Starting phenix.real_space_refine
on Tue Feb 11 12:06:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7vaf_31839/02_2025/7vaf_31839.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7vaf_31839/02_2025/7vaf_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_31839/02_2025/7vaf_31839.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7vaf_31839/02_2025/7vaf_31839.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7vaf_31839/02_2025/7vaf_31839.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7vaf_31839/02_2025/7vaf_31839.cif"
  }
  resolution = 3.11
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.55, per 1000 atoms: 0.63
  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: 1.38
  Conformation dependent library (CDL) restraints added in 633.3 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: 0.66
  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: 1.59

  Time building geometry restraints manager: 1.61 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:             0.450
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.480
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.090
-------------------------------------------------------------------------------
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   5761  Z= 0.143
  Angle     :  0.561   6.923   7827  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (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
 TRP   0.006   0.001   TRP L  56 
 HIS   0.003   0.000   HIS H  35 
 PHE   0.020   0.001   PHE A  48 
 TYR   0.011   0.001   TYR L  55 
 ARG   0.001   0.000   ARG A 180 

*********************** 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  : 0.619 
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: 0.6461 (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: 0.7946 (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: 0.1341
  time to fit residues: 40.7698
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  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 36 optimal weight:    0.0980
   chunk 29 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   chunk 65 optimal weight:    0.5980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.133931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.104394 restraints weight = 9370.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.93
r_work: 0.3112 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.089   5761  Z= 0.411
  Angle     :  0.718   8.053   7827  Z= 0.358
  Chirality :  0.048   0.174    911
  Planarity :  0.004   0.036    964
  Dihedral  :  4.297  15.814    781
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.10 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 12.95 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.32), residues: 728
  helix:  1.40 (0.33), residues: 249
  sheet:  0.63 (0.39), residues: 188
  loop : -1.25 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP L 168 
 HIS   0.006   0.001   HIS H  35 
 PHE   0.018   0.002   PHE L 140 
 TYR   0.023   0.002   TYR H 183 
 ARG   0.004   0.001   ARG L 160 

*********************** 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
  191 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 177
  time to evaluate  : 0.556 
Fit side-chains
REVERT: H  156 GLU cc_start: 0.8074 (tp30) cc_final: 0.7401 (tp30)
REVERT: H  179 GLN cc_start: 0.8628 (pp30) cc_final: 0.8170 (pp30)
REVERT: L  129 GLN cc_start: 0.8814 (tp-100) cc_final: 0.8329 (tp-100)
REVERT: L  139 CYS cc_start: 0.7958 (p) cc_final: 0.7444 (p)
REVERT: L  180 MET cc_start: 0.9046 (ttt) cc_final: 0.8764 (ttt)
REVERT: A   59 LYS cc_start: 0.7965 (tttm) cc_final: 0.7632 (ttmt)
REVERT: A  277 GLU cc_start: 0.8911 (mp0) cc_final: 0.8678 (mp0)
  outliers start: 14
  outliers final: 13
  residues processed: 186
  average time/residue: 0.1373
  time to fit residues: 34.9755
Evaluate side-chains
  182 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 169
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
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  130 LEU
Chi-restraints excluded: chain L residue  183 THR
Chi-restraints excluded: chain L residue  187 THR
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  267 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 16 optimal weight:    8.9990
   chunk 50 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.137064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.106660 restraints weight = 9409.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 3.09
r_work: 0.3152 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5761  Z= 0.223
  Angle     :  0.620   8.098   7827  Z= 0.307
  Chirality :  0.044   0.182    911
  Planarity :  0.004   0.036    964
  Dihedral  :  4.153  18.225    781
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 17.47 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.32), residues: 728
  helix:  1.56 (0.34), residues: 243
  sheet:  0.74 (0.40), residues: 186
  loop : -1.28 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.021   0.001   PHE A 285 
 TYR   0.019   0.001   TYR H 183 
 ARG   0.001   0.000   ARG L 193 

