: 3.813A  pdb=" N   HIS L 194 " --> pdb=" O   GLU L 190 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.706A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 8.678A  pdb=" N   TYR H  32 " --> pdb=" O   ASN H  52 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   ASN H  52 " --> pdb=" O   TYR H  32 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ILE H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   TYR H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.799A  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: 6.706A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   TYR H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
      removed outlier: 8.279A  pdb=" N   TYR H 100 " --> pdb=" O   PHE H 108 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   PHE H 108 " --> pdb=" O   TYR H 100 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 128 through 132
      removed outlier: 4.476A  pdb=" N   GLY H 147 " --> pdb=" O   LEU H 132 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   CYS H 148 " --> pdb=" O   SER H 187 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   SER H 187 " --> pdb=" O   CYS H 148 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   MET H 185 " --> pdb=" O   VAL H 150 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   THR H 184 " --> pdb=" O   ALA H 176 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   ALA H 176 " --> pdb=" O   THR H 184 " (cutoff:3.500A)
      removed outlier: 3.798A  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
    Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.390A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 110 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 21
      removed outlier: 3.880A  pdb=" N   VAL L  19 " --> pdb=" O   ILE L  81 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ILE L  81 " --> pdb=" O   VAL L  19 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 40 through 43
      removed outlier: 6.549A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 119 through 123
      removed outlier: 3.540A  pdb=" N   ASN L 143 " --> pdb=" O   TYR L 178 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   TYR L 178 " --> pdb=" O   ASN L 143 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 158 through 159

    287 hydrogen bonds defined for protein.
    798 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: 1.63

  Time building geometry restraints manager: 1.58 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: 1724
        1.35 -     1.47: 1453
        1.47 -     1.59: 2543
        1.59 -     1.71: 0
        1.71 -     1.83: 58
  Bond restraints: 5778
  Sorted by residual:
  bond pdb=" CB  MET A 256 "
       pdb=" CG  MET A 256 "
    ideal  model  delta    sigma   weight residual
    1.520  1.492  0.028 3.00e-02 1.11e+03 8.67e-01
  bond pdb=" CB  MET A 116 "
       pdb=" CG  MET A 116 "
    ideal  model  delta    sigma   weight residual
    1.520  1.493  0.027 3.00e-02 1.11e+03 8.27e-01
  bond pdb=" CA  VAL H 191 "
       pdb=" C   VAL H 191 "
    ideal  model  delta    sigma   weight residual
    1.524  1.515  0.009 1.05e-02 9.07e+03 8.01e-01
  bond pdb=" CB  LYS H 151 "
       pdb=" CG  LYS H 151 "
    ideal  model  delta    sigma   weight residual
    1.520  1.546 -0.026 3.00e-02 1.11e+03 7.46e-01
  bond pdb=" CA  ILE H  48 "
       pdb=" CB  ILE H  48 "
    ideal  model  delta    sigma   weight residual
    1.545  1.537  0.008 9.10e-03 1.21e+04 7.17e-01
  ... (remaining 5773 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 7730
        2.26 -     4.52: 98
        4.52 -     6.78: 17
        6.78 -     9.04: 4
        9.04 -    11.30: 1
  Bond angle restraints: 7850
  Sorted by residual:
  angle pdb=" C   ALA H  16 "
        pdb=" CA  ALA H  16 "
        pdb=" CB  ALA H  16 "
      ideal   model   delta    sigma   weight residual
     115.89  110.24    5.65 1.32e+00 5.74e-01 1.83e+01
  angle pdb=" CA  LEU A 150 "
        pdb=" CB  LEU A 150 "
        pdb=" CG  LEU A 150 "
      ideal   model   delta    sigma   weight residual
     116.30  127.60  -11.30 3.50e+00 8.16e-02 1.04e+01
  angle pdb=" CB  MET A  72 "
        pdb=" CG  MET A  72 "
        pdb=" SD  MET A  72 "
      ideal   model   delta    sigma   weight residual
     112.70  121.37   -8.67 3.00e+00 1.11e-01 8.36e+00
  angle pdb=" CB  MET A 256 "
        pdb=" CG  MET A 256 "
        pdb=" SD  MET A 256 "
      ideal   model   delta    sigma   weight residual
     112.70  104.69    8.01 3.00e+00 1.11e-01 7.14e+00
  angle pdb=" CB  LYS H 151 "
        pdb=" CG  LYS H 151 "
        pdb=" CD  LYS H 151 "
      ideal   model   delta    sigma   weight residual
     111.30  117.32   -6.02 2.30e+00 1.89e-01 6.84e+00
  ... (remaining 7845 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 3129
       17.97 -    35.94: 253
       35.94 -    53.91: 50
       53.91 -    71.88: 7
       71.88 -    89.84: 4
  Dihedral angle restraints: 3443
    sinusoidal: 1317
      harmonic: 2126
  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  171.35  -78.35     1      1.00e+01 1.00e-02 7.66e+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
      93.00  127.11  -34.11     1      1.00e+01 1.00e-02 1.65e+01
  dihedral pdb=" CA  LEU A 228 "
           pdb=" C   LEU A 228 "
           pdb=" N   MET A 229 "
           pdb=" CA  MET A 229 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.59  -16.41     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 3440 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 475
       0.026 -    0.053: 259
       0.053 -    0.079: 101
       0.079 -    0.106: 54
       0.106 -    0.132: 22
  Chirality restraints: 911
  Sorted by residual:
  chirality pdb=" CA  THR A 219 "
            pdb=" N   THR A 219 "
            pdb=" C   THR A 219 "
            pdb=" CB  THR A 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.39    0.13 2.00e-01 2.50e+01 4.35e-01
  chirality pdb=" CA  VAL H 191 "
            pdb=" N   VAL H 191 "
            pdb=" C   VAL H 191 "
            pdb=" CB  VAL H 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.85e-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    2.56   -0.12 2.00e-01 2.50e+01 3.79e-01
  ... (remaining 908 not shown)

