Starting phenix.real_space_refine
on Tue Mar  3 13:58:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vag_31840/03_2026/7vag_31840.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vag_31840/03_2026/7vag_31840.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vag_31840/03_2026/7vag_31840.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vag_31840/03_2026/7vag_31840.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vag_31840/03_2026/7vag_31840.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vag_31840/03_2026/7vag_31840.cif"
  }
  resolution = 3.32
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    3676      2.51       5
     N     912      2.21       5
     O    1066      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  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: 5697
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2344
          Classifications: {'peptide': 306}
          Link IDs: {'PTRANS': 17, 'TRANS': 288}
    Chain: "H"
      Number of atoms: 1669
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1669
          Classifications: {'peptide': 221}
          Link IDs: {'PTRANS': 15, 'TRANS': 205}
    Chain: "L"
      Number of atoms: 1684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1684
          Classifications: {'peptide': 216}
          Link IDs: {'PTRANS': 9, 'TRANS': 206}
  Time building chain proxies: 1.30, per 1000 atoms: 0.23
  Number of scatterers: 5697
  At special positions: 0
  Unit cell: (84.66, 72.21, 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      43     16.00
     O    1066      8.00
     N     912      7.00
     C    3676      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.44
  Conformation dependent library (CDL) restraints added in 353.4 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 9 sheets defined
      38.8% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 20
      removed outlier: 3.661A  pdb=" N   GLY A  19 " --> pdb=" O   PRO A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 45
      removed outlier: 4.106A  pdb=" N   THR A  45 " --> pdb=" O   SER A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 57
      removed outlier: 3.617A  pdb=" N   ILE A  51 " --> pdb=" O   GLU A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 71
      removed outlier: 3.840A  pdb=" N   ILE A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 83
    Processing helix  chain 'A' and resid 86 through 99
    Processing helix  chain 'A' and resid 102 through 113
      removed outlier: 3.698A  pdb=" N   ASN A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 142
      Proline residue:  A 135  - end of helix
    Processing helix  chain 'A' and resid 156 through 180
      Proline residue:  A 169  - end of helix
    Processing helix  chain 'A' and resid 183 through 209
      removed outlier: 3.510A  pdb=" N   VAL A 187 " --> pdb=" O   TYR A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 218
    Processing helix  chain 'A' and resid 219 through 244
      Proline residue:  A 230  - end of helix
      removed outlier: 3.526A  pdb=" N   PHE A 244 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 260
      removed outlier: 4.528A  pdb=" N   THR A 253 " --> pdb=" O   ARG A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 274
    Processing helix  chain 'A' and resid 280 through 283
    Processing helix  chain 'A' and resid 284 through 310
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.793A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 62 through 66
      removed outlier: 3.743A  pdb=" N   LYS H  65 " --> pdb=" O   GLU H  62 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   GLY H  66 " --> pdb=" O   LYS H  63 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 62 through 66'
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.866A  pdb=" N   SER H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 85 through 89
      removed outlier: 3.952A  pdb=" N   LEU L  89 " --> pdb=" O   ALA L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 126 through 132
      removed outlier: 3.514A  pdb=" N   LEU L 130 " --> pdb=" O   SER L 126 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   THR L 131 " --> pdb=" O   SER L 127 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.606A  pdb=" N   ILE H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   TYR H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.755A  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: 7.028A  pdb=" N   CYS H  96 " --> pdb=" O   TYR H 110 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   TYR H 110 " --> pdb=" O   CYS H  96 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   ARG H  98 " --> pdb=" O   PHE H 108 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   PHE H 108 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   TYR H 100 " --> pdb=" O   HIS H 106 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 130 through 132
      removed outlier: 4.340A  pdb=" N   GLY H 147 " --> pdb=" O   LEU H 132 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   CYS H 148 " --> pdb=" O   SER H 187 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   SER H 187 " --> pdb=" O   CYS H 148 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   THR H 184 " --> pdb=" O   ALA H 176 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   ALA H 176 " --> pdb=" O   THR H 184 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   SER H 186 " --> pdb=" O   PHE H 174 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 159 through 161
      removed outlier: 3.644A  pdb=" N   LYS H 216 " --> pdb=" O   CYS H 203 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 11 through 12
      removed outlier: 3.527A  pdb=" N   TYR L  92 " --> pdb=" O   THR L 107 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 21 through 23
      removed outlier: 3.673A  pdb=" N   CYS L  23 " --> pdb=" O   PHE L  77 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   PHE L  77 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 122 through 123
      removed outlier: 3.574A  pdb=" N   VAL L 138 " --> pdb=" O   PHE L 123 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ASN L 143 " --> pdb=" O   TYR L 178 " (cutoff:3.500A)
      removed outlier: 6.253A  pdb=" N   TYR L 178 " --> pdb=" O   ASN L 143 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 158 through 159

    283 hydrogen bonds defined for protein.
