Starting phenix.real_space_refine
on Tue Mar  3 13:52:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vae_31838/03_2026/7vae_31838.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vae_31838/03_2026/7vae_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_31838/03_2026/7vae_31838.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vae_31838/03_2026/7vae_31838.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vae_31838/03_2026/7vae_31838.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vae_31838/03_2026/7vae_31838.cif"
  }
  resolution = 3.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.32, per 1000 atoms: 0.23
  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: 0.34
  Conformation dependent library (CDL) restraints added in 281.8 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: 0.18
  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: 0.85

  Time building geometry restraints manager: 0.46 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:             0.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.660
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.860
-------------------------------------------------------------------------------
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   5782  Z= 0.134
  Angle     :  0.671  11.300   7858  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 : 11.65
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.008   0.001   ARG A 185 
 TYR   0.022   0.001   TYR H 130 
 PHE   0.018   0.001   PHE A 292 
 TRP   0.018   0.002   TRP L  41 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 5778)
  covalent geometry    : angle       0.67086 ( 7850)
  SS BOND              : bond        0.00352 (    4)
  SS BOND              : angle       1.05717 (    8)
  hydrogen bonds       : bond        0.15830 (  283)
  hydrogen bonds       : angle       6.83088 (  798)

*********************** 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  : 0.173 
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: 0.8629 (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: 0.7946 (t)
REVERT: A   36 LEU cc_start: 0.9076 (mm) cc_final: 0.8713 (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: 0.7993 (m-10)
REVERT: A  128 PHE cc_start: 0.8459 (t80) cc_final: 0.8242 (t80)
REVERT: H  130 TYR cc_start: 0.8180 (m-80) cc_final: 0.7305 (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: 0.7568 (m-80)
REVERT: L   94 CYS cc_start: 0.6419 (p) cc_final: 0.5436 (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: 0.0591
  time to fit residues: 21.6724
Evaluate side-chains
  239 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.150440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.123651 restraints weight = 10457.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.127192 restraints weight = 4928.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.129700 restraints weight = 2941.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.131136 restraints weight = 1981.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.132357 restraints weight = 1528.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5782  Z= 0.189
  Angle     :  0.706   7.963   7858  Z= 0.358
  Chirality :  0.046   0.174    911
  Planarity :  0.005   0.061    971
  Dihedral  :  4.517  18.443    787
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.71 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 17.03 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.31), residues: 730
  helix:  1.14 (0.33), residues: 247
  sheet:  0.52 (0.39), residues: 183
  loop : -1.25 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L 113 
 TYR   0.011   0.002   TYR H 183 
 PHE   0.019   0.002   PHE H 174 
 TRP   0.028   0.003   TRP L  41 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 5778)
  covalent geometry    : angle       0.70471 ( 7850)
  SS BOND              : bond        0.00503 (    4)
  SS BOND              : angle       1.26707 (    8)
  hydrogen bonds       : bond        0.05049 (  283)
  hydrogen bonds       : angle       5.46320 (  798)

*********************** 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
  270 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 247
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7596 (mpt-90) cc_final: 0.6615 (mtt180)
REVERT: A   34 MET cc_start: 0.8789 (ttm) cc_final: 0.8529 (ttm)
REVERT: A   36 LEU cc_start: 0.8925 (mm) cc_final: 0.8565 (mm)
REVERT: A   82 PHE cc_start: 0.8819 (t80) cc_final: 0.8397 (t80)
REVERT: A  117 ASN cc_start: 0.8142 (p0) cc_final: 0.7509 (p0)
REVERT: A  128 PHE cc_start: 0.8952 (t80) cc_final: 0.8515 (t80)
REVERT: H   36 TRP cc_start: 0.9170 (m100) cc_final: 0.8680 (m100)
REVERT: H   56 ASP cc_start: 0.8921 (t0) cc_final: 0.8696 (t0)
REVERT: H   73 ASP cc_start: 0.8170 (t0) cc_final: 0.7765 (t0)
REVERT: H  130 TYR cc_start: 0.8326 (m-80) cc_final: 0.7727 (m-10)
REVERT: H  185 MET cc_start: 0.9035 (ppp) cc_final: 0.8507 (ppp)
REVERT: L   17 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7647 (tp30)
REVERT: L   41 TRP cc_start: 0.9012 (m100) cc_final: 0.8614 (m100)
REVERT: L   42 TYR cc_start: 0.8582 (m-80) cc_final: 0.8229 (m-80)
REVERT: L   94 CYS cc_start: 0.6768 (p) cc_final: 0.6417 (p)
REVERT: L   96 GLN cc_start: 0.8892 (pp30) cc_final: 0.8469 (pp30)
REVERT: L  180 MET cc_start: 0.8135 (tmm) cc_final: 0.7631 (tmm)
REVERT: L  184 LEU cc_start: 0.9002 (mt) cc_final: 0.8701 (mt)
REVERT: L  200 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6298 (pm20)
REVERT: L  214 PHE cc_start: 0.6312 (t80) cc_final: 0.6026 (t80)
  outliers start: 23
  outliers final: 18
  residues processed: 252
  average time/residue: 0.0495
  time to fit residues: 17.5072
Evaluate side-chains
  252 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 233
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
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  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  294 VAL
Chi-restraints excluded: chain A residue  301 VAL
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  218 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue  182 SER
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 14 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0770
   chunk 2 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0010
   chunk 35 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.5944