  Planarity restraints: 971
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR H 125 "    0.055 5.00e-02 4.00e+02   8.26e-02 1.09e+01
        pdb=" N   PRO H 126 "   -0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO H 126 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO H 126 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  57 "    0.041 5.00e-02 4.00e+02   6.18e-02 6.10e+00
        pdb=" N   PRO A  58 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A  58 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A  58 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 219 "   -0.031 5.00e-02 4.00e+02   4.70e-02 3.53e+00
        pdb=" N   PRO A 220 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A 220 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 220 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 968 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 602
        2.75 -     3.29: 5851
        3.29 -     3.82: 9146
        3.82 -     4.36: 10288
        4.36 -     4.90: 18029
  Nonbonded interactions: 43916
  Sorted by model distance:
  nonbonded pdb=" O   VAL L   3 "
            pdb=" OG  SER L  26 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" O   VAL A 203 "
            pdb=" OG  SER A 206 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   GLY H   8 "
            pdb=" OG1 THR H 115 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" NH1 ARG L 160 "
            pdb=" O   ASN L 162 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" O   LEU A  85 "
            pdb=" NH1 ARG L  33 "
     model   vdw
     2.331 3.120
  ... (remaining 43911 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.620
  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:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     16.460
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
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   0.035   5778  Z= 0.187
  Angle     :  0.671  11.300   7850  Z= 0.340
  Chirality :  0.042   0.132    911
  Planarity :  0.005   0.083    971
  Dihedral  : 13.730  89.845   2073
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  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: -0.15 (0.32), residues: 730
  helix:  0.88 (0.34), residues: 237
  sheet:  0.38 (0.39), residues: 193
  loop : -1.19 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP L  41 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.018   0.001   PHE A 292 
 TYR   0.022   0.001   TYR H 130 
 ARG   0.008   0.001   ARG A 185 

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 271
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7448 (mpt-90) cc_final: 0.6778 (mtt180)
REVERT: A   27 LEU cc_start: 0.8904 (tt) cc_final: 0.8630 (tt)
REVERT: A   31 LEU cc_start: 0.9282 (mm) cc_final: 0.8958 (mm)
REVERT: A   32 VAL cc_start: 0.8386 (t) cc_final: 0.7945 (t)
REVERT: A   36 LEU cc_start: 0.9075 (mm) cc_final: 0.8712 (mm)
REVERT: A   99 SER cc_start: 0.8824 (m) cc_final: 0.8617 (p)
REVERT: A  108 PHE cc_start: 0.8213 (m-80) cc_final: 0.7994 (m-10)
REVERT: A  128 PHE cc_start: 0.8459 (t80) cc_final: 0.8241 (t80)
REVERT: H  130 TYR cc_start: 0.8180 (m-80) cc_final: 0.7304 (m-80)
REVERT: H  185 MET cc_start: 0.8801 (ppp) cc_final: 0.8565 (ppp)
REVERT: L   42 TYR cc_start: 0.7945 (m-80) cc_final: 0.7574 (m-80)
REVERT: L   94 CYS cc_start: 0.6419 (p) cc_final: 0.5440 (p)
REVERT: L  162 ASN cc_start: 0.8256 (m-40) cc_final: 0.8042 (m-40)
REVERT: L  180 MET cc_start: 0.7604 (tmm) cc_final: 0.6839 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 271
  average time/residue: 0.1511
  time to fit residues: 54.1801
Evaluate side-chains
  238 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0040
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.7594

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  84 GLN
A 293 GLN
L  43 GLN
** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.154214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.127368 restraints weight = 10212.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.131157 restraints weight = 4837.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.133602 restraints weight = 2852.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5778  Z= 0.236
  Angle     :  0.690   8.284   7850  Z= 0.349
  Chirality :  0.045   0.170    911
  Planarity :  0.005   0.063    971
  Dihedral  :  4.404  19.417    787
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.16 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 16.88 %
    Favored  : 80.62 %
  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: 730
  helix:  1.23 (0.33), residues: 246
  sheet:  0.49 (0.40), residues: 185
  loop : -1.19 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP L  41 
 HIS   0.002   0.001   HIS L 194 
 PHE   0.016   0.002   PHE H 174 
 TYR   0.011   0.001   TYR H 183 
 ARG   0.004   0.001   ARG L 113 