    753 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.85

  Time building geometry restraints manager: 0.60 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: 1734
        1.35 -     1.46: 1443
        1.46 -     1.58: 2593
        1.58 -     1.70: 0
        1.70 -     1.82: 65
  Bond restraints: 5835
  Sorted by residual:
  bond pdb=" CA  MET A 133 "
       pdb=" CB  MET A 133 "
    ideal  model  delta    sigma   weight residual
    1.530  1.549 -0.019 1.84e-02 2.95e+03 1.08e+00
  bond pdb=" CB  GLN H 179 "
       pdb=" CG  GLN H 179 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 1.00e+00
  bond pdb=" CA  GLN H 179 "
       pdb=" CB  GLN H 179 "
    ideal  model  delta    sigma   weight residual
    1.533  1.549 -0.016 1.69e-02 3.50e+03 8.61e-01
  bond pdb=" C   SER L   7 "
       pdb=" N   PRO L   8 "
    ideal  model  delta    sigma   weight residual
    1.334  1.353 -0.019 2.34e-02 1.83e+03 6.57e-01
  bond pdb=" CB  MET A 256 "
       pdb=" CG  MET A 256 "
    ideal  model  delta    sigma   weight residual
    1.520  1.496  0.024 3.00e-02 1.11e+03 6.25e-01
  ... (remaining 5830 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 7752
        1.88 -     3.76: 135
        3.76 -     5.64: 31
        5.64 -     7.52: 9
        7.52 -     9.39: 2
  Bond angle restraints: 7929
  Sorted by residual:
  angle pdb=" CA  GLN H 179 "
        pdb=" CB  GLN H 179 "
        pdb=" CG  GLN H 179 "
      ideal   model   delta    sigma   weight residual
     114.10  119.79   -5.69 2.00e+00 2.50e-01 8.09e+00
  angle pdb=" CA  LEU A 150 "
        pdb=" CB  LEU A 150 "
        pdb=" CG  LEU A 150 "
      ideal   model   delta    sigma   weight residual
     116.30  125.69   -9.39 3.50e+00 8.16e-02 7.20e+00
  angle pdb=" CB  MET A 133 "
        pdb=" CG  MET A 133 "
        pdb=" SD  MET A 133 "
      ideal   model   delta    sigma   weight residual
     112.70  120.74   -8.04 3.00e+00 1.11e-01 7.19e+00
  angle pdb=" N   MET A 133 "
        pdb=" CA  MET A 133 "
        pdb=" CB  MET A 133 "
      ideal   model   delta    sigma   weight residual
     111.66  107.78    3.88 1.56e+00 4.11e-01 6.18e+00
  angle pdb=" CB  MET A  39 "
        pdb=" CG  MET A  39 "
        pdb=" SD  MET A  39 "
      ideal   model   delta    sigma   weight residual
     112.70  119.71   -7.01 3.00e+00 1.11e-01 5.45e+00
  ... (remaining 7924 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3179
       17.95 -    35.90: 258
       35.90 -    53.85: 33
       53.85 -    71.80: 7
       71.80 -    89.75: 4
  Dihedral angle restraints: 3481
    sinusoidal: 1329
      harmonic: 2152
  Sorted by residual:
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  94 "
           pdb=" CB  CYS L  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.03  -72.03     1      1.00e+01 1.00e-02 6.64e+01
  dihedral pdb=" CB  GLU L 192 "
           pdb=" CG  GLU L 192 "
           pdb=" CD  GLU L 192 "
           pdb=" OE1 GLU L 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.75  -89.75     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CA  GLY A 132 "
           pdb=" C   GLY A 132 "
           pdb=" N   MET A 133 "
           pdb=" CA  MET A 133 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.19  -15.81     0      5.00e+00 4.00e-02 1.00e+01
  ... (remaining 3478 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 550
       0.029 -    0.058: 230
       0.058 -    0.088: 80
       0.088 -    0.117: 52
       0.117 -    0.146: 6
  Chirality restraints: 918
  Sorted by residual:
  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    2.58   -0.15 2.00e-01 2.50e+01 5.34e-01
  chirality pdb=" CG  LEU A 118 "
            pdb=" CB  LEU A 118 "
            pdb=" CD1 LEU A 118 "
            pdb=" CD2 LEU A 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.72    0.13 2.00e-01 2.50e+01 4.21e-01
  chirality pdb=" CB  ILE A 214 "
            pdb=" CA  ILE A 214 "
            pdb=" CG1 ILE A 214 "
            pdb=" CG2 ILE A 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.77   -0.13 2.00e-01 2.50e+01 3.98e-01
  ... (remaining 915 not shown)

  Planarity restraints: 980
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR H 213 "   -0.007 2.00e-02 2.50e+03   1.34e-02 1.78e+00
        pdb=" C   THR H 213 "    0.023 2.00e-02 2.50e+03
        pdb=" O   THR H 213 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   VAL H 214 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE H 174 "   -0.020 5.00e-02 4.00e+02   2.97e-02 1.41e+00
        pdb=" N   PRO H 175 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO H 175 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO H 175 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 280 "   -0.018 5.00e-02 4.00e+02   2.74e-02 1.20e+00
        pdb=" N   PRO A 281 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 281 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 281 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 977 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 77
        2.67 -     3.23: 5522
        3.23 -     3.78: 8655
        3.78 -     4.34: 11118
        4.34 -     4.90: 18741
  Nonbonded interactions: 44113
  Sorted by model distance:
  nonbonded pdb=" OG  SER H 198 "
            pdb=" OE1 GLN H 199 "
     model   vdw
     2.109 3.040