*********************** 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
  189 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 176
  time to evaluate  : 0.657 
Fit side-chains
REVERT: H  153 TYR cc_start: 0.7936 (p90) cc_final: 0.6963 (p90)
REVERT: H  179 GLN cc_start: 0.8660 (pp30) cc_final: 0.8406 (pp30)
REVERT: L  129 GLN cc_start: 0.8860 (tp-100) cc_final: 0.8472 (tp-100)
REVERT: L  159 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6675 (mm-30)
REVERT: A   59 LYS cc_start: 0.7962 (tttm) cc_final: 0.7642 (ttmt)
REVERT: A  106 ASN cc_start: 0.8558 (t0) cc_final: 0.8330 (t0)
REVERT: A  256 MET cc_start: 0.9133 (mmm) cc_final: 0.8928 (tpp)
REVERT: A  277 GLU cc_start: 0.8980 (mp0) cc_final: 0.8709 (mp0)
  outliers start: 13
  outliers final: 9
  residues processed: 182
  average time/residue: 0.1430
  time to fit residues: 35.3299
Evaluate side-chains
  174 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 165
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
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   53 LEU
Chi-restraints excluded: chain L residue   59 THR
Chi-restraints excluded: chain L residue  130 LEU
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  183 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 19 optimal weight:    0.3980
   chunk 10 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 35 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3644 r_free = 0.3644 target = 0.134686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.105047 restraints weight = 9454.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 3.00
r_work: 0.3111 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5761  Z= 0.252
  Angle     :  0.627   7.577   7827  Z= 0.310
  Chirality :  0.044   0.160    911
  Planarity :  0.004   0.037    964
  Dihedral  :  4.181  17.692    781
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 20.28 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.32), residues: 728
  helix:  1.50 (0.34), residues: 244
  sheet:  0.71 (0.40), residues: 186
  loop : -1.29 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.014   0.001   PHE H 154 
 TYR   0.018   0.001   TYR H 183 
 ARG   0.001   0.000   ARG L 193 

*********************** 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
  190 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 174
  time to evaluate  : 0.578 
Fit side-chains
REVERT: H  153 TYR cc_start: 0.8065 (p90) cc_final: 0.6806 (p90)
REVERT: H  156 GLU cc_start: 0.8032 (tp30) cc_final: 0.7233 (tp30)
REVERT: H  179 GLN cc_start: 0.8759 (pp30) cc_final: 0.8449 (pp30)
REVERT: H  185 MET cc_start: 0.9099 (ppp) cc_final: 0.8590 (ppp)
REVERT: L  129 GLN cc_start: 0.8884 (tp-100) cc_final: 0.8391 (tp-100)
REVERT: L  159 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6826 (mm-30)
REVERT: L  168 TRP cc_start: 0.9360 (m-90) cc_final: 0.8656 (m-90)
REVERT: L  180 MET cc_start: 0.8982 (ttt) cc_final: 0.8204 (ttt)
REVERT: A   59 LYS cc_start: 0.7997 (tttm) cc_final: 0.7693 (ttmt)
REVERT: A  277 GLU cc_start: 0.9011 (mp0) cc_final: 0.8720 (mp0)
REVERT: A  289 TYR cc_start: 0.9136 (t80) cc_final: 0.8805 (t80)
  outliers start: 16
  outliers final: 13
  residues processed: 182
  average time/residue: 0.1347
  time to fit residues: 33.8547
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  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 VAL
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  130 LEU
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  133 MET
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 61 optimal weight:    0.9980
   chunk 28 optimal weight:    0.2980
   chunk 36 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 43 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 54 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 44 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  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 = 0.3659 r_free = 0.3659 target = 0.136007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.105951 restraints weight = 9440.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 3.07
r_work: 0.3120 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5761  Z= 0.209
  Angle     :  0.616   7.508   7827  Z= 0.303
  Chirality :  0.043   0.149    911
  Planarity :  0.004   0.036    964
  Dihedral  :  4.118  16.834    781
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 20.90 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.32), residues: 728
  helix:  1.55 (0.34), residues: 243
  sheet:  0.72 (0.40), residues: 186
  loop : -1.35 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.013   0.001   PHE H 154 
 TYR   0.017   0.001   TYR H 183 
 ARG   0.001   0.000   ARG L 160 