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 244
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7558 (mpt-90) cc_final: 0.6592 (mtt180)
REVERT: A   34 MET cc_start: 0.8760 (ttm) cc_final: 0.8509 (ttm)
REVERT: A   36 LEU cc_start: 0.8919 (mm) cc_final: 0.8563 (mm)
REVERT: A   82 PHE cc_start: 0.8806 (t80) cc_final: 0.8394 (t80)
REVERT: A  117 ASN cc_start: 0.8076 (p0) cc_final: 0.7485 (p0)
REVERT: A  128 PHE cc_start: 0.8930 (t80) cc_final: 0.8506 (t80)
REVERT: A  189 LYS cc_start: 0.7443 (mmtt) cc_final: 0.6756 (tttm)
REVERT: A  292 PHE cc_start: 0.6584 (t80) cc_final: 0.6115 (t80)
REVERT: H   36 TRP cc_start: 0.9165 (m100) cc_final: 0.8760 (m100)
REVERT: H   56 ASP cc_start: 0.8939 (t0) cc_final: 0.8690 (t0)
REVERT: H   73 ASP cc_start: 0.8112 (t0) cc_final: 0.7713 (t0)
REVERT: H  130 TYR cc_start: 0.8274 (m-80) cc_final: 0.7538 (m-10)
REVERT: H  185 MET cc_start: 0.9036 (ppp) cc_final: 0.8476 (ppp)
REVERT: L   17 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7564 (tp30)
REVERT: L   41 TRP cc_start: 0.8961 (m100) cc_final: 0.8624 (m100)
REVERT: L   42 TYR cc_start: 0.8513 (m-80) cc_final: 0.8152 (m-80)
REVERT: L   94 CYS cc_start: 0.6963 (p) cc_final: 0.6507 (p)
REVERT: L  180 MET cc_start: 0.8127 (tmm) cc_final: 0.7617 (tmm)
REVERT: L  184 LEU cc_start: 0.8988 (mt) cc_final: 0.8728 (mt)
REVERT: L  200 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6248 (pm20)
REVERT: L  214 PHE cc_start: 0.6242 (t80) cc_final: 0.5992 (t80)
  outliers start: 16
  outliers final: 12
  residues processed: 248
  average time/residue: 0.1520
  time to fit residues: 51.0643
Evaluate side-chains
  245 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 232
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  125 THR
Chi-restraints excluded: chain H residue  149 LEU
Chi-restraints excluded: chain H residue  218 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   89 LEU
Chi-restraints excluded: chain L residue  197 TYR
Chi-restraints excluded: chain L residue  200 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 57 optimal weight:    5.9990
   chunk 60 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 64 optimal weight:    7.9990
   chunk 15 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 58 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 GLN
H   5 GLN
** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.149391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.122082 restraints weight = 10652.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.125727 restraints weight = 5027.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.127936 restraints weight = 2976.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5778  Z= 0.257
  Angle     :  0.694  10.621   7850  Z= 0.345
  Chirality :  0.045   0.174    911
  Planarity :  0.005   0.068    971
  Dihedral  :  4.524  22.167    787
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 19.69 %
    Favored  : 75.47 %
  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:  0.09 (0.31), residues: 730
  helix:  1.36 (0.32), residues: 246
  sheet:  0.55 (0.39), residues: 190
  loop : -1.42 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP L 168 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.016   0.001   PHE H 174 
 TYR   0.016   0.002   TYR H  50 
 ARG   0.010   0.001   ARG A  21 

