Starting phenix.real_space_refine
on Tue Mar  3 13:51:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vaf_31839/03_2026/7vaf_31839.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vaf_31839/03_2026/7vaf_31839.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7vaf_31839/03_2026/7vaf_31839.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vaf_31839/03_2026/7vaf_31839.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vaf_31839/03_2026/7vaf_31839.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vaf_31839/03_2026/7vaf_31839.cif"
  }
  resolution = 3.11
  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      40      5.16       5
     C    3629      2.51       5
     N     899      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 14 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: 5625
  Number of models: 1
  Model: ""
    Number of chains: 3
    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}
    Chain: "A"
      Number of atoms: 2272
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2272
          Classifications: {'peptide': 297}
          Link IDs: {'PTRANS': 16, 'TRANS': 280}
  Time building chain proxies: 1.41, per 1000 atoms: 0.25
  Number of scatterers: 5625
  At special positions: 0
  Unit cell: (85.905, 75.945, 141.93, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1057      8.00
     N     899      7.00
     C    3629      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=2.03

  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: 0.50
  Conformation dependent library (CDL) restraints added in 351.2 milliseconds
  

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1360

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 10 sheets defined
      36.8% alpha, 22.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.568A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 85 through 89
      removed outlier: 4.153A  pdb=" N   LEU L  89 " --> pdb=" O   ALA L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 126 through 132
    Processing helix  chain 'L' and resid 190 through 195
      removed outlier: 3.578A  pdb=" N   HIS L 194 " --> pdb=" O   GLU L 190 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ASN L 195 " --> pdb=" O   TYR L 191 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 190 through 195'
    Processing helix  chain 'A' and resid 23 through 44
    Processing helix  chain 'A' and resid 48 through 57
    Processing helix  chain 'A' and resid 59 through 71
      removed outlier: 3.706A  pdb=" N   VAL A  63 " --> pdb=" O   LYS A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 84
    Processing helix  chain 'A' and resid 86 through 98
    Processing helix  chain 'A' and resid 102 through 109
      removed outlier: 3.768A  pdb=" N   ASN A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 141
      removed outlier: 3.819A  pdb=" N   SER A 119 " --> pdb=" O   ASP A 115 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   ILE A 120 " --> pdb=" O   MET A 116 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   VAL A 121 " --> pdb=" O   ASN A 117 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLY A 132 " --> pdb=" O   PHE A 128 " (cutoff:3.500A)
      Proline residue:  A 135  - end of helix
      removed outlier: 3.921A  pdb=" N   TYR A 141 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 154
      removed outlier: 3.510A  pdb=" N   LYS A 153 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   VAL A 154 " --> pdb=" O   LYS A 151 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 150 through 154'
    Processing helix  chain 'A' and resid 156 through 180
      Proline residue:  A 169  - end of helix
    Processing helix  chain 'A' and resid 183 through 211
      removed outlier: 3.555A  pdb=" N   GLY A 190 " --> pdb=" O   TYR A 186 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   SER A 199 " --> pdb=" O   THR A 195 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   VAL A 200 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   LEU A 205 " --> pdb=" O   ALA A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 244
      Proline residue:  A 230  - end of helix
    Processing helix  chain 'A' and resid 247 through 260
      removed outlier: 3.810A  pdb=" N   PHE A 260 " --> pdb=" O   MET A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 274
      removed outlier: 4.271A  pdb=" N   CYS A 266 " --> pdb=" O   ASN A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 311
      removed outlier: 3.546A  pdb=" N   LYS A 311 " --> pdb=" O   TYR A 307 " (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: 6.503A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ILE H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   TYR H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLY H  57 " --> pdb=" O   ASN H  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.503A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   TYR H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
      removed outlier: 8.401A  pdb=" N   TYR H 100 " --> pdb=" O   PHE H 108 " (cutoff:3.500A)