*********************** 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
  199 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 180
  time to evaluate  : 0.774 
Fit side-chains
REVERT: H  153 TYR cc_start: 0.8178 (p90) cc_final: 0.6941 (p90)
REVERT: H  156 GLU cc_start: 0.7998 (tp30) cc_final: 0.7189 (tp30)
REVERT: H  179 GLN cc_start: 0.8694 (pp30) cc_final: 0.8368 (pp30)
REVERT: L   42 TYR cc_start: 0.9384 (m-80) cc_final: 0.9124 (m-80)
REVERT: L  129 GLN cc_start: 0.8816 (tp-100) cc_final: 0.8385 (tp-100)
REVERT: L  162 ASN cc_start: 0.8280 (m110) cc_final: 0.8062 (m-40)
REVERT: L  168 TRP cc_start: 0.9385 (m-90) cc_final: 0.8719 (m-90)
REVERT: L  180 MET cc_start: 0.8982 (ttt) cc_final: 0.8292 (ttt)
REVERT: A   59 LYS cc_start: 0.7983 (tttm) cc_final: 0.7667 (ttmt)
REVERT: A  115 ASP cc_start: 0.8277 (t0) cc_final: 0.7817 (t0)
REVERT: A  277 GLU cc_start: 0.9002 (mp0) cc_final: 0.8712 (mp0)
REVERT: A  283 PHE cc_start: 0.9429 (t80) cc_final: 0.9133 (t80)
REVERT: A  289 TYR cc_start: 0.9139 (t80) cc_final: 0.8782 (t80)
  outliers start: 19
  outliers final: 13
  residues processed: 188
  average time/residue: 0.1398
  time to fit residues: 36.2280
Evaluate side-chains
  184 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 171
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
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  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   66 VAL
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  133 MET
Chi-restraints excluded: chain A residue  183 TYR
Chi-restraints excluded: chain A residue  267 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 39 optimal weight:    5.9990
   chunk 42 optimal weight:    9.9990
   chunk 54 optimal weight:    2.9990
   chunk 67 optimal weight:    0.3980
   chunk 9 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0980
   chunk 0 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
H   5 GLN
** 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 = 0.3662 r_free = 0.3662 target = 0.135756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.106446 restraints weight = 9290.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.94
r_work: 0.3138 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5761  Z= 0.194
  Angle     :  0.616   7.396   7827  Z= 0.302
  Chirality :  0.043   0.177    911
  Planarity :  0.004   0.035    964
  Dihedral  :  4.064  15.493    781
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 22.62 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.32), residues: 728
  helix:  1.54 (0.34), residues: 244
  sheet:  0.71 (0.40), residues: 183
  loop : -1.33 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L 168 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.011   0.001   PHE L 140 
 TYR   0.015   0.001   TYR H 183 
 ARG   0.004   0.000   ARG L 216 