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 243
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7533 (mpt-90) cc_final: 0.6668 (mtt180)
REVERT: A   34 MET cc_start: 0.8754 (ttm) cc_final: 0.8447 (ttm)
REVERT: A   36 LEU cc_start: 0.8971 (mm) cc_final: 0.8565 (mm)
REVERT: A   50 LYS cc_start: 0.8320 (mmmm) cc_final: 0.8098 (mmmm)
REVERT: A   82 PHE cc_start: 0.8774 (t80) cc_final: 0.8374 (t80)
REVERT: A  116 MET cc_start: 0.7411 (tpp) cc_final: 0.7139 (tpp)
REVERT: A  117 ASN cc_start: 0.8103 (p0) cc_final: 0.7510 (p0)
REVERT: A  160 MET cc_start: 0.8416 (mmt) cc_final: 0.7843 (ppp)
REVERT: A  292 PHE cc_start: 0.6797 (t80) cc_final: 0.6430 (t80)
REVERT: H    5 GLN cc_start: 0.8735 (mm110) cc_final: 0.8366 (mm110)
REVERT: H   36 TRP cc_start: 0.9167 (m100) cc_final: 0.8776 (m100)
REVERT: H   73 ASP cc_start: 0.8232 (t0) cc_final: 0.7886 (t0)
REVERT: H  130 TYR cc_start: 0.8164 (m-80) cc_final: 0.7688 (m-10)
REVERT: H  151 LYS cc_start: 0.8281 (tppt) cc_final: 0.7890 (tppp)
REVERT: H  185 MET cc_start: 0.9137 (ppp) cc_final: 0.8526 (ppp)
REVERT: L   17 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7557 (tp30)
REVERT: L   41 TRP cc_start: 0.9026 (m100) cc_final: 0.8555 (m100)
REVERT: L   42 TYR cc_start: 0.8737 (m-80) cc_final: 0.8457 (m-80)
REVERT: L   96 GLN cc_start: 0.9118 (pp30) cc_final: 0.8686 (pp30)
REVERT: L  180 MET cc_start: 0.8179 (tmm) cc_final: 0.7656 (tmm)
REVERT: L  200 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6383 (pm20)
REVERT: L  214 PHE cc_start: 0.6661 (t80) cc_final: 0.6182 (t80)
  outliers start: 31
  outliers final: 23
  residues processed: 252
  average time/residue: 0.1565
  time to fit residues: 53.0595
Evaluate side-chains
  249 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 225
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  187 VAL
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  247 ASN
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  125 THR
Chi-restraints excluded: chain H residue  149 LEU
Chi-restraints excluded: chain H residue  183 TYR
Chi-restraints excluded: chain H residue  184 THR
Chi-restraints excluded: chain H residue  218 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  200 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 61 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 68 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 66 optimal weight:    0.3980
   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  54 HIS
A  84 GLN
** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 113 GLN
L  27 GLN
** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.149914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.122385 restraints weight = 10999.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.126229 restraints weight = 5152.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.128708 restraints weight = 3007.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5778  Z= 0.209
  Angle     :  0.673   8.289   7850  Z= 0.333
  Chirality :  0.044   0.150    911
  Planarity :  0.005   0.057    971
  Dihedral  :  4.483  23.376    787
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 24.06 %
    Favored  : 71.88 %
  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:  0.08 (0.31), residues: 730
  helix:  1.25 (0.32), residues: 247
  sheet:  0.58 (0.39), residues: 194
  loop : -1.39 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP L 168 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.012   0.001   PHE H 154 
 TYR   0.017   0.001   TYR L 145 
 ARG   0.007   0.000   ARG A  21 

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 246
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7499 (mpt-90) cc_final: 0.6709 (mtt180)
REVERT: A   34 MET cc_start: 0.8749 (ttm) cc_final: 0.8399 (ttm)
REVERT: A   36 LEU cc_start: 0.8924 (mm) cc_final: 0.8526 (mm)
REVERT: A   50 LYS cc_start: 0.8248 (mmmm) cc_final: 0.8047 (mmmm)
REVERT: A   82 PHE cc_start: 0.8790 (t80) cc_final: 0.8366 (t80)
REVERT: A  117 ASN cc_start: 0.8220 (p0) cc_final: 0.7688 (p0)
REVERT: A  160 MET cc_start: 0.8359 (mmt) cc_final: 0.7838 (ppp)
REVERT: H    5 GLN cc_start: 0.8688 (mm110) cc_final: 0.8288 (mm110)
REVERT: H   73 ASP cc_start: 0.8223 (t0) cc_final: 0.7877 (t0)
REVERT: H  130 TYR cc_start: 0.8134 (m-80) cc_final: 0.7644 (m-10)
REVERT: H  151 LYS cc_start: 0.8280 (tppt) cc_final: 0.8042 (tppp)
REVERT: H  179 GLN cc_start: 0.8530 (pp30) cc_final: 0.8131 (pp30)
REVERT: H  185 MET cc_start: 0.9194 (ppp) cc_final: 0.8581 (ppp)
REVERT: L   17 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7565 (tp30)
REVERT: L   41 TRP cc_start: 0.8998 (m100) cc_final: 0.8738 (m100)
REVERT: L   42 TYR cc_start: 0.8764 (m-80) cc_final: 0.8512 (m-80)
REVERT: L   96 GLN cc_start: 0.9030 (pp30) cc_final: 0.8654 (pp30)
REVERT: L  121 SER cc_start: 0.8404 (m) cc_final: 0.8109 (t)
REVERT: L  180 MET cc_start: 0.8142 (tmm) cc_final: 0.7487 (tmm)
REVERT: L  200 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6455 (pm20)
REVERT: L  214 PHE cc_start: 0.6576 (t80) cc_final: 0.6365 (t80)
  outliers start: 26
  outliers final: 24
  residues processed: 255
  average time/residue: 0.1356
  time to fit residues: 47.0413
Evaluate side-chains
  255 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 230
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  247 ASN
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  149 LEU
Chi-restraints excluded: chain H residue  183 TYR
Chi-restraints excluded: chain H residue  184 THR
Chi-restraints excluded: chain H residue  218 LEU
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  179 SER
Chi-restraints excluded: chain L residue  182 SER
Chi-restraints excluded: chain L residue  200 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 26 optimal weight:    0.2980
   chunk 30 optimal weight:    0.0770
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A 293 GLN
H 113 GLN
** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.150099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.122644 restraints weight = 10902.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.126410 restraints weight = 5155.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.128806 restraints weight = 3027.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5778  Z= 0.196
  Angle     :  0.676   8.948   7850  Z= 0.332
  Chirality :  0.044   0.147    911
  Planarity :  0.004   0.053    971
  Dihedral  :  4.388  21.787    787
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 25.94 %
    Favored  : 69.06 %
  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:  0.08 (0.32), residues: 730
  helix:  1.34 (0.33), residues: 247
  sheet:  0.53 (0.39), residues: 201
  loop : -1.49 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H 162 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.011   0.001   PHE L 144 
 TYR   0.019   0.001   TYR L 145 
 ARG   0.006   0.000   ARG A  21 

