Starting phenix.real_space_refine
on Fri Aug 22 16:49:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yqx_39509/08_2025/8yqx_39509.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yqx_39509/08_2025/8yqx_39509.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yqx_39509/08_2025/8yqx_39509.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yqx_39509/08_2025/8yqx_39509.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yqx_39509/08_2025/8yqx_39509.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yqx_39509/08_2025/8yqx_39509.map"
  }
  resolution = 2.97
  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=   0.001 sd=   0.084
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      32      5.16       5
     C    3952      2.51       5
     N    1062      2.21       5
     O    1121      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6167
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2125
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2125
          Classifications: {'peptide': 264}
          Link IDs: {'PTRANS': 14, 'TRANS': 249}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 2698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2698
          Classifications: {'peptide': 336}
          Link IDs: {'PTRANS': 13, 'TRANS': 322}
    Chain: "J"
      Number of atoms: 1344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 166, 1344
          Classifications: {'peptide': 166}
          Link IDs: {'PTRANS': 7, 'TRANS': 158}
  Time building chain proxies: 1.65, per 1000 atoms: 0.27
  Number of scatterers: 6167
  At special positions: 0
  Unit cell: (84.84, 101.808, 96.96, 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      32     16.00
     O    1121      8.00
     N    1062      7.00
     C    3952      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.45
  Conformation dependent library (CDL) restraints added in 236.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1458

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 9 sheets defined
      38.4% alpha, 18.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 25
    Processing helix  chain 'A' and resid 47 through 51
    Processing helix  chain 'A' and resid 87 through 96
    Processing helix  chain 'A' and resid 108 through 113
    Processing helix  chain 'A' and resid 116 through 127
      removed outlier: 4.668A  pdb=" N   LEU A 121 " --> pdb=" O   ARG A 117 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   ILE A 122 " --> pdb=" O   PRO A 118 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   SER A 127 " --> pdb=" O   GLU A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 175
    Processing helix  chain 'A' and resid 178 through 185
    Processing helix  chain 'A' and resid 192 through 195
    Processing helix  chain 'A' and resid 225 through 238
      removed outlier: 3.793A  pdb=" N   VAL A 229 " --> pdb=" O   ASP A 225 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU A 238 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 272
    Processing helix  chain 'F' and resid 15 through 20
    Processing helix  chain 'F' and resid 22 through 36
    Processing helix  chain 'F' and resid 171 through 194
      removed outlier: 4.104A  pdb=" N   LYS F 180 " --> pdb=" O   LEU F 176 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   LEU F 181 " --> pdb=" O   ASN F 177 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LYS F 194 " --> pdb=" O   GLU F 190 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 196 through 207
    Processing helix  chain 'F' and resid 239 through 248
      removed outlier: 3.568A  pdb=" N   LYS F 248 " --> pdb=" O   TYR F 244 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 288 through 314
    Processing helix  chain 'F' and resid 316 through 323
      removed outlier: 3.616A  pdb=" N   ILE F 320 " --> pdb=" O   ASN F 316 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 323 through 333
      removed outlier: 3.654A  pdb=" N   ARG F 333 " --> pdb=" O   LEU F 329 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 75 through 85
      removed outlier: 3.865A  pdb=" N   ASP J  85 " --> pdb=" O   GLN J  81 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 138 through 149
      removed outlier: 3.699A  pdb=" N   PHE J 142 " --> pdb=" O   SER J 138 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 152 through 163
    Processing helix  chain 'J' and resid 167 through 173
    Processing helix  chain 'J' and resid 193 through 211
      removed outlier: 3.576A  pdb=" N   ILE J 197 " --> pdb=" O   LYS J 193 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 215 through 236
      removed outlier: 3.506A  pdb=" N   ASN J 220 " --> pdb=" O   SER J 216 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29
      removed outlier: 4.823A  pdb=" N   GLN A  77 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
      removed outlier: 10.309A  pdb=" N   MET A  78 " --> pdb=" O   GLN A 202 " (cutoff:3.500A)
      removed outlier: 10.835A  pdb=" N   GLN A 202 " --> pdb=" O   MET A  78 " (cutoff:3.500A)