      removed outlier: 7.450A  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: 4.050A  pdb=" N   GLY H 147 " --> pdb=" O   LEU H 132 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   CYS H 148 " --> pdb=" O   SER H 187 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   SER H 187 " --> pdb=" O   CYS H 148 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL H 150 " --> pdb=" O   MET H 185 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   MET H 185 " --> pdb=" O   VAL H 150 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   THR H 184 " --> pdb=" O   ALA H 176 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   ALA H 176 " --> pdb=" O   THR H 184 " (cutoff:3.500A)
      removed outlier: 3.710A  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: 6.744A  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: 3.950A  pdb=" N   VAL L  19 " --> pdb=" O   ILE L  81 " (cutoff:3.500A)
      removed outlier: 3.780A  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: 6.613A  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: 3.826A  pdb=" N   ASN L 143 " --> pdb=" O   TYR L 178 " (cutoff:3.500A)
      removed outlier: 6.141A  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

    270 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: 0.84

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1711
        1.34 -     1.46: 1379
        1.46 -     1.58: 2608
        1.58 -     1.70: 0
        1.70 -     1.82: 63
  Bond restraints: 5761
  Sorted by residual:
  bond pdb=" N   ALA H  16 "
       pdb=" CA  ALA H  16 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.29e-02 6.01e+03 1.67e+00
  bond pdb=" CA  ALA H  16 "
       pdb=" CB  ALA H  16 "
    ideal  model  delta    sigma   weight residual
    1.530  1.514  0.016 1.69e-02 3.50e+03 8.66e-01
  bond pdb=" CA  VAL A 154 "
       pdb=" CB  VAL A 154 "
    ideal  model  delta    sigma   weight residual
    1.526  1.539 -0.013 1.55e-02 4.16e+03 7.53e-01
  bond pdb=" CB  ASN H  55 "
       pdb=" CG  ASN H  55 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 2.50e-02 1.60e+03 6.48e-01
  bond pdb=" CB  GLU L 159 "
       pdb=" CG  GLU L 159 "
    ideal  model  delta    sigma   weight residual
    1.520  1.543 -0.023 3.00e-02 1.11e+03 6.00e-01
  ... (remaining 5756 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 7597
        1.38 -     2.77: 167
        2.77 -     4.15: 42
        4.15 -     5.54: 17
        5.54 -     6.92: 4
  Bond angle restraints: 7827
  Sorted by residual:
  angle pdb=" C   TRP L  56 "
        pdb=" N   ALA L  57 "
        pdb=" CA  ALA L  57 "
      ideal   model   delta    sigma   weight residual
     121.54  126.44   -4.90 1.91e+00 2.74e-01 6.59e+00
  angle pdb=" C   PRO L   8 "
        pdb=" N   SER L   9 "
        pdb=" CA  SER L   9 "
      ideal   model   delta    sigma   weight residual
     121.54  126.38   -4.84 1.91e+00 2.74e-01 6.43e+00
  angle pdb=" C   ALA H  16 "
        pdb=" CA  ALA H  16 "
        pdb=" CB  ALA H  16 "
      ideal   model   delta    sigma   weight residual
     110.42  115.20   -4.78 1.99e+00 2.53e-01 5.76e+00
  angle pdb=" C   MET A 112 "
        pdb=" N   LYS A 113 "
        pdb=" CA  LYS A 113 "
      ideal   model   delta    sigma   weight residual
     121.54  125.49   -3.95 1.91e+00 2.74e-01 4.28e+00
  angle pdb=" CA  CYS L  94 "
        pdb=" CB  CYS L  94 "
        pdb=" SG  CYS L  94 "
      ideal   model   delta    sigma   weight residual
     114.40  119.11   -4.71 2.30e+00 1.89e-01 4.20e+00
  ... (remaining 7822 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.73: 3095
       16.73 -    33.45: 279
       33.45 -    50.18: 56
       50.18 -    66.91: 6
       66.91 -    83.64: 7
  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  166.24  -73.24     1      1.00e+01 1.00e-02 6.83e+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  138.20  -45.20     1      1.00e+01 1.00e-02 2.84e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   66.55   26.45     1      1.00e+01 1.00e-02 1.00e+01
  ... (remaining 3440 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 535
       0.028 -    0.057: 240
       0.057 -    0.085: 74
       0.085 -    0.113: 52
       0.113 -    0.142: 10
  Chirality restraints: 911
  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   -0.14 2.00e-01 2.50e+01 5.02e-01
  chirality pdb=" CB  THR A 268 "
            pdb=" CA  THR A 268 "
            pdb=" OG1 THR A 268 "
            pdb=" CG2 THR A 268 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.42    0.13 2.00e-01 2.50e+01 4.33e-01
  chirality pdb=" CA  VAL L 120 "
            pdb=" N   VAL L 120 "
            pdb=" C   VAL L 120 "
            pdb=" CB  VAL L 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.31e-01
  ... (remaining 908 not shown)

  Planarity restraints: 964
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR H 125 "    0.024 5.00e-02 4.00e+02   3.65e-02 2.13e+00
        pdb=" N   PRO H 126 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO H 126 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO H 126 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN L  85 "    0.006 2.00e-02 2.50e+03   1.16e-02 1.36e+00
        pdb=" CD  GLN L  85 "   -0.020 2.00e-02 2.50e+03
        pdb=" OE1 GLN L  85 "    0.008 2.00e-02 2.50e+03