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 238
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7364 (mpt-90) cc_final: 0.6587 (mtt180)
REVERT: A   34 MET cc_start: 0.8799 (ttm) cc_final: 0.8460 (ttm)
REVERT: A   36 LEU cc_start: 0.8923 (mm) cc_final: 0.8519 (mm)
REVERT: A   82 PHE cc_start: 0.8726 (t80) cc_final: 0.8357 (t80)
REVERT: A  117 ASN cc_start: 0.8281 (p0) cc_final: 0.7769 (p0)
REVERT: A  160 MET cc_start: 0.8397 (mmt) cc_final: 0.7808 (ptt)
REVERT: A  292 PHE cc_start: 0.6717 (t80) cc_final: 0.5968 (t80)
REVERT: H   73 ASP cc_start: 0.8249 (t0) cc_final: 0.7947 (t0)
REVERT: H  179 GLN cc_start: 0.8528 (pp30) cc_final: 0.8132 (pp30)
REVERT: H  185 MET cc_start: 0.9231 (ppp) cc_final: 0.8560 (ppp)
REVERT: L   17 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7567 (tp30)
REVERT: L   41 TRP cc_start: 0.8976 (m100) cc_final: 0.8713 (m100)
REVERT: L   42 TYR cc_start: 0.8778 (m-80) cc_final: 0.8462 (m-80)
REVERT: L   96 GLN cc_start: 0.9086 (pp30) cc_final: 0.8713 (pp30)
REVERT: L  121 SER cc_start: 0.8383 (m) cc_final: 0.8129 (t)
REVERT: L  184 LEU cc_start: 0.8824 (mt) cc_final: 0.8615 (mt)
REVERT: L  200 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6372 (pm20)
  outliers start: 32
  outliers final: 23
  residues processed: 247
  average time/residue: 0.1337
  time to fit residues: 45.1102
Evaluate side-chains
  257 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 233
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  247 ASN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain H residue    3 GLN
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  125 THR
Chi-restraints excluded: chain H residue  149 LEU
Chi-restraints excluded: chain H residue  183 TYR
Chi-restraints excluded: chain H residue  218 LEU
Chi-restraints excluded: chain L residue    3 VAL
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  151 VAL
Chi-restraints excluded: chain L residue  200 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 67 optimal weight:    0.0980
   chunk 62 optimal weight:    4.9990
   chunk 45 optimal weight:    8.9990
   chunk 36 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0470
   chunk 9 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0970
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.3276

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 GLN
H 113 GLN
L  27 GLN
** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.150877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.122125 restraints weight = 10922.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.126070 restraints weight = 5242.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.128595 restraints weight = 3113.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5778  Z= 0.181
  Angle     :  0.666   8.902   7850  Z= 0.326
  Chirality :  0.044   0.147    911
  Planarity :  0.005   0.058    971
  Dihedral  :  4.374  23.634    787
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 26.56 %
    Favored  : 69.53 %
  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:  0.08 (0.32), residues: 730
  helix:  1.39 (0.33), residues: 248
  sheet:  0.56 (0.39), residues: 199
  loop : -1.56 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H 162 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.016   0.001   PHE H 154 
 TYR   0.020   0.001   TYR L 145 
 ARG   0.006   0.000   ARG A  21 

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 241
  time to evaluate  : 0.614 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 PHE cc_start: 0.7991 (m-80) cc_final: 0.7223 (t80)
REVERT: A   25 ARG cc_start: 0.7413 (mpt-90) cc_final: 0.6611 (mtt180)
REVERT: A   34 MET cc_start: 0.8812 (ttm) cc_final: 0.8435 (ttm)
REVERT: A   36 LEU cc_start: 0.8843 (mm) cc_final: 0.8426 (mm)
REVERT: A   82 PHE cc_start: 0.8818 (t80) cc_final: 0.8356 (t80)
REVERT: A   93 ILE cc_start: 0.9043 (tp) cc_final: 0.8827 (tp)
REVERT: A  117 ASN cc_start: 0.8230 (p0) cc_final: 0.7598 (p0)
REVERT: A  160 MET cc_start: 0.8418 (mmt) cc_final: 0.8148 (mmp)
REVERT: A  292 PHE cc_start: 0.6709 (t80) cc_final: 0.6051 (t80)
REVERT: H    5 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8289 (mm110)
REVERT: H   56 ASP cc_start: 0.8944 (t0) cc_final: 0.8729 (t0)
REVERT: H   73 ASP cc_start: 0.8168 (t0) cc_final: 0.7837 (t0)
REVERT: H  146 LEU cc_start: 0.9415 (mt) cc_final: 0.9116 (mt)
REVERT: H  179 GLN cc_start: 0.8496 (pp30) cc_final: 0.8053 (pp30)
REVERT: H  185 MET cc_start: 0.9164 (ppp) cc_final: 0.8446 (ppp)
REVERT: L   17 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7652 (tp30)
REVERT: L   41 TRP cc_start: 0.8942 (m100) cc_final: 0.8602 (m100)
REVERT: L  107 THR cc_start: 0.9210 (m) cc_final: 0.8969 (t)
REVERT: L  121 SER cc_start: 0.8321 (m) cc_final: 0.8048 (t)
REVERT: L  184 LEU cc_start: 0.8804 (mt) cc_final: 0.8600 (mt)
REVERT: L  200 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6320 (pm20)
  outliers start: 25
  outliers final: 20
  residues processed: 249
  average time/residue: 0.1337
  time to fit residues: 45.6148
Evaluate side-chains
  252 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 231
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  247 ASN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  125 THR
Chi-restraints excluded: chain H residue  149 LEU
Chi-restraints excluded: chain H residue  183 TYR
Chi-restraints excluded: chain H residue  218 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  200 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0020
   chunk 47 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 31 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.6588