      removed outlier: 10.493A  pdb=" N   ALA A  80 " --> pdb=" O   ALA A 200 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ALA A 200 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36
      removed outlier: 3.848A  pdb=" N   LEU A  39 " --> pdb=" O   GLU A  36 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 146
      removed outlier: 4.606A  pdb=" N   PHE A 154 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'F' and resid 2 through 13
      removed outlier: 6.305A  pdb=" N   SER F  75 " --> pdb=" O   VAL F  51 " (cutoff:3.500A)
      removed outlier: 5.327A  pdb=" N   VAL F  51 " --> pdb=" O   SER F  75 " (cutoff:3.500A)
      removed outlier: 7.542A  pdb=" N   VAL F  77 " --> pdb=" O   THR F  49 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   THR F  49 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 8.108A  pdb=" N   SER F  79 " --> pdb=" O   ASN F  47 " (cutoff:3.500A)
      removed outlier: 9.563A  pdb=" N   ASN F  47 " --> pdb=" O   SER F  79 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 2 through 13
    Processing sheet with id=AA6, first strand: chain 'F' and resid 86 through 87
      removed outlier: 7.545A  pdb=" N   ILE F 154 " --> pdb=" O   PRO F 115 " (cutoff:3.500A)
      removed outlier: 7.527A  pdb=" N   ILE F  99 " --> pdb=" O   ASN F  95 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   ASN F  95 " --> pdb=" O   ILE F  99 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LEU F 101 " --> pdb=" O   ILE F  93 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'F' and resid 237 through 238
      removed outlier: 6.695A  pdb=" N   VAL F 163 " --> pdb=" O   ILE F 285 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   CYS F 287 " --> pdb=" O   VAL F 163 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   HIS F 165 " --> pdb=" O   CYS F 287 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 217 through 219
    Processing sheet with id=AA9, first strand: chain 'J' and resid 115 through 119
      removed outlier: 3.642A  pdb=" N   THR J 115 " --> pdb=" O   LEU J 111 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   ILE J  91 " --> pdb=" O   PHE J 110 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   VAL J  92 " --> pdb=" O   TYR J 128 " (cutoff:3.500A)

    263 hydrogen bonds defined for protein.
    744 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: 0.98

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2009
        1.34 -     1.46: 1353
        1.46 -     1.58: 2883
        1.58 -     1.70: 0
        1.70 -     1.82: 48
  Bond restraints: 6293
  Sorted by residual:
  bond pdb=" CB  ASN F 136 "
       pdb=" CG  ASN F 136 "
    ideal  model  delta    sigma   weight residual
    1.516  1.549 -0.033 2.50e-02 1.60e+03 1.69e+00
  bond pdb=" CA  GLY A  37 "
       pdb=" C   GLY A  37 "
    ideal  model  delta    sigma   weight residual
    1.514  1.531 -0.016 1.41e-02 5.03e+03 1.34e+00
  bond pdb=" N   GLY A  37 "
       pdb=" CA  GLY A  37 "
    ideal  model  delta    sigma   weight residual
    1.449  1.464 -0.015 1.45e-02 4.76e+03 1.07e+00
  bond pdb=" CB  GLU F 282 "
       pdb=" CG  GLU F 282 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 1.03e+00
  bond pdb=" CB  GLU A 113 "
       pdb=" CG  GLU A 113 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.23e-01
  ... (remaining 6288 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 8366
        1.67 -     3.33: 121
        3.33 -     5.00: 16
        5.00 -     6.66: 5
        6.66 -     8.33: 2
  Bond angle restraints: 8510
  Sorted by residual:
  angle pdb=" N   VAL F 123 "
        pdb=" CA  VAL F 123 "
        pdb=" C   VAL F 123 "
      ideal   model   delta    sigma   weight residual
     112.96  107.95    5.01 1.00e+00 1.00e+00 2.51e+01
  angle pdb=" CG  ARG A 111 "
        pdb=" CD  ARG A 111 "
        pdb=" NE  ARG A 111 "
      ideal   model   delta    sigma   weight residual
     112.00  118.92   -6.92 2.20e+00 2.07e-01 9.89e+00
  angle pdb=" CB  MET F 328 "
        pdb=" CG  MET F 328 "
        pdb=" SD  MET F 328 "
      ideal   model   delta    sigma   weight residual
     112.70  121.03   -8.33 3.00e+00 1.11e-01 7.71e+00
  angle pdb=" C   ILE J 112 "
        pdb=" N   ASN J 113 "
        pdb=" CA  ASN J 113 "
      ideal   model   delta    sigma   weight residual
     125.66  130.77   -5.11 1.85e+00 2.92e-01 7.64e+00
  angle pdb=" CA  LYS J 174 "
        pdb=" CB  LYS J 174 "
        pdb=" CG  LYS J 174 "
      ideal   model   delta    sigma   weight residual
     114.10  119.42   -5.32 2.00e+00 2.50e-01 7.07e+00
  ... (remaining 8505 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 3372
       18.00 -    35.99: 342
       35.99 -    53.98: 98
       53.98 -    71.98: 19
       71.98 -    89.97: 9
  Dihedral angle restraints: 3840
    sinusoidal: 1592
      harmonic: 2248
  Sorted by residual:
  dihedral pdb=" CA  LYS J 174 "
           pdb=" C   LYS J 174 "
           pdb=" N   CYS J 175 "
           pdb=" CA  CYS J 175 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.62   19.38     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CG  ARG A 111 "
           pdb=" CD  ARG A 111 "