        pdb=" NE2 GLN L  85 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  48 "   -0.006 2.00e-02 2.50e+03   8.72e-03 1.33e+00
        pdb=" CG  PHE A  48 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  48 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  48 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  48 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  48 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  48 "    0.000 2.00e-02 2.50e+03
  ... (remaining 961 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1281
        2.79 -     3.32: 5356
        3.32 -     3.85: 9073
        3.85 -     4.37: 10154
        4.37 -     4.90: 17991
  Nonbonded interactions: 43855
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 138 "
            pdb=" OG  SER A 142 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OE1 GLN L   6 "
            pdb=" OG1 THR L 107 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" NE2 GLN L  96 "
            pdb=" O   LEU L 100 "
     model   vdw
     2.321 3.120
  nonbonded pdb=" OD1 ASN A 106 "
            pdb=" OG  SER A 119 "
     model   vdw
     2.321 3.040
  nonbonded pdb=" OG  SER L 126 "
            pdb=" OE1 GLU L 128 "
     model   vdw
     2.349 3.040
  ... (remaining 43850 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:             0.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.190
  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:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
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   0.028   5764  Z= 0.100
  Angle     :  0.561   6.923   7833  Z= 0.275
  Chirality :  0.041   0.142    911
  Planarity :  0.003   0.036    964
  Dihedral  : 13.384  83.635   2074
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  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: 728
  helix:  1.38 (0.34), residues: 245
  sheet:  0.71 (0.39), residues: 194
  loop : -1.17 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 180 
 TYR   0.011   0.001   TYR L  55 
 PHE   0.020   0.001   PHE A  48 
 TRP   0.006   0.001   TRP L  56 
 HIS   0.003   0.000   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 5761)
  covalent geometry    : angle       0.56141 ( 7827)
  SS BOND              : bond        0.00261 (    3)
  SS BOND              : angle       0.16802 (    6)
  hydrogen bonds       : bond        0.12520 (  266)
  hydrogen bonds       : angle       6.03596 (  753)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.176 
Fit side-chains
REVERT: L   20 THR cc_start: 0.8750 (p) cc_final: 0.8519 (p)
REVERT: L  129 GLN cc_start: 0.8601 (tp-100) cc_final: 0.8335 (tp40)
REVERT: L  139 CYS cc_start: 0.6902 (p) cc_final: 0.6462 (p)
REVERT: L  153 TRP cc_start: 0.8296 (m100) cc_final: 0.7897 (m100)
REVERT: L  180 MET cc_start: 0.8417 (ttt) cc_final: 0.7945 (ttt)
REVERT: A   59 LYS cc_start: 0.7783 (tttm) cc_final: 0.7362 (ttmt)
REVERT: A  143 LYS cc_start: 0.8221 (tttm) cc_final: 0.7955 (mmtt)
REVERT: A  239 ILE cc_start: 0.9301 (mm) cc_final: 0.9096 (mm)
REVERT: A  298 LEU cc_start: 0.8742 (mt) cc_final: 0.8514 (mt)
REVERT: A  299 LEU cc_start: 0.8865 (tp) cc_final: 0.8471 (tp)
REVERT: A  307 TYR cc_start: 0.8253 (t80) cc_final: 0.8006 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 222
  average time/residue: 0.0525
  time to fit residues: 16.4371
Evaluate side-chains
  174 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0570
   overall best weight:    0.8500

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.140718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.110936 restraints weight = 9364.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 2.98
r_work: 0.3216 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5764  Z= 0.152
  Angle     :  0.627   8.489   7833  Z= 0.309
  Chirality :  0.045   0.173    911
  Planarity :  0.004   0.036    964
  Dihedral  :  3.888  14.070    781
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.17 %
    Favored  : 86.27 %
  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:  0.52 (0.32), residues: 728
  helix:  1.62 (0.34), residues: 245
  sheet:  0.73 (0.39), residues: 196
  loop : -1.07 (0.37), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 216 
 TYR   0.019   0.001   TYR L  55 
 PHE   0.021   0.001   PHE A  48 
 TRP   0.011   0.001   TRP L 168 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 5761)
  covalent geometry    : angle       0.62764 ( 7827)
  SS BOND              : bond        0.00328 (    3)
  SS BOND              : angle       0.33256 (    6)
  hydrogen bonds       : bond        0.03581 (  266)
  hydrogen bonds       : angle       4.51081 (  753)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 185
  time to evaluate  : 0.218 
Fit side-chains
REVERT: H  153 TYR cc_start: 0.7654 (p90) cc_final: 0.6713 (p90)
REVERT: L    4 MET cc_start: 0.9054 (mmm) cc_final: 0.8574 (mmm)
REVERT: L   17 GLU cc_start: 0.7646 (pm20) cc_final: 0.7417 (pm20)
REVERT: L   27 GLN cc_start: 0.8403 (pm20) cc_final: 0.8110 (pm20)
REVERT: L  129 GLN cc_start: 0.8843 (tp-100) cc_final: 0.8274 (tp-100)
REVERT: L  139 CYS cc_start: 0.8039 (p) cc_final: 0.7568 (p)
REVERT: L  168 TRP cc_start: 0.9268 (m-90) cc_final: 0.8851 (m-90)