*********************** 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
  198 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 182
  time to evaluate  : 0.629 
Fit side-chains
REVERT: H  113 GLN cc_start: 0.9279 (pt0) cc_final: 0.8760 (pm20)
REVERT: H  153 TYR cc_start: 0.8198 (p90) cc_final: 0.6943 (p90)
REVERT: H  156 GLU cc_start: 0.8041 (tp30) cc_final: 0.7199 (tp30)
REVERT: H  179 GLN cc_start: 0.8692 (pp30) cc_final: 0.8353 (pp30)
REVERT: L   42 TYR cc_start: 0.9385 (m-80) cc_final: 0.9095 (m-80)
REVERT: L   44 GLN cc_start: 0.9506 (OUTLIER) cc_final: 0.8580 (tt0)
REVERT: L  129 GLN cc_start: 0.8757 (tp-100) cc_final: 0.8545 (tp40)
REVERT: L  162 ASN cc_start: 0.8189 (m110) cc_final: 0.7972 (m-40)
REVERT: L  168 TRP cc_start: 0.9389 (m-90) cc_final: 0.8773 (m-90)
REVERT: L  180 MET cc_start: 0.8989 (ttt) cc_final: 0.8261 (ttt)
REVERT: A   46 MET cc_start: 0.7558 (ptm) cc_final: 0.6614 (tmm)
REVERT: A   59 LYS cc_start: 0.7952 (tttm) cc_final: 0.7602 (ttmt)
REVERT: A  115 ASP cc_start: 0.8297 (t0) cc_final: 0.7758 (t0)
REVERT: A  277 GLU cc_start: 0.8996 (mp0) cc_final: 0.8676 (mp0)
REVERT: A  289 TYR cc_start: 0.9130 (t80) cc_final: 0.8789 (t80)
  outliers start: 16
  outliers final: 11
  residues processed: 190
  average time/residue: 0.1361
  time to fit residues: 35.6767
Evaluate side-chains
  190 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 178
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
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  130 LEU
Chi-restraints excluded: chain L residue  141 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  121 VAL
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 14 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 67 optimal weight:    0.0170
   chunk 17 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    1.1620

-------------------------------------------------------------------------------
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 = 0.133277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.103544 restraints weight = 9326.489|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 2.97
r_work: 0.3091 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5761  Z= 0.284
  Angle     :  0.657   7.958   7827  Z= 0.327
  Chirality :  0.045   0.161    911
  Planarity :  0.004   0.035    964
  Dihedral  :  4.200  15.445    781
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 22.46 %
    Favored  : 74.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.32), residues: 728
  helix:  1.39 (0.34), residues: 246
  sheet:  0.68 (0.40), residues: 186
  loop : -1.30 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L 168 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.015   0.001   PHE H 154 
 TYR   0.017   0.001   TYR H 183 
 ARG   0.001   0.000   ARG A 252 

*********************** 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
  199 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 178
  time to evaluate  : 0.609 
Fit side-chains
REVERT: H  156 GLU cc_start: 0.8065 (tp30) cc_final: 0.7317 (tp30)
REVERT: H  179 GLN cc_start: 0.8745 (pp30) cc_final: 0.8323 (pp30)
REVERT: L   44 GLN cc_start: 0.9549 (OUTLIER) cc_final: 0.8684 (tt0)
REVERT: L  129 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8533 (tp40)
REVERT: L  168 TRP cc_start: 0.9414 (m-90) cc_final: 0.8808 (m-90)
REVERT: A   59 LYS cc_start: 0.7966 (tttm) cc_final: 0.7646 (ttmt)
REVERT: A  115 ASP cc_start: 0.8356 (t0) cc_final: 0.7881 (t0)
REVERT: A  277 GLU cc_start: 0.9044 (mp0) cc_final: 0.8697 (mp0)
  outliers start: 21
  outliers final: 15
  residues processed: 191
  average time/residue: 0.1306
  time to fit residues: 34.3042
Evaluate side-chains
  189 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 173
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  125 THR
Chi-restraints excluded: chain H residue  150 VAL
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  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   37 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  175 VAL
Chi-restraints excluded: chain A residue  183 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 42 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 71 optimal weight:    0.2980
   chunk 47 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0020
   overall best weight:    0.5188

-------------------------------------------------------------------------------
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**
A 117 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.136897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.106614 restraints weight = 9282.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3259 rms_B_bonded: 3.01
r_work: 0.3135 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5761  Z= 0.198
  Angle     :  0.635   7.950   7827  Z= 0.311
  Chirality :  0.043   0.167    911
  Planarity :  0.004   0.033    964
  Dihedral  :  4.106  15.236    781
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 23.71 %
    Favored  : 73.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.32), residues: 728
  helix:  1.48 (0.34), residues: 245
  sheet:  0.71 (0.40), residues: 183
  loop : -1.41 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.012   0.001   PHE H 154 
 TYR   0.016   0.001   TYR A 289 
 ARG   0.002   0.000   ARG L 216 