  nonbonded pdb=" OE1 GLN H   6 "
            pdb=" OG1 THR H 115 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OH  TYR A  69 "
            pdb=" O   SER A 126 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" OE2 GLU A  47 "
            pdb=" NZ  LYS A  50 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" NH2 ARG L  60 "
            pdb=" O   VAL L  64 "
     model   vdw
     2.317 3.120
  ... (remaining 44108 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.520
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.410
  Find NCS groups from input model:        0.030
  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:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
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      :  0.002   0.030   5838  Z= 0.111
  Angle     :  0.655   9.395   7935  Z= 0.311
  Chirality :  0.041   0.146    918
  Planarity :  0.004   0.031    980
  Dihedral  : 13.266  89.754   2096
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.28 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.77 %
    Favored  : 99.07 %
  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:  0.41 (0.32), residues: 737
  helix:  1.46 (0.33), residues: 250
  sheet:  0.88 (0.41), residues: 168
  loop : -1.04 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 251 
 TYR   0.010   0.001   TYR A 146 
 PHE   0.014   0.001   PHE A 292 
 TRP   0.006   0.001   TRP L  56 
 HIS   0.002   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 5835)
  covalent geometry    : angle       0.65510 ( 7929)
  SS BOND              : bond        0.00417 (    3)
  SS BOND              : angle       0.31508 (    6)
  hydrogen bonds       : bond        0.16855 (  278)
  hydrogen bonds       : angle       6.48913 (  753)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 215
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  180 ARG cc_start: 0.8007 (mtt90) cc_final: 0.7666 (ttm-80)
REVERT: A  229 MET cc_start: 0.8523 (tpt) cc_final: 0.8039 (tpt)
REVERT: A  308 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7435 (tp30)
REVERT: H   91 SER cc_start: 0.8947 (m) cc_final: 0.8706 (p)
REVERT: H  153 TYR cc_start: 0.6429 (p90) cc_final: 0.5833 (p90)
REVERT: L  144 PHE cc_start: 0.8461 (p90) cc_final: 0.8190 (p90)
REVERT: L  180 MET cc_start: 0.8413 (ttp) cc_final: 0.8086 (ttt)
  outliers start: 1
  outliers final: 0
  residues processed: 215
  average time/residue: 0.0609
  time to fit residues: 17.7523
Evaluate side-chains
  185 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.4980
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
A 293 GLN
H  39 GLN
H 113 GLN
H 179 GLN
** L  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 195 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.162666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.127158 restraints weight = 9374.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 3.63
r_work: 0.3397 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5838  Z= 0.166
  Angle     :  0.713   9.983   7935  Z= 0.349
  Chirality :  0.045   0.175    918
  Planarity :  0.004   0.039    980
  Dihedral  :  4.171  17.485    794
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 14.55 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.47 (0.32), residues: 737
  helix:  1.63 (0.34), residues: 248
  sheet:  0.77 (0.41), residues: 169
  loop : -1.02 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 251 
 TYR   0.021   0.002   TYR A 146 
 PHE   0.028   0.002   PHE A 274 
 TRP   0.011   0.001   TRP H 196 
 HIS   0.003   0.001   HIS H 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 5835)
  covalent geometry    : angle       0.71263 ( 7929)
  SS BOND              : bond        0.00084 (    3)
  SS BOND              : angle       0.86980 (    6)
  hydrogen bonds       : bond        0.03849 (  278)
  hydrogen bonds       : angle       4.72424 (  753)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 206
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: A  180 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7821 (ttm170)
REVERT: A  182 GLN cc_start: 0.5441 (pm20) cc_final: 0.5187 (pm20)
REVERT: A  184 MET cc_start: 0.5199 (mmp) cc_final: 0.4818 (mmt)
REVERT: A  229 MET cc_start: 0.9007 (tpt) cc_final: 0.8394 (tpt)
REVERT: A  231 PHE cc_start: 0.8590 (t80) cc_final: 0.8215 (t80)
REVERT: A  271 ASN cc_start: 0.9006 (m-40) cc_final: 0.8774 (m-40)
REVERT: H   39 GLN cc_start: 0.8676 (tt0) cc_final: 0.8368 (tt0)
REVERT: H   61 ASN cc_start: 0.8796 (t0) cc_final: 0.8089 (t0)
REVERT: H  153 TYR cc_start: 0.6993 (p90) cc_final: 0.6210 (p90)
REVERT: H  179 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6925 (pp30)
REVERT: L    2 ILE cc_start: 0.9193 (mt) cc_final: 0.8955 (mm)
REVERT: L   87 GLU cc_start: 0.8587 (pm20) cc_final: 0.8296 (pm20)
REVERT: L   88 ASP cc_start: 0.8933 (m-30) cc_final: 0.8653 (m-30)
REVERT: L  144 PHE cc_start: 0.8540 (p90) cc_final: 0.8203 (p90)
REVERT: L  161 GLN cc_start: 0.6009 (mp10) cc_final: 0.4973 (pm20)
  outliers start: 13
  outliers final: 8
  residues processed: 209
  average time/residue: 0.0559
  time to fit residues: 16.2772
Evaluate side-chains
  205 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 196
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  293 GLN