REVERT: A   59 LYS cc_start: 0.7917 (tttm) cc_final: 0.7500 (ttmt)
REVERT: A  115 ASP cc_start: 0.8144 (t0) cc_final: 0.7943 (t0)
REVERT: A  143 LYS cc_start: 0.8739 (tttm) cc_final: 0.7766 (mmtt)
REVERT: A  247 ASN cc_start: 0.8031 (t0) cc_final: 0.7821 (t0)
REVERT: A  299 LEU cc_start: 0.8476 (tp) cc_final: 0.8159 (tp)
  outliers start: 10
  outliers final: 8
  residues processed: 189
  average time/residue: 0.0563
  time to fit residues: 14.9583
Evaluate side-chains
  181 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 173
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   54 ILE
Chi-restraints excluded: chain L residue   59 THR
Chi-restraints excluded: chain L residue  130 LEU
Chi-restraints excluded: chain L residue  183 THR
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  205 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 59 optimal weight:    9.9990
   chunk 14 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
** L  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  43 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.131027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.101256 restraints weight = 9369.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.90
r_work: 0.3088 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063   5764  Z= 0.248
  Angle     :  0.691   8.227   7833  Z= 0.349
  Chirality :  0.047   0.160    911
  Planarity :  0.004   0.041    964
  Dihedral  :  4.425  17.551    781
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 16.22 %
    Favored  : 80.19 %
  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:  0.17 (0.32), residues: 728
  helix:  1.32 (0.34), residues: 246
  sheet:  0.56 (0.40), residues: 188
  loop : -1.23 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L 216 
 TYR   0.025   0.002   TYR H 183 
 PHE   0.022   0.002   PHE H 154 
 TRP   0.010   0.001   TRP L 168 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00587 ( 5761)
  covalent geometry    : angle       0.69110 ( 7827)
  SS BOND              : bond        0.00441 (    3)
  SS BOND              : angle       0.59738 (    6)
  hydrogen bonds       : bond        0.03985 (  266)
  hydrogen bonds       : angle       4.76225 (  753)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 181
  time to evaluate  : 0.223 
Fit side-chains
REVERT: H  156 GLU cc_start: 0.8030 (tp30) cc_final: 0.7364 (tp30)
REVERT: L   27 GLN cc_start: 0.8594 (pm20) cc_final: 0.8322 (pm20)
REVERT: L   31 ASN cc_start: 0.8821 (t0) cc_final: 0.8330 (t0)
REVERT: L   42 TYR cc_start: 0.9418 (m-80) cc_final: 0.9099 (m-80)
REVERT: L  129 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8561 (tp40)
REVERT: L  159 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7175 (mm-30)
REVERT: L  180 MET cc_start: 0.9023 (ttt) cc_final: 0.8823 (ttt)
REVERT: A   59 LYS cc_start: 0.8036 (tttm) cc_final: 0.7746 (ttmt)
REVERT: A  256 MET cc_start: 0.9099 (mmm) cc_final: 0.8854 (tpp)
REVERT: A  277 GLU cc_start: 0.8996 (mp0) cc_final: 0.8725 (mp0)
  outliers start: 23
  outliers final: 16
  residues processed: 194
  average time/residue: 0.0620
  time to fit residues: 16.4590
Evaluate side-chains
  188 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 172
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  125 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   59 THR
Chi-restraints excluded: chain L residue   95 LYS
Chi-restraints excluded: chain L residue  130 LEU
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  183 THR
Chi-restraints excluded: chain L residue  187 THR
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  253 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 43 optimal weight:    8.9990
   chunk 52 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
H   5 GLN
** L  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  43 GLN
** L 203 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 = 0.3635 r_free = 0.3635 target = 0.133910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.104254 restraints weight = 9335.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 2.89
r_work: 0.3112 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5764  Z= 0.145
  Angle     :  0.633   7.576   7833  Z= 0.315
  Chirality :  0.044   0.184    911
  Planarity :  0.004   0.039    964
  Dihedral  :  4.253  18.619    781
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 19.66 %
    Favored  : 77.54 %
  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:  0.22 (0.32), residues: 728
  helix:  1.46 (0.34), residues: 244
  sheet:  0.64 (0.40), residues: 188
  loop : -1.34 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L 216 
 TYR   0.018   0.001   TYR H 183 
 PHE   0.013   0.001   PHE H 154 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 5761)
  covalent geometry    : angle       0.63305 ( 7827)
  SS BOND              : bond        0.00284 (    3)
  SS BOND              : angle       0.45839 (    6)
  hydrogen bonds       : bond        0.03394 (  266)
  hydrogen bonds       : angle       4.60211 (  753)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 177
  time to evaluate  : 0.138 
Fit side-chains
REVERT: H  156 GLU cc_start: 0.8001 (tp30) cc_final: 0.7323 (tp30)