           pdb=" NE  ARG A 111 "
           pdb=" CZ  ARG A 111 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -40.26  -49.74     2      1.50e+01 4.44e-03 1.24e+01
  dihedral pdb=" CA  ASP J 235 "
           pdb=" CB  ASP J 235 "
           pdb=" CG  ASP J 235 "
           pdb=" OD1 ASP J 235 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.47   57.47     1      2.00e+01 2.50e-03 1.11e+01
  ... (remaining 3837 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 650
       0.037 -    0.074: 221
       0.074 -    0.112: 67
       0.112 -    0.149: 24
       0.149 -    0.186: 1
  Chirality restraints: 963
  Sorted by residual:
  chirality pdb=" CB  VAL J  89 "
            pdb=" CA  VAL J  89 "
            pdb=" CG1 VAL J  89 "
            pdb=" CG2 VAL J  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 8.66e-01
  chirality pdb=" CA  ASN F 122 "
            pdb=" N   ASN F 122 "
            pdb=" C   ASN F 122 "
            pdb=" CB  ASN F 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.47e-01
  chirality pdb=" CA  ILE F 156 "
            pdb=" N   ILE F 156 "
            pdb=" C   ILE F 156 "
            pdb=" CB  ILE F 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.67e-01
  ... (remaining 960 not shown)

  Planarity restraints: 1086
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU F 283 "    0.034 5.00e-02 4.00e+02   5.13e-02 4.21e+00
        pdb=" N   PRO F 284 "   -0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO F 284 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO F 284 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 117 "    0.032 5.00e-02 4.00e+02   4.93e-02 3.88e+00
        pdb=" N   PRO A 118 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 118 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 118 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN F 136 "    0.007 2.00e-02 2.50e+03   1.40e-02 1.95e+00
        pdb=" C   ASN F 136 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   ASN F 136 "    0.009 2.00e-02 2.50e+03
        pdb=" N   SER F 137 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1083 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 443
        2.74 -     3.28: 5929
        3.28 -     3.82: 10013
        3.82 -     4.36: 12140
        4.36 -     4.90: 20677
  Nonbonded interactions: 49202
  Sorted by model distance:
  nonbonded pdb=" OH  TYR F 208 "
            pdb=" O   ASN F 262 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" N   GLU J 186 "
            pdb=" OE1 GLU J 186 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" NH2 ARG J 221 "
            pdb=" OE1 GLU J 224 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" N   GLU F 282 "
            pdb=" OE1 GLU F 282 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" OE1 GLU F 118 "
            pdb=" NE2 GLN F 120 "
     model   vdw
     2.324 3.120
  ... (remaining 49197 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:             4.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.760
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6293  Z= 0.120
  Angle     :  0.523   8.330   8510  Z= 0.289
  Chirality :  0.043   0.186    963
  Planarity :  0.004   0.051   1086
  Dihedral  : 16.268  89.972   2382
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 21.42 %
    Favored  : 77.86 %
  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 aren not related in a simple way.
  whole: -0.18 (0.30), residues: 758
  helix:  0.71 (0.30), residues: 279
  sheet: -0.25 (0.52), residues: 89
  loop : -0.65 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 111 
 TYR   0.011   0.001   TYR F 207 
 PHE   0.009   0.001   PHE F   7 
 TRP   0.006   0.001   TRP F 327 
 HIS   0.002   0.001   HIS A  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6293)
  covalent geometry    : angle       0.52312 ( 8510)
  hydrogen bonds       : bond        0.15255 (  251)
  hydrogen bonds       : angle       6.24982 (  744)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 110
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 114
  average time/residue: 0.5105
  time to fit residues: 61.3436
Evaluate side-chains
  111 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 107
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  146 LYS
Chi-restraints excluded: chain J residue   91 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS
A 245 GLN
A 264 GLN
F  22 ASN
F 122 ASN
F 238 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.174369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.128961 restraints weight = 6973.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 1.95
r_work: 0.3225 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.1130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   6293  Z= 0.231
  Angle     :  0.577   6.952   8510  Z= 0.302
  Chirality :  0.047   0.177    963
  Planarity :  0.005   0.045   1086
  Dihedral  :  5.498  49.903    837
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 17.95 %
    Favored  : 77.86 %
  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 aren not related in a simple way.