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain H residue  179 GLN
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  137 VAL
Chi-restraints excluded: chain L residue  141 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 22 optimal weight:    0.5980
   chunk 36 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 64 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
A 293 GLN
H  43 GLN
** L  37 ASN ** 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 = 0.3919 r_free = 0.3919 target = 0.159685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.123415 restraints weight = 9342.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 3.56
r_work: 0.3351 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5838  Z= 0.177
  Angle     :  0.699   8.602   7935  Z= 0.346
  Chirality :  0.045   0.210    918
  Planarity :  0.004   0.036    980
  Dihedral  :  4.392  17.924    794
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 17.18 %
    Favored  : 78.95 %
  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:  0.41 (0.32), residues: 737
  helix:  1.66 (0.34), residues: 247
  sheet:  0.73 (0.41), residues: 168
  loop : -1.10 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 251 
 TYR   0.016   0.001   TYR A 146 
 PHE   0.026   0.002   PHE A 292 
 TRP   0.007   0.001   TRP L 153 
 HIS   0.004   0.001   HIS H 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 5835)
  covalent geometry    : angle       0.69867 ( 7929)
  SS BOND              : bond        0.00267 (    3)
  SS BOND              : angle       0.54679 (    6)
  hydrogen bonds       : bond        0.03770 (  278)
  hydrogen bonds       : angle       4.54681 (  753)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 197
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 TYR cc_start: 0.8121 (t80) cc_final: 0.7913 (t80)
REVERT: A  184 MET cc_start: 0.5163 (mmp) cc_final: 0.4823 (mmt)
REVERT: A  229 MET cc_start: 0.9094 (tpt) cc_final: 0.8554 (tpt)
REVERT: H   39 GLN cc_start: 0.8680 (tt0) cc_final: 0.8428 (tt0)
REVERT: H   61 ASN cc_start: 0.8881 (t0) cc_final: 0.8490 (t0)
REVERT: H  153 TYR cc_start: 0.7297 (p90) cc_final: 0.6455 (p90)
REVERT: L    2 ILE cc_start: 0.9240 (mt) cc_final: 0.8938 (mm)
REVERT: L   27 GLN cc_start: 0.8058 (pm20) cc_final: 0.7443 (pm20)
REVERT: L   88 ASP cc_start: 0.8920 (m-30) cc_final: 0.8703 (m-30)
REVERT: L  144 PHE cc_start: 0.8529 (p90) cc_final: 0.8187 (p90)
  outliers start: 25
  outliers final: 17
  residues processed: 203
  average time/residue: 0.0548
  time to fit residues: 15.6001
Evaluate side-chains
  206 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 189
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   99 SER
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  245 CYS
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  137 VAL
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  194 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 72 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   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 209 ASN
** L  37 ASN ** 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 = 0.3909 r_free = 0.3909 target = 0.158402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.122619 restraints weight = 9431.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 3.61
r_work: 0.3347 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5838  Z= 0.141
  Angle     :  0.686   9.524   7935  Z= 0.330
  Chirality :  0.044   0.200    918
  Planarity :  0.004   0.037    980
  Dihedral  :  4.338  18.317    794
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 21.21 %
    Favored  : 75.54 %
  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:  0.32 (0.32), residues: 737
  helix:  1.60 (0.34), residues: 254
  sheet:  0.64 (0.41), residues: 172
  loop : -1.23 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 251 
 TYR   0.016   0.001   TYR L 145 
 PHE   0.020   0.001   PHE A 292 
 TRP   0.008   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 5835)
  covalent geometry    : angle       0.68597 ( 7929)
  SS BOND              : bond        0.00368 (    3)
  SS BOND              : angle       0.35882 (    6)
  hydrogen bonds       : bond        0.03491 (  278)
  hydrogen bonds       : angle       4.36214 (  753)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 203
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 LEU cc_start: 0.6709 (tp) cc_final: 0.6440 (mm)
REVERT: A   34 MET cc_start: 0.8833 (tmm) cc_final: 0.8608 (ttm)
REVERT: A   42 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8984 (mp)
REVERT: A  184 MET cc_start: 0.5192 (mmp) cc_final: 0.4890 (mmt)
REVERT: A  229 MET cc_start: 0.9121 (tpt) cc_final: 0.8595 (tpt)
REVERT: A  253 THR cc_start: 0.9016 (t) cc_final: 0.8735 (t)
REVERT: A  310 PHE cc_start: 0.6883 (m-10) cc_final: 0.6661 (m-80)
REVERT: H   39 GLN cc_start: 0.8658 (tt0) cc_final: 0.8418 (tt0)
REVERT: H   61 ASN cc_start: 0.8911 (t0) cc_final: 0.8516 (t0)
REVERT: H  153 TYR cc_start: 0.7408 (p90) cc_final: 0.6570 (p90)
REVERT: H  185 MET cc_start: 0.8430 (ppp) cc_final: 0.8227 (ppp)
REVERT: L    2 ILE cc_start: 0.9240 (mt) cc_final: 0.8832 (mm)
REVERT: L   27 GLN cc_start: 0.8005 (pm20) cc_final: 0.7199 (pm20)
REVERT: L   61 GLU cc_start: 0.9252 (tp30) cc_final: 0.9052 (tp30)