-------------------------------------------------------------------------------
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**
A 293 GLN
H   5 GLN
H  39 GLN
** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.151281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.123445 restraints weight = 10786.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.127259 restraints weight = 5102.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.129676 restraints weight = 2999.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.131384 restraints weight = 2058.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.132315 restraints weight = 1556.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.2540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5782  Z= 0.136
  Angle     :  0.684   8.884   7858  Z= 0.338
  Chirality :  0.045   0.171    911
  Planarity :  0.005   0.078    971
  Dihedral  :  4.461  22.675    787
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 22.03 %
    Favored  : 73.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.31), residues: 730
  helix:  1.35 (0.32), residues: 246
  sheet:  0.56 (0.40), residues: 183
  loop : -1.33 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  21 
 TYR   0.017   0.001   TYR L 145 
 PHE   0.013   0.001   PHE H 174 
 TRP   0.016   0.002   TRP L  41 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 5778)
  covalent geometry    : angle       0.68312 ( 7850)
  SS BOND              : bond        0.00503 (    4)
  SS BOND              : angle       1.06687 (    8)
  hydrogen bonds       : bond        0.04355 (  283)
  hydrogen bonds       : angle       5.16963 (  798)

*********************** 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
  267 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 240
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7446 (mpt-90) cc_final: 0.6598 (mtt180)
REVERT: A   34 MET cc_start: 0.8746 (ttm) cc_final: 0.8457 (ttm)
REVERT: A   36 LEU cc_start: 0.9005 (mm) cc_final: 0.8586 (mm)
REVERT: A   82 PHE cc_start: 0.8729 (t80) cc_final: 0.8380 (t80)
REVERT: A  128 PHE cc_start: 0.8924 (t80) cc_final: 0.8513 (t80)
REVERT: A  138 LEU cc_start: 0.9548 (mt) cc_final: 0.9336 (mt)
REVERT: H    5 GLN cc_start: 0.8745 (mm110) cc_final: 0.8337 (mm110)
REVERT: H   73 ASP cc_start: 0.8141 (t0) cc_final: 0.7751 (t0)
REVERT: H  130 TYR cc_start: 0.8138 (m-80) cc_final: 0.7696 (m-10)
REVERT: H  185 MET cc_start: 0.9180 (ppp) cc_final: 0.8567 (ppp)
REVERT: L   41 TRP cc_start: 0.9015 (m100) cc_final: 0.8702 (m100)
REVERT: L   42 TYR cc_start: 0.8632 (m-80) cc_final: 0.8329 (m-80)
REVERT: L   88 ASP cc_start: 0.9129 (m-30) cc_final: 0.8892 (m-30)
REVERT: L   94 CYS cc_start: 0.6512 (p) cc_final: 0.5768 (p)
REVERT: L   96 GLN cc_start: 0.8956 (pp30) cc_final: 0.8616 (pp30)
REVERT: L  200 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6411 (pm20)
REVERT: L  214 PHE cc_start: 0.6436 (t80) cc_final: 0.6024 (t80)
  outliers start: 27
  outliers final: 20
  residues processed: 251
  average time/residue: 0.0513
  time to fit residues: 18.0100
Evaluate side-chains
  250 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 229
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
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  213 SER
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 A residue  301 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  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  182 SER
Chi-restraints excluded: chain L residue  197 TYR
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 3 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0670
   chunk 17 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0970
   chunk 9 optimal weight:    0.9980
   chunk 68 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0050
   chunk 8 optimal weight:    0.0040
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.1742