*********************** 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
  196 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 180
  time to evaluate  : 0.624 
Fit side-chains
REVERT: H  113 GLN cc_start: 0.9278 (pt0) cc_final: 0.8769 (pm20)
REVERT: H  153 TYR cc_start: 0.8266 (p90) cc_final: 0.7107 (p90)
REVERT: H  156 GLU cc_start: 0.8079 (tp30) cc_final: 0.7050 (tp30)
REVERT: H  179 GLN cc_start: 0.8742 (pp30) cc_final: 0.8175 (pp30)
REVERT: L  129 GLN cc_start: 0.8797 (tp-100) cc_final: 0.8337 (tp-100)
REVERT: L  168 TRP cc_start: 0.9381 (m-90) cc_final: 0.8664 (m-90)
REVERT: L  180 MET cc_start: 0.8781 (ttt) cc_final: 0.8077 (ttt)
REVERT: A   59 LYS cc_start: 0.7924 (tttm) cc_final: 0.7583 (ttmt)
REVERT: A  115 ASP cc_start: 0.8329 (t0) cc_final: 0.7766 (t0)
REVERT: A  277 GLU cc_start: 0.9015 (mp0) cc_final: 0.8676 (mp0)
REVERT: A  289 TYR cc_start: 0.9111 (t80) cc_final: 0.8788 (t80)
  outliers start: 16
  outliers final: 14
  residues processed: 189
  average time/residue: 0.1302
  time to fit residues: 34.1098
Evaluate side-chains
  192 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 178
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue  150 VAL
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  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   66 VAL
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  183 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 55 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0570
   chunk 19 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 26 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.6298

-------------------------------------------------------------------------------
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 = 0.3661 r_free = 0.3661 target = 0.135713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.106039 restraints weight = 9272.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.95
r_work: 0.3129 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5761  Z= 0.210
  Angle     :  0.651   8.925   7827  Z= 0.318
  Chirality :  0.044   0.167    911
  Planarity :  0.004   0.032    964
  Dihedral  :  4.137  14.867    781
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 23.71 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.32), residues: 728
  helix:  1.50 (0.34), residues: 245
  sheet:  0.66 (0.40), residues: 183
  loop : -1.41 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP L 168 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.012   0.001   PHE H 154 
 TYR   0.015   0.001   TYR A 289 
 ARG   0.001   0.000   ARG L 216 

*********************** 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
  197 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 180
  time to evaluate  : 0.715 
Fit side-chains
REVERT: H  113 GLN cc_start: 0.9279 (pt0) cc_final: 0.8751 (pm20)
REVERT: H  153 TYR cc_start: 0.8280 (p90) cc_final: 0.7168 (p90)
REVERT: H  156 GLU cc_start: 0.8084 (tp30) cc_final: 0.7057 (tp30)
REVERT: H  179 GLN cc_start: 0.8759 (pp30) cc_final: 0.8201 (pp30)
REVERT: L   44 GLN cc_start: 0.9520 (OUTLIER) cc_final: 0.8618 (tt0)
REVERT: L  129 GLN cc_start: 0.8742 (tp-100) cc_final: 0.8220 (tp-100)
REVERT: L  168 TRP cc_start: 0.9374 (m-90) cc_final: 0.8709 (m-90)
REVERT: L  180 MET cc_start: 0.8816 (ttt) cc_final: 0.8182 (ttt)
REVERT: A   59 LYS cc_start: 0.7926 (tttm) cc_final: 0.7579 (ttmt)
REVERT: A  115 ASP cc_start: 0.8310 (t0) cc_final: 0.7769 (t0)
REVERT: A  277 GLU cc_start: 0.8999 (mp0) cc_final: 0.8680 (mp0)
REVERT: A  289 TYR cc_start: 0.9099 (t80) cc_final: 0.8768 (t80)
  outliers start: 17
  outliers final: 14
  residues processed: 190
  average time/residue: 0.1246
  time to fit residues: 32.8612
Evaluate side-chains
  194 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 179
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  150 VAL
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  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   66 VAL
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  121 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 35 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 59 optimal weight:    0.4980
   chunk 4 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0000
   chunk 30 optimal weight:    0.0670
   chunk 64 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.4322