REVERT: L   88 ASP cc_start: 0.8960 (m-30) cc_final: 0.8724 (m-30)
REVERT: L  144 PHE cc_start: 0.8510 (p90) cc_final: 0.8097 (p90)
REVERT: L  161 GLN cc_start: 0.6007 (mp10) cc_final: 0.5075 (pm20)
  outliers start: 21
  outliers final: 16
  residues processed: 208
  average time/residue: 0.0547
  time to fit residues: 15.9729
Evaluate side-chains
  214 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 197
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   99 SER
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain H residue   99 SER
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue  137 VAL
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  194 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 34 optimal weight:    0.3980
   chunk 37 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0040
   chunk 69 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.5992

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
** L  37 ASN ** 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 = 0.3910 r_free = 0.3910 target = 0.158696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.122990 restraints weight = 9563.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 3.65
r_work: 0.3356 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.2779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5838  Z= 0.125
  Angle     :  0.682   9.455   7935  Z= 0.325
  Chirality :  0.044   0.208    918
  Planarity :  0.003   0.036    980
  Dihedral  :  4.282  18.633    794
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 22.45 %
    Favored  : 73.68 %
  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:  0.37 (0.32), residues: 737
  helix:  1.68 (0.34), residues: 254
  sheet:  0.78 (0.43), residues: 164
  loop : -1.27 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 249 
 TYR   0.014   0.001   TYR H 183 
 PHE   0.021   0.001   PHE A 292 
 TRP   0.007   0.001   TRP L 168 
 HIS   0.002   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 5835)
  covalent geometry    : angle       0.68252 ( 7929)
  SS BOND              : bond        0.00355 (    3)
  SS BOND              : angle       0.27930 (    6)
  hydrogen bonds       : bond        0.03289 (  278)
  hydrogen bonds       : angle       4.28367 (  753)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 204
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A   27 LEU cc_start: 0.6744 (tp) cc_final: 0.6468 (mm)
REVERT: A   42 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8981 (mp)
REVERT: A  127 THR cc_start: 0.8911 (m) cc_final: 0.8574 (p)
REVERT: A  180 ARG cc_start: 0.8253 (ttm170) cc_final: 0.7603 (ttm110)
REVERT: A  229 MET cc_start: 0.9099 (tpt) cc_final: 0.8574 (tpt)
REVERT: A  253 THR cc_start: 0.9169 (t) cc_final: 0.8881 (t)
REVERT: H   39 GLN cc_start: 0.8681 (tt0) cc_final: 0.8472 (tt0)
REVERT: H   61 ASN cc_start: 0.8913 (t0) cc_final: 0.8521 (t0)
REVERT: H  153 TYR cc_start: 0.7346 (p90) cc_final: 0.6485 (p90)
REVERT: H  179 GLN cc_start: 0.7386 (tm-30) cc_final: 0.7131 (tm-30)
REVERT: L    2 ILE cc_start: 0.9234 (mt) cc_final: 0.8826 (mm)
REVERT: L   27 GLN cc_start: 0.8178 (pm20) cc_final: 0.7211 (pm20)
REVERT: L   61 GLU cc_start: 0.9318 (tp30) cc_final: 0.9114 (tp30)
REVERT: L  144 PHE cc_start: 0.8534 (p90) cc_final: 0.8186 (p90)
REVERT: L  180 MET cc_start: 0.8571 (ttt) cc_final: 0.8038 (ttt)
  outliers start: 25
  outliers final: 19
  residues processed: 212
  average time/residue: 0.0595
  time to fit residues: 17.4274
Evaluate side-chains
  218 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 198
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   99 SER
Chi-restraints excluded: chain A residue  125 CYS
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  258 THR
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain H residue   99 SER
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue  137 VAL
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  151 VAL
Chi-restraints excluded: chain L residue  194 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 1 optimal weight:    0.0670
   chunk 6 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 20 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0070
   chunk 64 optimal weight:    7.9990
   chunk 27 optimal weight:    0.0980
   chunk 54 optimal weight:    0.0870
   chunk 28 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.1714

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
A 293 GLN
** L  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 194 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.161923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.125870 restraints weight = 9467.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 3.64
r_work: 0.3393 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5838  Z= 0.115
  Angle     :  0.696   8.679   7935  Z= 0.325
  Chirality :  0.044   0.207    918
  Planarity :  0.003   0.037    980
  Dihedral  :  4.161  18.339    794
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 23.22 %
    Favored  : 73.84 %
  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:  0.36 (0.32), residues: 737
  helix:  1.80 (0.34), residues: 247
  sheet:  0.70 (0.43), residues: 162
  loop : -1.27 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 249 