-------------------------------------------------------------------------------
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 113 GLN
L  27 GLN
** L 129 GLN ** 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 = 0.3964 r_free = 0.3964 target = 0.154666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.127436 restraints weight = 10687.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.131145 restraints weight = 5003.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.133524 restraints weight = 2942.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.135067 restraints weight = 2028.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.135944 restraints weight = 1540.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.2888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   5782  Z= 0.132
  Angle     :  0.691  10.212   7858  Z= 0.337
  Chirality :  0.044   0.158    911
  Planarity :  0.004   0.055    971
  Dihedral  :  4.406  23.393    787
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 25.16 %
    Favored  : 72.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.05 (0.31), residues: 730
  helix:  1.15 (0.32), residues: 248
  sheet:  0.59 (0.40), residues: 189
  loop : -1.32 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  21 
 TYR   0.018   0.001   TYR L 145 
 PHE   0.011   0.001   PHE A 292 
 TRP   0.024   0.002   TRP L 168 
 HIS   0.004   0.001   HIS L 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 5778)
  covalent geometry    : angle       0.69020 ( 7850)
  SS BOND              : bond        0.00743 (    4)
  SS BOND              : angle       1.00350 (    8)
  hydrogen bonds       : bond        0.04053 (  283)
  hydrogen bonds       : angle       5.09267 (  798)

*********************** 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
  266 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 248
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 PHE cc_start: 0.8212 (m-80) cc_final: 0.7604 (t80)
REVERT: A   25 ARG cc_start: 0.7418 (mpt-90) cc_final: 0.6608 (mtt180)
REVERT: A   34 MET cc_start: 0.8809 (ttm) cc_final: 0.8475 (ttm)
REVERT: A   36 LEU cc_start: 0.8977 (mm) cc_final: 0.8589 (mm)
REVERT: A   82 PHE cc_start: 0.8717 (t80) cc_final: 0.8362 (t80)
REVERT: A  117 ASN cc_start: 0.8120 (p0) cc_final: 0.7657 (p0)
REVERT: H    5 GLN cc_start: 0.8672 (mm110) cc_final: 0.8296 (mm110)
REVERT: H   73 ASP cc_start: 0.8175 (t0) cc_final: 0.7720 (t0)
REVERT: H  130 TYR cc_start: 0.8123 (m-80) cc_final: 0.7705 (m-10)
REVERT: H  151 LYS cc_start: 0.8151 (tppt) cc_final: 0.7786 (tppp)
REVERT: H  185 MET cc_start: 0.9216 (ppp) cc_final: 0.8545 (ppp)
REVERT: L   41 TRP cc_start: 0.8873 (m100) cc_final: 0.8628 (m100)
REVERT: L   42 TYR cc_start: 0.8720 (m-80) cc_final: 0.8407 (m-80)
REVERT: L   94 CYS cc_start: 0.6409 (p) cc_final: 0.5927 (p)
REVERT: L  121 SER cc_start: 0.8349 (m) cc_final: 0.8071 (t)
REVERT: L  180 MET cc_start: 0.7970 (tmm) cc_final: 0.7343 (tmm)
REVERT: L  214 PHE cc_start: 0.6353 (t80) cc_final: 0.6042 (t80)
  outliers start: 18
  outliers final: 17
  residues processed: 253
  average time/residue: 0.0531
  time to fit residues: 18.7111
Evaluate side-chains
  242 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 225
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
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  187 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  247 ASN
Chi-restraints excluded: chain H residue    3 GLN
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  218 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  140 PHE
Chi-restraints excluded: chain L residue  141 LEU
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 52 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 58 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0470
   chunk 37 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 68 optimal weight:    7.9990
   chunk 8 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.9682

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

Flipped N/Q/H residues before XYZ refinement:
A 293 GLN
H  39 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.148484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.120546 restraints weight = 11184.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.124349 restraints weight = 5212.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.126768 restraints weight = 3046.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.128350 restraints weight = 2066.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.129436 restraints weight = 1583.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.3142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5782  Z= 0.153
  Angle     :  0.680   9.196   7858  Z= 0.336
  Chirality :  0.044   0.147    911
  Planarity :  0.004   0.051    971
  Dihedral  :  4.455  20.968    787
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 25.00 %
    Favored  : 69.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.31), residues: 730
  helix:  1.29 (0.32), residues: 247
  sheet:  0.44 (0.39), residues: 194
  loop : -1.49 (0.35), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  21 
 TYR   0.020   0.002   TYR H  50 
 PHE   0.013   0.001   PHE H 154 
 TRP   0.018   0.002   TRP L 168 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 5778)
  covalent geometry    : angle       0.67966 ( 7850)
  SS BOND              : bond        0.00676 (    4)
  SS BOND              : angle       1.10316 (    8)
  hydrogen bonds       : bond        0.03975 (  283)
  hydrogen bonds       : angle       5.05000 (  798)