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.138164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.107615 restraints weight = 9533.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 3.12
r_work: 0.3148 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5761  Z= 0.191
  Angle     :  0.651  10.236   7827  Z= 0.317
  Chirality :  0.044   0.160    911
  Planarity :  0.004   0.031    964
  Dihedral  :  4.061  14.814    781
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 24.34 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.32), residues: 728
  helix:  1.56 (0.34), residues: 244
  sheet:  0.67 (0.40), residues: 183
  loop : -1.43 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP L 168 
 HIS   0.002   0.000   HIS H  35 
 PHE   0.011   0.001   PHE H 154 
 TYR   0.014   0.001   TYR A 289 
 ARG   0.002   0.000   ARG L 216 

********************** 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
  195 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 181
  time to evaluate  : 0.674 
Fit side-chains
REVERT: H   52 ASN cc_start: 0.8793 (t0) cc_final: 0.8469 (t0)
REVERT: H  113 GLN cc_start: 0.9249 (pt0) cc_final: 0.8750 (pm20)
REVERT: H  153 TYR cc_start: 0.8243 (p90) cc_final: 0.7066 (p90)
REVERT: H  156 GLU cc_start: 0.8067 (tp30) cc_final: 0.7026 (tp30)
REVERT: H  179 GLN cc_start: 0.8778 (pp30) cc_final: 0.8162 (pp30)
REVERT: L   42 TYR cc_start: 0.9308 (m-80) cc_final: 0.9043 (m-80)
REVERT: L   44 GLN cc_start: 0.9501 (OUTLIER) cc_final: 0.8650 (tt0)
REVERT: L  129 GLN cc_start: 0.8676 (tp-100) cc_final: 0.8110 (tp-100)
REVERT: L  168 TRP cc_start: 0.9371 (m-90) cc_final: 0.8657 (m-90)
REVERT: L  180 MET cc_start: 0.8854 (ttt) cc_final: 0.8089 (ttt)
REVERT: A   59 LYS cc_start: 0.7924 (tttm) cc_final: 0.7545 (ttmt)
REVERT: A  115 ASP cc_start: 0.8327 (t0) cc_final: 0.7806 (t0)
REVERT: A  277 GLU cc_start: 0.8891 (mp0) cc_final: 0.8599 (mp0)
  outliers start: 14
  outliers final: 12
  residues processed: 188
  average time/residue: 0.1320
  time to fit residues: 34.3223
Evaluate side-chains
  192 residues out of total 641 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 179
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
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  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 A residue   46 MET
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  105 SER
Chi-restraints excluded: chain A residue  121 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 10 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0980
   chunk 26 optimal weight:    0.2980
   chunk 33 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0870
   chunk 2 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.3958

-------------------------------------------------------------------------------
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  43 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.137606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.108125 restraints weight = 9379.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.98
r_work: 0.3162 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.2885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5761  Z= 0.190
  Angle     :  0.671  11.969   7827  Z= 0.322
  Chirality :  0.044   0.164    911
  Planarity :  0.004   0.031    964
  Dihedral  :  4.015  14.375    781
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 24.65 %
    Favored  : 73.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.32), residues: 728
  helix:  1.56 (0.34), residues: 243
  sheet:  0.70 (0.40), residues: 183
  loop : -1.44 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L 168 
 HIS   0.002   0.000   HIS H  35 
 PHE   0.010   0.001   PHE H 154 
 TYR   0.022   0.001   TYR A 289 
 ARG   0.003   0.000   ARG L 216 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3014.00 seconds
wall clock time: 54 minutes 25.45 seconds (3265.45 seconds total)