 TYR   0.020   0.001   TYR L 145 
 PHE   0.016   0.001   PHE A 292 
 TRP   0.007   0.001   TRP L 168 
 HIS   0.002   0.001   HIS L 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 5835)
  covalent geometry    : angle       0.69613 ( 7929)
  SS BOND              : bond        0.00215 (    3)
  SS BOND              : angle       0.16636 (    6)
  hydrogen bonds       : bond        0.03096 (  278)
  hydrogen bonds       : angle       4.26163 (  753)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 198
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 THR cc_start: 0.8911 (m) cc_final: 0.8673 (p)
REVERT: A  163 LEU cc_start: 0.9008 (tp) cc_final: 0.8675 (mp)
REVERT: A  229 MET cc_start: 0.9122 (tpt) cc_final: 0.8571 (tpt)
REVERT: A  253 THR cc_start: 0.9077 (t) cc_final: 0.8785 (t)
REVERT: A  294 LEU cc_start: 0.8683 (tt) cc_final: 0.8462 (tt)
REVERT: H   39 GLN cc_start: 0.8718 (tt0) cc_final: 0.8514 (tt0)
REVERT: H   61 ASN cc_start: 0.8823 (t0) cc_final: 0.8409 (t0)
REVERT: H  100 TYR cc_start: 0.8732 (t80) cc_final: 0.8490 (t80)
REVERT: H  153 TYR cc_start: 0.7376 (p90) cc_final: 0.6469 (p90)
REVERT: H  179 GLN cc_start: 0.7340 (tm-30) cc_final: 0.7099 (tm-30)
REVERT: L   61 GLU cc_start: 0.9324 (tp30) cc_final: 0.9090 (tp30)
REVERT: L  144 PHE cc_start: 0.8498 (p90) cc_final: 0.8156 (p90)
REVERT: L  161 GLN cc_start: 0.5720 (mp10) cc_final: 0.4551 (pm20)
REVERT: L  180 MET cc_start: 0.8564 (ttt) cc_final: 0.7990 (ttt)
  outliers start: 19
  outliers final: 15
  residues processed: 203
  average time/residue: 0.0585
  time to fit residues: 16.5542
Evaluate side-chains
  207 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 192
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain H residue   99 SER
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain L residue   17 GLU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  137 VAL
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  151 VAL
Chi-restraints excluded: chain L residue  194 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 36 optimal weight:    0.0570
   chunk 25 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0000
   chunk 3 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0770
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.3660

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN
A 209 ASN
A 293 GLN
** L  37 ASN ** 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 = 0.3960 r_free = 0.3960 target = 0.163248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.126749 restraints weight = 9328.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 3.68
r_work: 0.3395 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5838  Z= 0.116
  Angle     :  0.696  11.016   7935  Z= 0.327
  Chirality :  0.043   0.206    918
  Planarity :  0.003   0.037    980
  Dihedral  :  4.119  18.353    794
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 23.84 %
    Favored  : 73.37 %
  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:  0.35 (0.32), residues: 737
  helix:  1.82 (0.34), residues: 247
  sheet:  0.66 (0.42), residues: 162
  loop : -1.28 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 249 
 TYR   0.016   0.001   TYR L 145 
 PHE   0.017   0.001   PHE A 292 
 TRP   0.007   0.001   TRP L 168 
 HIS   0.009   0.001   HIS L 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 5835)
  covalent geometry    : angle       0.69665 ( 7929)
  SS BOND              : bond        0.00287 (    3)
  SS BOND              : angle       0.22696 (    6)
  hydrogen bonds       : bond        0.03050 (  278)
  hydrogen bonds       : angle       4.18820 (  753)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 196
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 MET cc_start: 0.9105 (tpt) cc_final: 0.8636 (tpt)
REVERT: A  253 THR cc_start: 0.9008 (t) cc_final: 0.8720 (t)
REVERT: H   61 ASN cc_start: 0.8881 (t0) cc_final: 0.8472 (t0)
REVERT: H  100 TYR cc_start: 0.8738 (t80) cc_final: 0.8500 (t80)
REVERT: H  153 TYR cc_start: 0.7332 (p90) cc_final: 0.6455 (p90)
REVERT: H  179 GLN cc_start: 0.7368 (tm-30) cc_final: 0.7116 (tm-30)
REVERT: L    2 ILE cc_start: 0.8827 (mm) cc_final: 0.8574 (mm)
REVERT: L   27 GLN cc_start: 0.8214 (pm20) cc_final: 0.7604 (pm20)
REVERT: L   61 GLU cc_start: 0.9335 (tp30) cc_final: 0.9095 (tp30)
REVERT: L  144 PHE cc_start: 0.8428 (p90) cc_final: 0.8092 (p90)
REVERT: L  161 GLN cc_start: 0.5715 (mp10) cc_final: 0.4549 (pm20)
REVERT: L  180 MET cc_start: 0.8552 (ttt) cc_final: 0.7974 (ttt)
  outliers start: 18
  outliers final: 14
  residues processed: 200
  average time/residue: 0.0589
  time to fit residues: 16.2969
Evaluate side-chains
  204 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 190
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain L residue   17 GLU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  137 VAL
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  151 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   chunk 42 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 63 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 293 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 ASN ** 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 = 0.3942 r_free = 0.3942 target = 0.161287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.125264 restraints weight = 9233.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 3.58