*********************** 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
  275 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 238
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.8182 (p0)
REVERT: A   25 ARG cc_start: 0.7376 (mpt-90) cc_final: 0.6560 (mtt180)
REVERT: A   34 MET cc_start: 0.8802 (ttm) cc_final: 0.8432 (ttm)
REVERT: A   36 LEU cc_start: 0.8935 (mm) cc_final: 0.8526 (mm)
REVERT: A   50 LYS cc_start: 0.8220 (mmmt) cc_final: 0.7986 (mmmm)
REVERT: A   58 PRO cc_start: 0.8399 (Cg_exo) cc_final: 0.8175 (Cg_exo)
REVERT: A   82 PHE cc_start: 0.8761 (t80) cc_final: 0.8394 (t80)
REVERT: A  117 ASN cc_start: 0.8358 (p0) cc_final: 0.7708 (p0)
REVERT: A  229 MET cc_start: 0.8233 (tpp) cc_final: 0.8012 (tpp)
REVERT: A  231 PHE cc_start: 0.8681 (t80) cc_final: 0.8454 (t80)
REVERT: H    5 GLN cc_start: 0.8673 (mm110) cc_final: 0.8308 (mm110)
REVERT: H   56 ASP cc_start: 0.8865 (t0) cc_final: 0.8623 (t0)
REVERT: H   73 ASP cc_start: 0.8284 (t0) cc_final: 0.8006 (t70)
REVERT: H  179 GLN cc_start: 0.8466 (pp30) cc_final: 0.8195 (pp30)
REVERT: H  185 MET cc_start: 0.9181 (ppp) cc_final: 0.8532 (ppp)
REVERT: L   17 GLU cc_start: 0.7409 (tp30) cc_final: 0.7178 (tp30)
REVERT: L   41 TRP cc_start: 0.9019 (m100) cc_final: 0.8672 (m100)
REVERT: L   42 TYR cc_start: 0.8824 (m-80) cc_final: 0.8519 (m-80)
REVERT: L   94 CYS cc_start: 0.6385 (p) cc_final: 0.5690 (p)
REVERT: L   96 GLN cc_start: 0.9088 (pp30) cc_final: 0.8643 (pp30)
REVERT: L  121 SER cc_start: 0.8544 (m) cc_final: 0.8313 (t)
REVERT: L  180 MET cc_start: 0.8190 (tmm) cc_final: 0.7520 (tmm)
REVERT: L  184 LEU cc_start: 0.8850 (mt) cc_final: 0.8643 (mt)
REVERT: L  200 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6578 (pm20)
  outliers start: 37
  outliers final: 29
  residues processed: 250
  average time/residue: 0.0496
  time to fit residues: 17.6905
Evaluate side-chains
  270 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 239
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 ASP
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  127 THR
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   51 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    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  151 VAL
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 42 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 70 optimal weight:    0.6980
   chunk 37 optimal weight:    0.3980
   chunk 40 optimal weight:    1.9990
   chunk 51 optimal weight:    0.2980
   chunk 12 optimal weight:    0.8980
   chunk 0 optimal weight:    8.9990
   chunk 69 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 293 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.148584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.121222 restraints weight = 10758.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.124921 restraints weight = 5059.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.127212 restraints weight = 2970.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.128761 restraints weight = 2045.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.129679 restraints weight = 1556.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5782  Z= 0.143
  Angle     :  0.682   8.125   7858  Z= 0.336
  Chirality :  0.045   0.146    911
  Planarity :  0.004   0.053    971
  Dihedral  :  4.505  23.578    787
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  6.09 %
    Allowed  : 24.84 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.31), residues: 730
  helix:  1.40 (0.33), residues: 247
  sheet:  0.44 (0.39), residues: 192
  loop : -1.56 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  21 
 TYR   0.020   0.001   TYR L 145 
 PHE   0.023   0.001   PHE L 214 
 TRP   0.013   0.002   TRP L 168 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 5778)
  covalent geometry    : angle       0.68196 ( 7850)
  SS BOND              : bond        0.00506 (    4)
  SS BOND              : angle       1.06821 (    8)
  hydrogen bonds       : bond        0.03905 (  283)
  hydrogen bonds       : angle       5.08541 (  798)