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 GLN
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 113 GLN
** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.150188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.122601 restraints weight = 10937.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.126370 restraints weight = 5142.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.128683 restraints weight = 3005.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.3428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5778  Z= 0.207
  Angle     :  0.696   8.589   7850  Z= 0.336
  Chirality :  0.045   0.180    911
  Planarity :  0.004   0.054    971
  Dihedral  :  4.370  26.943    787
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 26.56 %
    Favored  : 68.12 %
  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:  0.11 (0.32), residues: 730
  helix:  1.48 (0.33), residues: 248
  sheet:  0.59 (0.40), residues: 191
  loop : -1.57 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H 162 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.016   0.001   PHE H 154 
 TYR   0.022   0.001   TYR L 145 
 ARG   0.007   0.000   ARG A  21 

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 234
  time to evaluate  : 0.631 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7427 (mpt-90) cc_final: 0.6654 (mtt180)
REVERT: A   34 MET cc_start: 0.8773 (ttm) cc_final: 0.8386 (ttm)
REVERT: A   36 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8624 (mm)
REVERT: A   82 PHE cc_start: 0.8761 (t80) cc_final: 0.8394 (t80)
REVERT: A   93 ILE cc_start: 0.9119 (tp) cc_final: 0.8896 (tp)
REVERT: A  116 MET cc_start: 0.7596 (tpp) cc_final: 0.7259 (tpp)
REVERT: A  117 ASN cc_start: 0.8315 (p0) cc_final: 0.7935 (p0)
REVERT: A  160 MET cc_start: 0.8319 (mmt) cc_final: 0.8097 (mmp)
REVERT: A  189 LYS cc_start: 0.7189 (mmtt) cc_final: 0.5941 (pttt)
REVERT: A  218 MET cc_start: 0.7853 (ppp) cc_final: 0.7546 (ppp)
REVERT: H    5 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8336 (mm110)
REVERT: H   73 ASP cc_start: 0.8139 (t0) cc_final: 0.7776 (t0)
REVERT: H  146 LEU cc_start: 0.9413 (mt) cc_final: 0.9155 (mt)
REVERT: H  179 GLN cc_start: 0.8591 (pp30) cc_final: 0.8327 (pp30)
REVERT: H  185 MET cc_start: 0.9211 (ppp) cc_final: 0.8436 (ppp)
REVERT: L   17 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7504 (tp30)
REVERT: L   41 TRP cc_start: 0.9028 (m100) cc_final: 0.8643 (m100)
REVERT: L   95 LYS cc_start: 0.9253 (tmmt) cc_final: 0.8986 (ttpt)
REVERT: L   96 GLN cc_start: 0.9097 (pp30) cc_final: 0.8723 (pp30)
REVERT: L  107 THR cc_start: 0.9290 (m) cc_final: 0.8994 (t)
REVERT: L  200 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6203 (pm20)
  outliers start: 34
  outliers final: 26
  residues processed: 247
  average time/residue: 0.1308
  time to fit residues: 44.1228
Evaluate side-chains
  262 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 234
  time to evaluate  : 0.580 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  247 ASN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  125 THR
Chi-restraints excluded: chain H residue  149 LEU
Chi-restraints excluded: chain H residue  183 TYR
Chi-restraints excluded: chain H residue  184 THR
Chi-restraints excluded: chain H residue  218 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  151 VAL
Chi-restraints excluded: chain L residue  179 SER
Chi-restraints excluded: chain L residue  200 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 47 optimal weight:    8.9990
   chunk 34 optimal weight:    0.0980
   chunk 12 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 43 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 GLN
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 113 GLN
** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.149862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.122511 restraints weight = 10679.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.126203 restraints weight = 5055.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.128542 restraints weight = 2972.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5778  Z= 0.207
  Angle     :  0.693   8.584   7850  Z= 0.335
  Chirality :  0.044   0.173    911
  Planarity :  0.005   0.062    971
  Dihedral  :  4.416  25.774    787
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 26.56 %
    Favored  : 68.44 %
  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:  0.11 (0.31), residues: 730
  helix:  1.53 (0.32), residues: 248
  sheet:  0.56 (0.40), residues: 191
  loop : -1.60 (0.34), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H 162 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.014   0.001   PHE H 154 
 TYR   0.022   0.001   TYR L 145 
 ARG   0.006   0.000   ARG A  21 