r_work: 0.3355 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5838  Z= 0.145
  Angle     :  0.726   9.817   7935  Z= 0.341
  Chirality :  0.044   0.210    918
  Planarity :  0.004   0.040    980
  Dihedral  :  4.276  19.913    794
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 22.91 %
    Favored  : 73.22 %
  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:  0.25 (0.32), residues: 737
  helix:  1.74 (0.34), residues: 246
  sheet:  0.57 (0.42), residues: 162
  loop : -1.32 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 249 
 TYR   0.016   0.001   TYR L 145 
 PHE   0.024   0.002   PHE A 292 
 TRP   0.009   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 5835)
  covalent geometry    : angle       0.72617 ( 7929)
  SS BOND              : bond        0.00419 (    3)
  SS BOND              : angle       0.45374 (    6)
  hydrogen bonds       : bond        0.03354 (  278)
  hydrogen bonds       : angle       4.27537 (  753)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 195
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 MET cc_start: 0.9226 (tpt) cc_final: 0.8701 (tpt)
REVERT: A  253 THR cc_start: 0.9235 (t) cc_final: 0.8899 (t)
REVERT: H   61 ASN cc_start: 0.8932 (t0) cc_final: 0.8255 (t0)
REVERT: H  100 TYR cc_start: 0.8768 (t80) cc_final: 0.8500 (t80)
REVERT: H  153 TYR cc_start: 0.7358 (p90) cc_final: 0.6414 (p90)
REVERT: H  179 GLN cc_start: 0.7691 (tm-30) cc_final: 0.7442 (tm-30)
REVERT: L    2 ILE cc_start: 0.8864 (mm) cc_final: 0.8621 (mm)
REVERT: L   61 GLU cc_start: 0.9298 (tp30) cc_final: 0.9049 (tp30)
REVERT: L  144 PHE cc_start: 0.8392 (p90) cc_final: 0.8092 (p90)
REVERT: L  180 MET cc_start: 0.8527 (ttt) cc_final: 0.7874 (ttt)
  outliers start: 25
  outliers final: 20
  residues processed: 201
  average time/residue: 0.0591
  time to fit residues: 16.4564
Evaluate side-chains
  212 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 192
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   47 GLU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain H residue   99 SER
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain L residue   17 GLU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  137 VAL
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  151 VAL
Chi-restraints excluded: chain L residue  194 HIS
Chi-restraints excluded: chain L residue  214 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0170
   chunk 39 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.9424

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

Flipped N/Q/H residues before XYZ refinement:
A 293 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 ASN ** 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 = 0.3928 r_free = 0.3928 target = 0.160004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.123658 restraints weight = 9293.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 3.62
r_work: 0.3330 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5838  Z= 0.151
  Angle     :  0.752  12.815   7935  Z= 0.354
  Chirality :  0.045   0.213    918
  Planarity :  0.004   0.040    980
  Dihedral  :  4.370  20.364    794
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 24.61 %
    Favored  : 72.14 %
  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: 737
  helix:  1.70 (0.34), residues: 247
  sheet:  0.51 (0.42), residues: 162
  loop : -1.42 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 249 
 TYR   0.021   0.001   TYR L 145 
 PHE   0.025   0.001   PHE A 292 
 TRP   0.009   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 5835)
  covalent geometry    : angle       0.75219 ( 7929)
  SS BOND              : bond        0.00450 (    3)
  SS BOND              : angle       0.49787 (    6)
  hydrogen bonds       : bond        0.03425 (  278)
  hydrogen bonds       : angle       4.33064 (  753)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 196
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.9235 (tpp) cc_final: 0.8919 (tpp)
REVERT: A  229 MET cc_start: 0.9172 (tpt) cc_final: 0.8606 (tpt)
REVERT: A  253 THR cc_start: 0.9263 (t) cc_final: 0.8950 (t)
REVERT: A  271 ASN cc_start: 0.9162 (m-40) cc_final: 0.8888 (m110)
REVERT: A  294 LEU cc_start: 0.8720 (tt) cc_final: 0.8496 (tt)
REVERT: H   61 ASN cc_start: 0.8956 (t0) cc_final: 0.8570 (t0)
REVERT: H  100 TYR cc_start: 0.8762 (t80) cc_final: 0.8479 (t80)
REVERT: H  153 TYR cc_start: 0.7491 (p90) cc_final: 0.6646 (p90)
REVERT: H  179 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7529 (tm-30)
REVERT: L    2 ILE cc_start: 0.8917 (mm) cc_final: 0.8662 (mm)
REVERT: L   61 GLU cc_start: 0.9323 (tp30) cc_final: 0.9092 (tp30)
REVERT: L   67 ARG cc_start: 0.8579 (ptt-90) cc_final: 0.8318 (ptt-90)
REVERT: L  144 PHE cc_start: 0.8310 (p90) cc_final: 0.8096 (p90)
REVERT: L  180 MET cc_start: 0.8507 (ttt) cc_final: 0.7877 (ttt)
  outliers start: 21
  outliers final: 20
  residues processed: 201
  average time/residue: 0.0608
  time to fit residues: 16.7955
Evaluate side-chains
  214 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 194
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain H residue   99 SER
Chi-restraints excluded: chain H residue  104 ILE