*********************** 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
  284 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 245
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7406 (mpt-90) cc_final: 0.6621 (mtt180)
REVERT: A   34 MET cc_start: 0.8821 (ttm) cc_final: 0.8492 (ttm)
REVERT: A   36 LEU cc_start: 0.8916 (mm) cc_final: 0.8524 (mm)
REVERT: A   50 LYS cc_start: 0.8257 (mmmt) cc_final: 0.8040 (mmmm)
REVERT: A   58 PRO cc_start: 0.8287 (Cg_exo) cc_final: 0.8055 (Cg_exo)
REVERT: A   82 PHE cc_start: 0.8772 (t80) cc_final: 0.8406 (t80)
REVERT: A  116 MET cc_start: 0.7687 (tpp) cc_final: 0.7406 (tpp)
REVERT: A  117 ASN cc_start: 0.8363 (p0) cc_final: 0.7949 (p0)
REVERT: A  231 PHE cc_start: 0.8753 (t80) cc_final: 0.8439 (t80)
REVERT: A  283 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8248 (m-80)
REVERT: H   47 TRP cc_start: 0.9085 (t60) cc_final: 0.8402 (t60)
REVERT: H   73 ASP cc_start: 0.8272 (t0) cc_final: 0.8012 (t70)
REVERT: H  146 LEU cc_start: 0.9418 (mt) cc_final: 0.9130 (mt)
REVERT: H  179 GLN cc_start: 0.8630 (pp30) cc_final: 0.8327 (pp30)
REVERT: H  185 MET cc_start: 0.9211 (ppp) cc_final: 0.8566 (ppp)
REVERT: L   17 GLU cc_start: 0.7442 (tp30) cc_final: 0.7164 (tp30)
REVERT: L   41 TRP cc_start: 0.9037 (m100) cc_final: 0.8732 (m100)
REVERT: L   42 TYR cc_start: 0.8815 (m-80) cc_final: 0.8484 (m-80)
REVERT: L   94 CYS cc_start: 0.6321 (p) cc_final: 0.5934 (p)
REVERT: L   96 GLN cc_start: 0.9071 (pp30) cc_final: 0.8657 (pp30)
REVERT: L  184 LEU cc_start: 0.8873 (mt) cc_final: 0.8659 (mt)
REVERT: L  200 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6600 (pm20)
  outliers start: 39
  outliers final: 31
  residues processed: 260
  average time/residue: 0.0547
  time to fit residues: 19.8387
Evaluate side-chains
  274 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 241
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
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  140 LEU
Chi-restraints excluded: chain A residue  192 ILE
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 H residue    2 VAL
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  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   11 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  119 THR
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  165 LEU
Chi-restraints excluded: chain L residue  179 SER
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 52 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 43 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0770
   chunk 51 optimal weight:    0.0870
   chunk 1 optimal weight:    0.9980
   chunk 50 optimal weight:    7.9990
   chunk 71 optimal weight:   10.0000
   overall best weight:    0.5916

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

Flipped N/Q/H residues before XYZ refinement:
A 293 GLN
** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 162 ASN
** 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 = 0.149964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.122345 restraints weight = 10870.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.126094 restraints weight = 5144.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.128433 restraints weight = 3018.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.130011 restraints weight = 2055.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.130833 restraints weight = 1558.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.3472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5782  Z= 0.134
  Angle     :  0.692   8.540   7858  Z= 0.338
  Chirality :  0.044   0.146    911
  Planarity :  0.004   0.049    971
  Dihedral  :  4.501  22.900    787
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 27.03 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.32), residues: 730
  helix:  1.39 (0.33), residues: 249
  sheet:  0.47 (0.40), residues: 190
  loop : -1.56 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  21 
 TYR   0.021   0.001   TYR L 145 
 PHE   0.017   0.001   PHE H 154 
 TRP   0.011   0.002   TRP L 168 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 5778)
  covalent geometry    : angle       0.69153 ( 7850)
  SS BOND              : bond        0.00529 (    4)
  SS BOND              : angle       0.97454 (    8)
  hydrogen bonds       : bond        0.03802 (  283)
  hydrogen bonds       : angle       5.01980 (  798)