REVERT: L   27 GLN cc_start: 0.8448 (pm20) cc_final: 0.8190 (pm20)
REVERT: L   42 TYR cc_start: 0.9375 (m-80) cc_final: 0.9112 (m-80)
REVERT: L  129 GLN cc_start: 0.8760 (tp-100) cc_final: 0.8505 (tp40)
REVERT: L  159 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6943 (mm-30)
REVERT: A   59 LYS cc_start: 0.7992 (tttm) cc_final: 0.7674 (ttmt)
REVERT: A  115 ASP cc_start: 0.8289 (t0) cc_final: 0.7789 (t0)
REVERT: A  141 TYR cc_start: 0.9185 (m-10) cc_final: 0.8903 (m-80)
REVERT: A  256 MET cc_start: 0.9100 (mmm) cc_final: 0.8897 (tpp)
REVERT: A  277 GLU cc_start: 0.8971 (mp0) cc_final: 0.8669 (mp0)
  outliers start: 18
  outliers final: 13
  residues processed: 186
  average time/residue: 0.0525
  time to fit residues: 13.6766
Evaluate side-chains
  185 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 172
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   43 GLN
Chi-restraints excluded: chain L residue   53 LEU
Chi-restraints excluded: chain L residue   59 THR
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   95 LYS
Chi-restraints excluded: chain L residue  128 GLU
Chi-restraints excluded: chain L residue  130 LEU
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain A residue  294 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 21 optimal weight:    9.9990
   chunk 65 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 35 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   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  37 ASN ** 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 = 0.3630 r_free = 0.3630 target = 0.133591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.104046 restraints weight = 9490.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.96
r_work: 0.3101 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5764  Z= 0.147
  Angle     :  0.629   7.021   7833  Z= 0.313
  Chirality :  0.044   0.168    911
  Planarity :  0.004   0.036    964
  Dihedral  :  4.237  19.597    781
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.97 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 21.37 %
    Favored  : 75.82 %
  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:  0.22 (0.32), residues: 728
  helix:  1.42 (0.34), residues: 245
  sheet:  0.67 (0.40), residues: 188
  loop : -1.32 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 305 
 TYR   0.017   0.001   TYR H 183 
 PHE   0.013   0.001   PHE H 154 
 TRP   0.010   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 5761)
  covalent geometry    : angle       0.62960 ( 7827)
  SS BOND              : bond        0.00274 (    3)
  SS BOND              : angle       0.40212 (    6)
  hydrogen bonds       : bond        0.03314 (  266)
  hydrogen bonds       : angle       4.57275 (  753)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 178
  time to evaluate  : 0.220 
Fit side-chains
REVERT: H  156 GLU cc_start: 0.8081 (tp30) cc_final: 0.7385 (tp30)
REVERT: L   27 GLN cc_start: 0.8400 (pm20) cc_final: 0.8164 (pm20)
REVERT: L   44 GLN cc_start: 0.9482 (OUTLIER) cc_final: 0.8510 (tt0)
REVERT: L  129 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8556 (tp40)
REVERT: L  162 ASN cc_start: 0.8246 (m110) cc_final: 0.8018 (m-40)
REVERT: L  168 TRP cc_start: 0.9400 (m-90) cc_final: 0.8711 (m-90)
REVERT: L  180 MET cc_start: 0.8940 (ttt) cc_final: 0.8205 (ttt)
REVERT: A   46 MET cc_start: 0.7776 (ptm) cc_final: 0.6640 (tmm)
REVERT: A   59 LYS cc_start: 0.7981 (tttm) cc_final: 0.7683 (ttmt)
REVERT: A  115 ASP cc_start: 0.8302 (t0) cc_final: 0.7783 (t0)
REVERT: A  277 GLU cc_start: 0.9007 (mp0) cc_final: 0.8720 (mp0)
  outliers start: 18
  outliers final: 14
  residues processed: 188
  average time/residue: 0.0567
  time to fit residues: 15.0373
Evaluate side-chains
  191 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 176
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   44 GLN
Chi-restraints excluded: chain L residue   53 LEU
Chi-restraints excluded: chain L residue   59 THR
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   95 LYS
Chi-restraints excluded: chain L residue  128 GLU
Chi-restraints excluded: chain L residue  130 LEU
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  187 THR
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  183 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 15 optimal weight:    0.4980
   chunk 57 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0020
   chunk 51 optimal weight:    0.5980
   chunk 16 optimal weight:    7.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
** L  37 ASN ** 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 = 0.3651 r_free = 0.3651 target = 0.135032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.105688 restraints weight = 9362.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.98
r_work: 0.3126 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5764  Z= 0.124
  Angle     :  0.622   7.004   7833  Z= 0.307
  Chirality :  0.044   0.210    911
  Planarity :  0.004   0.035    964
  Dihedral  :  4.132  19.457    781
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 21.84 %
    Favored  : 74.73 %
  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:  0.27 (0.32), residues: 728