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain L residue   17 GLU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  137 VAL
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  151 VAL
Chi-restraints excluded: chain L residue  194 HIS
Chi-restraints excluded: chain L residue  214 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 72 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 293 GLN
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** 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 = 0.3919 r_free = 0.3919 target = 0.158945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.122445 restraints weight = 9404.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 3.62
r_work: 0.3325 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.3486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5838  Z= 0.142
  Angle     :  0.747   9.500   7935  Z= 0.354
  Chirality :  0.045   0.211    918
  Planarity :  0.004   0.040    980
  Dihedral  :  4.396  20.736    794
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 24.92 %
    Favored  : 71.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.06 (0.31), residues: 737
  helix:  1.60 (0.34), residues: 247
  sheet:  0.49 (0.42), residues: 162
  loop : -1.46 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 249 
 TYR   0.024   0.002   TYR L 145 
 PHE   0.021   0.001   PHE A 292 
 TRP   0.010   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5835)
  covalent geometry    : angle       0.74694 ( 7929)
  SS BOND              : bond        0.00464 (    3)
  SS BOND              : angle       0.44936 (    6)
  hydrogen bonds       : bond        0.03298 (  278)
  hydrogen bonds       : angle       4.37807 (  753)

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

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

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

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 195
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.9204 (tpp) cc_final: 0.8913 (tpp)
REVERT: A  192 MET cc_start: 0.5872 (mtm) cc_final: 0.5635 (mtp)
REVERT: A  229 MET cc_start: 0.9159 (tpt) cc_final: 0.8592 (tpt)
REVERT: A  253 THR cc_start: 0.9277 (t) cc_final: 0.8989 (t)
REVERT: A  294 LEU cc_start: 0.8677 (tt) cc_final: 0.8470 (tt)
REVERT: H   61 ASN cc_start: 0.8961 (t0) cc_final: 0.8578 (t0)
REVERT: H  100 TYR cc_start: 0.8726 (t80) cc_final: 0.8433 (t80)
REVERT: H  153 TYR cc_start: 0.7514 (p90) cc_final: 0.6607 (p90)
REVERT: H  179 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7557 (tm-30)
REVERT: L    2 ILE cc_start: 0.8905 (mm) cc_final: 0.8667 (mm)
REVERT: L   61 GLU cc_start: 0.9324 (tp30) cc_final: 0.9096 (tp30)
REVERT: L   67 ARG cc_start: 0.8580 (ptt-90) cc_final: 0.8315 (ptt-90)
REVERT: L  144 PHE cc_start: 0.8321 (p90) cc_final: 0.8113 (p90)
REVERT: L  180 MET cc_start: 0.8456 (ttt) cc_final: 0.7873 (ttt)
  outliers start: 20
  outliers final: 20
  residues processed: 200
  average time/residue: 0.0597
  time to fit residues: 16.4930
Evaluate side-chains
  212 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 192
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  154 VAL
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  174 ILE
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain H residue   99 SER
Chi-restraints excluded: chain H residue  104 ILE
Chi-restraints excluded: chain H residue  118 THR
Chi-restraints excluded: chain L residue   17 GLU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   52 LEU
Chi-restraints excluded: chain L residue  110 GLU
Chi-restraints excluded: chain L residue  137 VAL
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  151 VAL
Chi-restraints excluded: chain L residue  194 HIS
Chi-restraints excluded: chain L residue  214 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 73
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 60 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 9 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** L   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.160470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.124359 restraints weight = 9163.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 3.59
r_work: 0.3339 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5838  Z= 0.145
  Angle     :  0.750   9.358   7935  Z= 0.357
  Chirality :  0.045   0.207    918
  Planarity :  0.004   0.040    980
  Dihedral  :  4.418  20.856    794
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 24.77 %
    Favored  : 71.36 %
  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:  0.01 (0.31), residues: 737
  helix:  1.59 (0.35), residues: 247
  sheet:  0.46 (0.42), residues: 162
  loop : -1.53 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 249 
 TYR   0.015   0.001   TYR A 146 
 PHE   0.025   0.001   PHE A 292 
 TRP   0.009   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 5835)
  covalent geometry    : angle       0.74970 ( 7929)
  SS BOND              : bond        0.00448 (    3)
  SS BOND              : angle       0.45784 (    6)
  hydrogen bonds       : bond        0.03303 (  278)
  hydrogen bonds       : angle       4.33550 (  753)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1493.65 seconds
wall clock time: 26 minutes 20.20 seconds (1580.20 seconds total)