*********************** 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
  279 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 243
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7325 (mpt-90) cc_final: 0.6585 (mtt180)
REVERT: A   34 MET cc_start: 0.8800 (ttm) cc_final: 0.8437 (ttm)
REVERT: A   36 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8524 (mm)
REVERT: A   58 PRO cc_start: 0.8278 (Cg_exo) cc_final: 0.8029 (Cg_exo)
REVERT: A   82 PHE cc_start: 0.8763 (t80) cc_final: 0.8397 (t80)
REVERT: A   93 ILE cc_start: 0.9083 (tp) cc_final: 0.8880 (tp)
REVERT: A  231 PHE cc_start: 0.8764 (t80) cc_final: 0.8474 (t80)
REVERT: A  283 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8239 (m-80)
REVERT: H    5 GLN cc_start: 0.8603 (mm-40) cc_final: 0.8318 (mm110)
REVERT: H   73 ASP cc_start: 0.8113 (t0) cc_final: 0.7768 (t0)
REVERT: H  146 LEU cc_start: 0.9411 (mt) cc_final: 0.9124 (mt)
REVERT: H  179 GLN cc_start: 0.8620 (pp30) cc_final: 0.8301 (pp30)
REVERT: H  185 MET cc_start: 0.9237 (ppp) cc_final: 0.8538 (ppp)
REVERT: L   41 TRP cc_start: 0.9049 (m100) cc_final: 0.8689 (m100)
REVERT: L   42 TYR cc_start: 0.8785 (m-80) cc_final: 0.8437 (m-80)
REVERT: L   94 CYS cc_start: 0.6358 (p) cc_final: 0.5652 (p)
REVERT: L   96 GLN cc_start: 0.9018 (pp30) cc_final: 0.8667 (pp30)
REVERT: L  200 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6601 (pm20)
  outliers start: 36
  outliers final: 31
  residues processed: 256
  average time/residue: 0.0512
  time to fit residues: 18.4877
Evaluate side-chains
  267 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 233
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
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  104 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  122 MET
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  192 ILE
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  247 ASN
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  283 PHE
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  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   11 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  119 THR
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  165 LEU
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 42 optimal weight:    6.9990
   chunk 11 optimal weight:    0.4980
   chunk 6 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 54 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 17 optimal weight:    0.2980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** H   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.150004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.122344 restraints weight = 10877.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.126132 restraints weight = 5113.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.128562 restraints weight = 2994.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.129980 restraints weight = 2034.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.131189 restraints weight = 1578.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.3632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   5782  Z= 0.138
  Angle     :  0.731   8.726   7858  Z= 0.352
  Chirality :  0.045   0.159    911
  Planarity :  0.004   0.057    971
  Dihedral  :  4.520  26.020    787
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 27.66 %
    Favored  : 67.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.31), residues: 730
  helix:  1.38 (0.32), residues: 249
  sheet:  0.48 (0.40), residues: 190
  loop : -1.55 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  21 
 TYR   0.023   0.001   TYR L 145 
 PHE   0.015   0.001   PHE H 154 
 TRP   0.013   0.002   TRP H 162 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 5778)
  covalent geometry    : angle       0.73059 ( 7850)
  SS BOND              : bond        0.00431 (    4)
  SS BOND              : angle       0.91293 (    8)
  hydrogen bonds       : bond        0.03795 (  283)
  hydrogen bonds       : angle       4.99715 (  798)

*********************** 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
  274 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 241
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7319 (mpt-90) cc_final: 0.6558 (mtt180)
REVERT: A   34 MET cc_start: 0.8792 (ttm) cc_final: 0.8427 (ttm)
REVERT: A   36 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8602 (mm)
REVERT: A   58 PRO cc_start: 0.8297 (Cg_exo) cc_final: 0.8049 (Cg_exo)
REVERT: A   82 PHE cc_start: 0.8755 (t80) cc_final: 0.8392 (t80)
REVERT: A   93 ILE cc_start: 0.9069 (tp) cc_final: 0.8869 (tp)
REVERT: A  116 MET cc_start: 0.7693 (mmm) cc_final: 0.7472 (tpp)
REVERT: A  117 ASN cc_start: 0.8378 (p0) cc_final: 0.7884 (p0)
REVERT: A  231 PHE cc_start: 0.8698 (t80) cc_final: 0.8420 (t80)
REVERT: H    5 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8270 (mm110)
REVERT: H   73 ASP cc_start: 0.8116 (t0) cc_final: 0.7777 (t0)
REVERT: H  146 LEU cc_start: 0.9413 (mt) cc_final: 0.9133 (mt)
REVERT: H  179 GLN cc_start: 0.8624 (pp30) cc_final: 0.8295 (pp30)
REVERT: H  185 MET cc_start: 0.9219 (ppp) cc_final: 0.8495 (ppp)
REVERT: L   41 TRP cc_start: 0.9048 (m100) cc_final: 0.8661 (m100)
REVERT: L   61 GLU cc_start: 0.8941 (tp30) cc_final: 0.8263 (tm-30)
REVERT: L   94 CYS cc_start: 0.6358 (p) cc_final: 0.5655 (p)
REVERT: L   96 GLN cc_start: 0.9026 (pp30) cc_final: 0.8670 (pp30)
REVERT: L  107 THR cc_start: 0.9220 (m) cc_final: 0.8919 (t)
REVERT: L  200 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6604 (pm20)
  outliers start: 33
  outliers final: 28
  residues processed: 251
  average time/residue: 0.0490
  time to fit residues: 17.6623
Evaluate side-chains
  266 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 236
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
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  104 LEU
Chi-restraints excluded: chain A residue  122 MET
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  247 ASN
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  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  119 THR
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  165 LEU
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 3 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0270
   chunk 47 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    1.3242