  helix:  1.48 (0.34), residues: 245
  sheet:  0.69 (0.40), residues: 188
  loop : -1.31 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L 216 
 TYR   0.016   0.001   TYR A 289 
 PHE   0.012   0.001   PHE L 140 
 TRP   0.011   0.001   TRP L 168 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 5761)
  covalent geometry    : angle       0.62260 ( 7827)
  SS BOND              : bond        0.00237 (    3)
  SS BOND              : angle       0.32973 (    6)
  hydrogen bonds       : bond        0.03155 (  266)
  hydrogen bonds       : angle       4.49223 (  753)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 178
  time to evaluate  : 0.219 
Fit side-chains
REVERT: H  113 GLN cc_start: 0.9270 (pt0) cc_final: 0.8744 (pm20)
REVERT: H  153 TYR cc_start: 0.8162 (p90) cc_final: 0.7036 (p90)
REVERT: H  156 GLU cc_start: 0.8076 (tp30) cc_final: 0.7192 (tp30)
REVERT: L  129 GLN cc_start: 0.8827 (tp-100) cc_final: 0.8561 (tp40)
REVERT: L  168 TRP cc_start: 0.9398 (m-90) cc_final: 0.8770 (m-90)
REVERT: L  180 MET cc_start: 0.8992 (ttt) cc_final: 0.8218 (ttt)
REVERT: A   59 LYS cc_start: 0.7960 (tttm) cc_final: 0.7618 (ttmt)
REVERT: A  115 ASP cc_start: 0.8294 (t0) cc_final: 0.7681 (t0)
REVERT: A  277 GLU cc_start: 0.8995 (mp0) cc_final: 0.8736 (mp0)
REVERT: A  289 TYR cc_start: 0.9149 (t80) cc_final: 0.8790 (t80)
  outliers start: 22
  outliers final: 14
  residues processed: 192
  average time/residue: 0.0572
  time to fit residues: 15.4638
Evaluate side-chains
  187 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 173
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   59 THR
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   95 LYS
Chi-restraints excluded: chain L residue  128 GLU
Chi-restraints excluded: chain L residue  130 LEU
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  187 THR
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  267 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
H   5 GLN
** L  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 117 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.132882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.103379 restraints weight = 9558.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 3.01
r_work: 0.3112 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.2939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5764  Z= 0.169
  Angle     :  0.659   6.727   7833  Z= 0.329
  Chirality :  0.045   0.170    911
  Planarity :  0.004   0.035    964
  Dihedral  :  4.262  19.869    781
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 22.93 %
    Favored  : 73.48 %
  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:  0.19 (0.32), residues: 728
  helix:  1.35 (0.34), residues: 245
  sheet:  0.63 (0.40), residues: 188
  loop : -1.28 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 305 
 TYR   0.016   0.001   TYR H 183 
 PHE   0.020   0.001   PHE A 274 
 TRP   0.011   0.001   TRP L 168 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 5761)
  covalent geometry    : angle       0.65941 ( 7827)
  SS BOND              : bond        0.00279 (    3)
  SS BOND              : angle       0.38487 (    6)
  hydrogen bonds       : bond        0.03358 (  266)
  hydrogen bonds       : angle       4.57031 (  753)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 183
  time to evaluate  : 0.252 
Fit side-chains
REVERT: H  156 GLU cc_start: 0.8050 (tp30) cc_final: 0.7253 (tp30)
REVERT: L   44 GLN cc_start: 0.9549 (OUTLIER) cc_final: 0.8730 (tt0)
REVERT: L  129 GLN cc_start: 0.8686 (tp-100) cc_final: 0.8412 (tp40)
REVERT: L  168 TRP cc_start: 0.9418 (m-90) cc_final: 0.8815 (m-90)
REVERT: A   46 MET cc_start: 0.7302 (ptt) cc_final: 0.7082 (tmm)
REVERT: A   59 LYS cc_start: 0.7973 (tttm) cc_final: 0.7653 (ttmt)
REVERT: A  115 ASP cc_start: 0.8252 (t0) cc_final: 0.7722 (t0)
REVERT: A  277 GLU cc_start: 0.9033 (mp0) cc_final: 0.8715 (mp0)
REVERT: A  289 TYR cc_start: 0.9183 (t80) cc_final: 0.8820 (t80)
  outliers start: 23
  outliers final: 18
  residues processed: 198
  average time/residue: 0.0586
  time to fit residues: 16.0702
Evaluate side-chains
  198 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 179
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   44 GLN
Chi-restraints excluded: chain L residue   59 THR
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   95 LYS
Chi-restraints excluded: chain L residue  128 GLU
Chi-restraints excluded: chain L residue  130 LEU
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  183 THR
Chi-restraints excluded: chain L residue  187 THR
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  267 SER
Chi-restraints excluded: chain A residue  301 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0980
   chunk 45 optimal weight:    0.7980
   chunk 67 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
L  31 ASN
** L  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 162 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.131485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.101819 restraints weight = 9211.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 2.99
r_work: 0.3065 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5764  Z= 0.157