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 239
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7392 (mpt-90) cc_final: 0.6626 (mtt180)
REVERT: A   34 MET cc_start: 0.8749 (ttm) cc_final: 0.8384 (ttm)
REVERT: A   36 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8613 (mm)
REVERT: A   82 PHE cc_start: 0.8752 (t80) cc_final: 0.8398 (t80)
REVERT: A   93 ILE cc_start: 0.9123 (tp) cc_final: 0.8920 (tp)
REVERT: A  117 ASN cc_start: 0.8416 (p0) cc_final: 0.7713 (p0)
REVERT: A  160 MET cc_start: 0.8344 (mmt) cc_final: 0.8134 (mmp)
REVERT: A  229 MET cc_start: 0.8229 (tpp) cc_final: 0.7940 (tpp)
REVERT: A  283 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8187 (m-80)
REVERT: H    5 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8448 (mm110)
REVERT: H   47 TRP cc_start: 0.9067 (t60) cc_final: 0.8432 (t60)
REVERT: H   73 ASP cc_start: 0.8045 (t0) cc_final: 0.7724 (t0)
REVERT: H  146 LEU cc_start: 0.9415 (mt) cc_final: 0.9155 (mt)
REVERT: H  179 GLN cc_start: 0.8625 (pp30) cc_final: 0.8193 (pp30)
REVERT: H  185 MET cc_start: 0.9195 (ppp) cc_final: 0.8467 (ppp)
REVERT: L   17 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7450 (tp30)
REVERT: L   41 TRP cc_start: 0.9035 (m100) cc_final: 0.8581 (m100)
REVERT: L   61 GLU cc_start: 0.8993 (tp30) cc_final: 0.8269 (tm-30)
REVERT: L  107 THR cc_start: 0.9255 (m) cc_final: 0.8990 (t)
REVERT: L  200 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6243 (pm20)
  outliers start: 32
  outliers final: 28
  residues processed: 250
  average time/residue: 0.1375
  time to fit residues: 47.4856
Evaluate side-chains
  264 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 233
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   45 THR
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  247 ASN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  283 PHE
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  125 THR
Chi-restraints excluded: chain H residue  149 LEU
Chi-restraints excluded: chain H residue  183 TYR
Chi-restraints excluded: chain H residue  184 THR
Chi-restraints excluded: chain H residue  218 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  151 VAL
Chi-restraints excluded: chain L residue  179 SER
Chi-restraints excluded: chain L residue  200 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 53 optimal weight:    0.0060
   chunk 29 optimal weight:    4.9990
   chunk 42 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0270
   chunk 8 optimal weight:    0.3980
   overall best weight:    0.3054

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 GLN
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.153474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.126093 restraints weight = 10695.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.129924 restraints weight = 5047.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.132303 restraints weight = 2950.656|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.3696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5778  Z= 0.189
  Angle     :  0.716  11.158   7850  Z= 0.342
  Chirality :  0.044   0.207    911
  Planarity :  0.005   0.060    971
  Dihedral  :  4.399  26.825    787
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 28.75 %
    Favored  : 67.34 %
  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:  0.14 (0.32), residues: 730
  helix:  1.56 (0.32), residues: 248
  sheet:  0.56 (0.40), residues: 190
  loop : -1.57 (0.35), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H 162 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.013   0.001   PHE H 154 
 TYR   0.022   0.001   TYR L 145 
 ARG   0.006   0.000   ARG A  21 

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 240
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7341 (mpt-90) cc_final: 0.6570 (mtt180)
REVERT: A   34 MET cc_start: 0.8742 (ttm) cc_final: 0.8365 (ttm)
REVERT: A   36 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8608 (mm)
REVERT: A   82 PHE cc_start: 0.8719 (t80) cc_final: 0.8354 (t80)
REVERT: A  117 ASN cc_start: 0.8449 (p0) cc_final: 0.7937 (p0)
REVERT: A  153 LYS cc_start: 0.8726 (mttp) cc_final: 0.8472 (mtmm)
REVERT: A  292 PHE cc_start: 0.6862 (t80) cc_final: 0.6211 (t80)
REVERT: H   54 TYR cc_start: 0.8607 (t80) cc_final: 0.8384 (t80)
REVERT: H   73 ASP cc_start: 0.8026 (t0) cc_final: 0.7714 (t0)
REVERT: H  146 LEU cc_start: 0.9417 (mt) cc_final: 0.9171 (mt)
REVERT: H  179 GLN cc_start: 0.8555 (pp30) cc_final: 0.8255 (pp30)
REVERT: H  185 MET cc_start: 0.9195 (ppp) cc_final: 0.8393 (ppp)
REVERT: L   17 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7427 (tp30)
REVERT: L   41 TRP cc_start: 0.8985 (m100) cc_final: 0.8579 (m100)
REVERT: L   61 GLU cc_start: 0.9000 (tp30) cc_final: 0.8315 (tm-30)
REVERT: L   95 LYS cc_start: 0.9270 (tmmt) cc_final: 0.9007 (ttpt)
  outliers start: 25
  outliers final: 23
  residues processed: 250
  average time/residue: 0.1321
  time to fit residues: 45.5445
Evaluate side-chains
  255 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 231
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  139 TYR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  247 ASN
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  125 THR
Chi-restraints excluded: chain H residue  149 LEU
Chi-restraints excluded: chain H residue  183 TYR
Chi-restraints excluded: chain H residue  184 THR
Chi-restraints excluded: chain H residue  218 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  151 VAL
Chi-restraints excluded: chain L residue  179 SER
Chi-restraints excluded: chain L residue  200 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 45 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 54 optimal weight:    0.1980
   chunk 70 optimal weight:    0.0670
   chunk 28 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.8120