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.145815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.118359 restraints weight = 11059.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.122042 restraints weight = 5159.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.124368 restraints weight = 3013.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.125935 restraints weight = 2043.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.126958 restraints weight = 1567.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.3794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   5782  Z= 0.185
  Angle     :  0.764   9.741   7858  Z= 0.371
  Chirality :  0.047   0.213    911
  Planarity :  0.004   0.059    971
  Dihedral  :  4.727  24.261    787
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  5.78 %
    Allowed  : 27.81 %
    Favored  : 66.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.32), residues: 730
  helix:  1.41 (0.32), residues: 249
  sheet:  0.36 (0.40), residues: 190
  loop : -1.55 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  21 
 TYR   0.023   0.002   TYR L 145 
 PHE   0.018   0.002   PHE H 154 
 TRP   0.011   0.002   TRP L 168 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 5778)
  covalent geometry    : angle       0.76390 ( 7850)
  SS BOND              : bond        0.00582 (    4)
  SS BOND              : angle       1.10107 (    8)
  hydrogen bonds       : bond        0.04074 (  283)
  hydrogen bonds       : angle       5.11449 (  798)

*********************** 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
  274 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 237
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7369 (mpt-90) cc_final: 0.6621 (mtt180)
REVERT: A   34 MET cc_start: 0.8790 (ttm) cc_final: 0.8420 (ttm)
REVERT: A   36 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8662 (mm)
REVERT: A   58 PRO cc_start: 0.8386 (Cg_exo) cc_final: 0.8119 (Cg_exo)
REVERT: A   82 PHE cc_start: 0.8827 (t80) cc_final: 0.8433 (t80)
REVERT: A  117 ASN cc_start: 0.8398 (p0) cc_final: 0.7642 (p0)
REVERT: A  231 PHE cc_start: 0.8799 (t80) cc_final: 0.8458 (t80)
REVERT: A  283 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8257 (m-80)
REVERT: H    5 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8276 (mm110)
REVERT: H   47 TRP cc_start: 0.9104 (t60) cc_final: 0.8409 (t60)
REVERT: H   73 ASP cc_start: 0.8225 (t0) cc_final: 0.7946 (t70)
REVERT: H  146 LEU cc_start: 0.9402 (mt) cc_final: 0.9142 (mt)
REVERT: H  179 GLN cc_start: 0.8536 (pp30) cc_final: 0.7755 (pm20)
REVERT: H  185 MET cc_start: 0.9200 (ppp) cc_final: 0.8527 (ppp)
REVERT: L   41 TRP cc_start: 0.9218 (m100) cc_final: 0.8706 (m100)
REVERT: L   61 GLU cc_start: 0.9062 (tp30) cc_final: 0.8240 (tm-30)
REVERT: L   94 CYS cc_start: 0.6456 (p) cc_final: 0.5909 (p)
REVERT: L   96 GLN cc_start: 0.9092 (pp30) cc_final: 0.8627 (pp30)
REVERT: L  123 PHE cc_start: 0.8002 (m-80) cc_final: 0.7510 (m-80)
REVERT: L  200 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6668 (pm20)
  outliers start: 37
  outliers final: 32
  residues processed: 250
  average time/residue: 0.0528
  time to fit residues: 18.7803
Evaluate side-chains
  267 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 232
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
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  104 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  171 THR
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  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    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  119 THR
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  165 LEU
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 39 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 65 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9990
   chunk 70 optimal weight:    6.9990
   chunk 49 optimal weight:    7.9990
   chunk 15 optimal weight:    0.3980
   chunk 57 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.150582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.123634 restraints weight = 10939.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.127172 restraints weight = 4982.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.129547 restraints weight = 2972.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.130730 restraints weight = 2014.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.131887 restraints weight = 1590.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.3933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5782  Z= 0.138
  Angle     :  0.772  11.851   7858  Z= 0.366
  Chirality :  0.046   0.199    911
  Planarity :  0.004   0.060    971
  Dihedral  :  4.683  28.328    787
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 29.06 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.32), residues: 730
  helix:  1.53 (0.32), residues: 249
  sheet:  0.44 (0.40), residues: 190
  loop : -1.64 (0.34), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  21 
 TYR   0.023   0.001   TYR L 145 
 PHE   0.015   0.001   PHE H 154 
 TRP   0.013   0.002   TRP H 162 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 5778)
  covalent geometry    : angle       0.77212 ( 7850)
  SS BOND              : bond        0.00462 (    4)
  SS BOND              : angle       0.91298 (    8)
  hydrogen bonds       : bond        0.03803 (  283)
  hydrogen bonds       : angle       5.03687 (  798)