  Angle     :  0.663   7.430   7833  Z= 0.330
  Chirality :  0.045   0.176    911
  Planarity :  0.004   0.034    964
  Dihedral  :  4.323  20.803    781
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 24.18 %
    Favored  : 73.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.17 (0.32), residues: 728
  helix:  1.36 (0.34), residues: 245
  sheet:  0.63 (0.40), residues: 188
  loop : -1.31 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  35 
 TYR   0.015   0.001   TYR H 183 
 PHE   0.019   0.001   PHE A 274 
 TRP   0.011   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 5761)
  covalent geometry    : angle       0.66275 ( 7827)
  SS BOND              : bond        0.00298 (    3)
  SS BOND              : angle       0.36495 (    6)
  hydrogen bonds       : bond        0.03298 (  266)
  hydrogen bonds       : angle       4.59799 (  753)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 181
  time to evaluate  : 0.148 
Fit side-chains
REVERT: H  156 GLU cc_start: 0.8086 (tp30) cc_final: 0.7231 (tp30)
REVERT: L   44 GLN cc_start: 0.9552 (OUTLIER) cc_final: 0.8761 (tt0)
REVERT: L  129 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8432 (tp40)
REVERT: L  168 TRP cc_start: 0.9393 (m-90) cc_final: 0.8743 (m-90)
REVERT: L  180 MET cc_start: 0.8800 (ttt) cc_final: 0.8123 (ttt)
REVERT: A   46 MET cc_start: 0.7460 (ptt) cc_final: 0.7157 (tmm)
REVERT: A   59 LYS cc_start: 0.7982 (tttm) cc_final: 0.7661 (ttmt)
REVERT: A  115 ASP cc_start: 0.8278 (t0) cc_final: 0.7752 (t0)
REVERT: A  277 GLU cc_start: 0.9036 (mp0) cc_final: 0.8757 (mp0)
REVERT: A  289 TYR cc_start: 0.9175 (t80) cc_final: 0.8848 (t80)
  outliers start: 17
  outliers final: 15
  residues processed: 193
  average time/residue: 0.0589
  time to fit residues: 15.6813
Evaluate side-chains
  194 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 178
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   44 GLN
Chi-restraints excluded: chain L residue   59 THR
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   95 LYS
Chi-restraints excluded: chain L residue  128 GLU
Chi-restraints excluded: chain L residue  130 LEU
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  183 THR
Chi-restraints excluded: chain L residue  187 THR
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  267 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 14 optimal weight:    0.4980
   chunk 67 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 11 optimal weight:    0.4980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
L  31 ASN
** L  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 162 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.132159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.102553 restraints weight = 9311.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 3.01
r_work: 0.3074 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.3042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5764  Z= 0.141
  Angle     :  0.669   7.922   7833  Z= 0.332
  Chirality :  0.045   0.176    911
  Planarity :  0.004   0.033    964
  Dihedral  :  4.287  20.914    781
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 24.34 %
    Favored  : 72.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.17 (0.32), residues: 728
  helix:  1.37 (0.34), residues: 246
  sheet:  0.61 (0.40), residues: 188
  loop : -1.32 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG L  35 
 TYR   0.017   0.001   TYR H 153 
 PHE   0.017   0.001   PHE A 274 
 TRP   0.010   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 5761)
  covalent geometry    : angle       0.66938 ( 7827)
  SS BOND              : bond        0.00247 (    3)
  SS BOND              : angle       0.34095 (    6)
  hydrogen bonds       : bond        0.03257 (  266)
  hydrogen bonds       : angle       4.56226 (  753)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 181
  time to evaluate  : 0.222 
Fit side-chains
REVERT: H  113 GLN cc_start: 0.9296 (pt0) cc_final: 0.8814 (pm20)
REVERT: H  153 TYR cc_start: 0.8228 (p90) cc_final: 0.7013 (p90)
REVERT: H  156 GLU cc_start: 0.8060 (tp30) cc_final: 0.7020 (tp30)
REVERT: L   44 GLN cc_start: 0.9541 (OUTLIER) cc_final: 0.8731 (tt0)
REVERT: L  129 GLN cc_start: 0.8719 (tp-100) cc_final: 0.8437 (tp40)
REVERT: L  168 TRP cc_start: 0.9392 (m-90) cc_final: 0.8725 (m-90)
REVERT: L  180 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8082 (ttt)
REVERT: A   46 MET cc_start: 0.7678 (ptt) cc_final: 0.7081 (tmm)
REVERT: A   59 LYS cc_start: 0.7980 (tttm) cc_final: 0.7647 (ttmt)
REVERT: A  115 ASP cc_start: 0.8291 (t0) cc_final: 0.7762 (t0)
REVERT: A  277 GLU cc_start: 0.9028 (mp0) cc_final: 0.8752 (mp0)
REVERT: A  289 TYR cc_start: 0.9161 (t80) cc_final: 0.8866 (t80)
  outliers start: 18
  outliers final: 14
  residues processed: 192
  average time/residue: 0.0525
  time to fit residues: 14.3361
Evaluate side-chains
  198 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 182
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   44 GLN
Chi-restraints excluded: chain L residue   59 THR
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   95 LYS
Chi-restraints excluded: chain L residue  128 GLU
Chi-restraints excluded: chain L residue  130 LEU