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 GLN
H  39 GLN
** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.151808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.124369 restraints weight = 10846.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.128135 restraints weight = 5129.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.130447 restraints weight = 3000.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.3796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   5778  Z= 0.235
  Angle     :  0.758  12.082   7850  Z= 0.362
  Chirality :  0.045   0.200    911
  Planarity :  0.005   0.058    971
  Dihedral  :  4.471  30.843    787
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 30.00 %
    Favored  : 66.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.08 (0.31), residues: 730
  helix:  1.55 (0.32), residues: 249
  sheet:  0.46 (0.40), residues: 191
  loop : -1.61 (0.34), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  36 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.015   0.001   PHE H 154 
 TYR   0.022   0.001   TYR L 145 
 ARG   0.007   0.000   ARG A  21 

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

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

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1460 Ramachandran restraints generated.
    730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 237
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7288 (mpt-90) cc_final: 0.6531 (mtt180)
REVERT: A   34 MET cc_start: 0.8741 (ttm) cc_final: 0.8374 (ttm)
REVERT: A   36 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8620 (mm)
REVERT: A   82 PHE cc_start: 0.8765 (t80) cc_final: 0.8380 (t80)
REVERT: A  117 ASN cc_start: 0.8462 (p0) cc_final: 0.7731 (p0)
REVERT: A  160 MET cc_start: 0.9094 (mmp) cc_final: 0.7830 (ptt)
REVERT: H   47 TRP cc_start: 0.9114 (t60) cc_final: 0.8464 (t60)
REVERT: H   54 TYR cc_start: 0.8669 (t80) cc_final: 0.8433 (t80)
REVERT: H   73 ASP cc_start: 0.8082 (t0) cc_final: 0.7756 (t0)
REVERT: H  146 LEU cc_start: 0.9436 (mt) cc_final: 0.9213 (mt)
REVERT: H  179 GLN cc_start: 0.8588 (pp30) cc_final: 0.8273 (pp30)
REVERT: H  185 MET cc_start: 0.9178 (ppp) cc_final: 0.8448 (ppp)
REVERT: L   17 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7359 (tp30)
REVERT: L   41 TRP cc_start: 0.9081 (m100) cc_final: 0.8610 (m100)
REVERT: L   61 GLU cc_start: 0.9051 (tp30) cc_final: 0.8283 (tm-30)
REVERT: L   95 LYS cc_start: 0.9310 (tmmt) cc_final: 0.9077 (ttpt)
REVERT: L  200 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6220 (pm20)
  outliers start: 25
  outliers final: 22
  residues processed: 246
  average time/residue: 0.1336
  time to fit residues: 44.9948
Evaluate side-chains
  260 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 236
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  139 TYR
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  217 VAL
Chi-restraints excluded: chain A residue  247 ASN
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue  116 THR
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  125 THR
Chi-restraints excluded: chain H residue  149 LEU
Chi-restraints excluded: chain H residue  183 TYR
Chi-restraints excluded: chain H residue  184 THR
Chi-restraints excluded: chain H residue  218 LEU
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  151 VAL
Chi-restraints excluded: chain L residue  179 SER
Chi-restraints excluded: chain L residue  200 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 65 optimal weight:    0.2980
   chunk 24 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 57 optimal weight:    0.4980
   chunk 36 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 GLN
H  39 GLN
** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.150317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.123551 restraints weight = 10819.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.127228 restraints weight = 5047.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.129662 restraints weight = 2928.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5778  Z= 0.212
  Angle     :  0.771  13.271   7850  Z= 0.364
  Chirality :  0.045   0.208    911
  Planarity :  0.005   0.057    971
  Dihedral  :  4.477  31.520    787
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 30.94 %
    Favored  : 65.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: 730
  helix:  1.58 (0.32), residues: 248
  sheet:  0.42 (0.40), residues: 191
  loop : -1.64 (0.34), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H 162 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.013   0.001   PHE H 154 
 TYR   0.023   0.001   TYR L 145 
 ARG   0.006   0.000   ARG A  21 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2235.77 seconds
wall clock time: 40 minutes 50.71 seconds (2450.71 seconds total)