********************** 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
  270 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 236
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 ARG cc_start: 0.7307 (mpt-90) cc_final: 0.6632 (mtt180)
REVERT: A   34 MET cc_start: 0.8733 (ttm) cc_final: 0.8361 (ttm)
REVERT: A   36 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8621 (mm)
REVERT: A   58 PRO cc_start: 0.8272 (Cg_exo) cc_final: 0.8015 (Cg_exo)
REVERT: A   74 LEU cc_start: 0.8469 (tt) cc_final: 0.8238 (tt)
REVERT: A   82 PHE cc_start: 0.8792 (t80) cc_final: 0.8391 (t80)
REVERT: A  116 MET cc_start: 0.7728 (tpp) cc_final: 0.7436 (tpp)
REVERT: A  117 ASN cc_start: 0.8374 (p0) cc_final: 0.7849 (p0)
REVERT: A  212 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7288 (tptt)
REVERT: A  231 PHE cc_start: 0.8784 (t80) cc_final: 0.8522 (t80)
REVERT: A  283 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8234 (m-80)
REVERT: H    5 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8222 (mm110)
REVERT: H   73 ASP cc_start: 0.8065 (t0) cc_final: 0.7714 (t0)
REVERT: H  146 LEU cc_start: 0.9433 (mt) cc_final: 0.9187 (mt)
REVERT: H  179 GLN cc_start: 0.8469 (pp30) cc_final: 0.7699 (pm20)
REVERT: H  185 MET cc_start: 0.9221 (ppp) cc_final: 0.8508 (ppp)
REVERT: L   41 TRP cc_start: 0.9131 (m100) cc_final: 0.8596 (m100)
REVERT: L   61 GLU cc_start: 0.9037 (tp30) cc_final: 0.8281 (tm-30)
REVERT: L   94 CYS cc_start: 0.6402 (p) cc_final: 0.5748 (p)
REVERT: L   96 GLN cc_start: 0.9133 (pp30) cc_final: 0.8730 (pp30)
REVERT: L  107 THR cc_start: 0.9255 (m) cc_final: 0.8956 (t)
REVERT: L  200 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6638 (pm20)
  outliers start: 34
  outliers final: 29
  residues processed: 249
  average time/residue: 0.0516
  time to fit residues: 18.0374
Evaluate side-chains
  268 residues out of total 640 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 235
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
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  104 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  212 LYS
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 A residue  300 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  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   11 LEU
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  119 THR
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  165 LEU
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 20 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0020
   chunk 16 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   overall best weight:    1.1392

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

Flipped N/Q/H residues before XYZ refinement:
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.145587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.118434 restraints weight = 10992.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.122040 restraints weight = 5137.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.124377 restraints weight = 3005.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.125970 restraints weight = 2036.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.126851 restraints weight = 1546.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.4054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5782  Z= 0.169
  Angle     :  0.796  12.816   7858  Z= 0.380
  Chirality :  0.046   0.223    911
  Planarity :  0.004   0.058    971
  Dihedral  :  4.785  31.162    787
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 15.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 29.69 %
    Favored  : 65.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.32), residues: 730
  helix:  1.53 (0.33), residues: 250
  sheet:  0.30 (0.40), residues: 190
  loop : -1.59 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  21 
 TYR   0.023   0.002   TYR L 145 
 PHE   0.016   0.001   PHE H 154 
 TRP   0.011   0.002   TRP H 162 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 5778)
  covalent geometry    : angle       0.79559 ( 7850)
  SS BOND              : bond        0.00530 (    4)
  SS BOND              : angle       0.97200 (    8)
  hydrogen bonds       : bond        0.03930 (  283)
  hydrogen bonds       : angle       5.08436 (  798)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1136.70 seconds
wall clock time: 20 minutes 18.73 seconds (1218.73 seconds total)