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  180 MET
Chi-restraints excluded: chain L residue  183 THR
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  267 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 35 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 21 optimal weight:    5.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
H   5 GLN
L  31 ASN
** L  37 ASN ** 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 = 0.3583 r_free = 0.3583 target = 0.130653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.100742 restraints weight = 9474.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 3.02
r_work: 0.3047 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5764  Z= 0.178
  Angle     :  0.703   9.708   7833  Z= 0.349
  Chirality :  0.046   0.179    911
  Planarity :  0.004   0.032    964
  Dihedral  :  4.411  20.436    781
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 24.34 %
    Favored  : 72.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.08 (0.32), residues: 728
  helix:  1.28 (0.34), residues: 246
  sheet:  0.55 (0.40), residues: 188
  loop : -1.34 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 252 
 TYR   0.015   0.001   TYR A 146 
 PHE   0.018   0.001   PHE A 274 
 TRP   0.011   0.001   TRP L 168 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 5761)
  covalent geometry    : angle       0.70283 ( 7827)
  SS BOND              : bond        0.00293 (    3)
  SS BOND              : angle       0.39362 (    6)
  hydrogen bonds       : bond        0.03512 (  266)
  hydrogen bonds       : angle       4.62962 (  753)

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 186
  time to evaluate  : 0.143 
Fit side-chains
REVERT: H  153 TYR cc_start: 0.8276 (p90) cc_final: 0.7066 (p90)
REVERT: H  156 GLU cc_start: 0.8077 (tp30) cc_final: 0.7041 (tp30)
REVERT: L   44 GLN cc_start: 0.9576 (OUTLIER) cc_final: 0.8800 (tt0)
REVERT: L  129 GLN cc_start: 0.8686 (tp-100) cc_final: 0.8385 (tp40)
REVERT: L  168 TRP cc_start: 0.9397 (m-90) cc_final: 0.8748 (m-90)
REVERT: L  180 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8136 (ttt)
REVERT: A   59 LYS cc_start: 0.7998 (tttm) cc_final: 0.7691 (ttmt)
REVERT: A  115 ASP cc_start: 0.8340 (t0) cc_final: 0.7817 (t0)
REVERT: A  277 GLU cc_start: 0.9054 (mp0) cc_final: 0.8704 (mp0)
REVERT: A  289 TYR cc_start: 0.9171 (t80) cc_final: 0.8864 (t80)
  outliers start: 18
  outliers final: 15
  residues processed: 196
  average time/residue: 0.0568
  time to fit residues: 15.6292
Evaluate side-chains
  205 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 188
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue  202 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   44 GLN
Chi-restraints excluded: chain L residue   59 THR
Chi-restraints excluded: chain L residue   69 THR
Chi-restraints excluded: chain L residue   95 LYS
Chi-restraints excluded: chain L residue  128 GLU
Chi-restraints excluded: chain L residue  130 LEU
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain L residue  180 MET
Chi-restraints excluded: chain L residue  183 THR
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   41 SER
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  183 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 35 optimal weight:    7.9990
   chunk 68 optimal weight:    0.0870
   chunk 14 optimal weight:    0.0870
   chunk 7 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0870
   chunk 29 optimal weight:    0.0970
   chunk 31 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.2112

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

Flipped N/Q/H residues before XYZ refinement:
L  31 ASN
** L  37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 103 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 = 0.3589 r_free = 0.3589 target = 0.131051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.101141 restraints weight = 9261.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 3.05
r_work: 0.3044 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.214   5764  Z= 0.247
  Angle     :  1.163  59.197   7833  Z= 0.660
  Chirality :  0.046   0.234    911
  Planarity :  0.004   0.032    964
  Dihedral  :  4.401  18.932    781
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.38 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 24.80 %
    Favored  : 72.85 %
  Cbeta Deviations :  0.15 %
  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:  0.09 (0.32), residues: 728
  helix:  1.29 (0.34), residues: 246
  sheet:  0.54 (0.40), residues: 188
  loop : -1.33 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 252 
 TYR   0.015   0.001   TYR A 146 
 PHE   0.017   0.001   PHE A 274 
 TRP   0.010   0.001   TRP L 168 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 ( 5761)
  covalent geometry    : angle       1.16317 ( 7827)
  SS BOND              : bond        0.00203 (    3)
  SS BOND              : angle       0.44662 (    6)
  hydrogen bonds       : bond        0.03545 (  266)
  hydrogen bonds       : angle       4.64000 (  753)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1473.24 seconds
wall clock time: 25 minutes 58.38 seconds (1558.38 seconds total)