  whole: -0.51 (0.29), residues: 758
  helix:  0.59 (0.30), residues: 280
  sheet: -0.90 (0.52), residues: 82
  loop : -0.85 (0.30), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 111 
 TYR   0.015   0.002   TYR A 112 
 PHE   0.017   0.002   PHE J 199 
 TRP   0.006   0.001   TRP A 155 
 HIS   0.006   0.001   HIS J 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00568 ( 6293)
  covalent geometry    : angle       0.57718 ( 8510)
  hydrogen bonds       : bond        0.04511 (  251)
  hydrogen bonds       : angle       4.77124 (  744)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 96
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: A  111 ARG cc_start: 0.8079 (mtp85) cc_final: 0.7702 (ttm-80)
REVERT: A  123 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7434 (mp0)
REVERT: A  147 ASP cc_start: 0.7529 (t0) cc_final: 0.7084 (t0)
REVERT: F    1 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7290 (tpp)
REVERT: F  187 MET cc_start: 0.8049 (ptt) cc_final: 0.7820 (ptp)
REVERT: F  333 ARG cc_start: 0.6327 (mmm-85) cc_final: 0.5566 (mtt180)
  outliers start: 29
  outliers final: 14
  residues processed: 116
  average time/residue: 0.5585
  time to fit residues: 67.8681
Evaluate side-chains
  111 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain F residue  122 ASN
Chi-restraints excluded: chain F residue  132 VAL
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  237 CYS
Chi-restraints excluded: chain F residue  269 LEU
Chi-restraints excluded: chain F residue  332 GLN
Chi-restraints excluded: chain J residue   91 ILE
Chi-restraints excluded: chain J residue  101 VAL
Chi-restraints excluded: chain J residue  171 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 55 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS
F 122 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.185293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.145745 restraints weight = 6876.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 1.84
r_work: 0.3307 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.1070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6293  Z= 0.125
  Angle     :  0.481   7.192   8510  Z= 0.256
  Chirality :  0.044   0.161    963
  Planarity :  0.004   0.041   1086
  Dihedral  :  4.873  42.434    831
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 18.81 %
    Favored  : 76.85 %
  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 aren not related in a simple way.
  whole: -0.26 (0.29), residues: 758
  helix:  0.86 (0.30), residues: 281
  sheet: -0.76 (0.53), residues: 82
  loop : -0.77 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 111 
 TYR   0.012   0.001   TYR F 207 
 PHE   0.009   0.001   PHE J 199 
 TRP   0.005   0.001   TRP A 155 
 HIS   0.002   0.001   HIS J 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6293)
  covalent geometry    : angle       0.48141 ( 8510)
  hydrogen bonds       : bond        0.03677 (  251)
  hydrogen bonds       : angle       4.53654 (  744)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 97
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7709 (ttm-80)
REVERT: A  123 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7459 (mp0)
REVERT: A  147 ASP cc_start: 0.7402 (t0) cc_final: 0.6910 (t0)
REVERT: A  172 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8307 (tp30)
REVERT: F  187 MET cc_start: 0.8170 (ptt) cc_final: 0.7927 (ptp)
REVERT: F  333 ARG cc_start: 0.6407 (mmm-85) cc_final: 0.5771 (mtt180)
  outliers start: 30
  outliers final: 13
  residues processed: 118
  average time/residue: 0.4733
  time to fit residues: 58.6772
Evaluate side-chains
  105 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   17 THR
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain F residue  118 GLU
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain F residue  269 LEU
Chi-restraints excluded: chain J residue   91 ILE
Chi-restraints excluded: chain J residue  101 VAL
Chi-restraints excluded: chain J residue  171 VAL
Chi-restraints excluded: chain J residue  222 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 44 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 14 optimal weight:    0.2980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.184756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.141552 restraints weight = 6873.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 1.81
r_work: 0.3317 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.1195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6293  Z= 0.140
  Angle     :  0.504   8.423   8510  Z= 0.263
  Chirality :  0.044   0.157    963
  Planarity :  0.004   0.038   1086
  Dihedral  :  4.854  42.246    831
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 20.26 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.29), residues: 758
  helix:  0.99 (0.30), residues: 281
  sheet: -0.82 (0.51), residues: 88
  loop : -0.76 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 111 
 TYR   0.012   0.001   TYR J 207 
 PHE   0.011   0.001   PHE J 199 
 TRP   0.006   0.001   TRP J 181 
 HIS   0.003   0.001   HIS J 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6293)
  covalent geometry    : angle       0.50369 ( 8510)
  hydrogen bonds       : bond        0.03614 (  251)
  hydrogen bonds       : angle       4.46784 (  744)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 102
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.7967 (mtp85) cc_final: 0.7639 (ttm-80)
REVERT: A  123 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7506 (mp0)
REVERT: A  147 ASP cc_start: 0.7314 (t0) cc_final: 0.6893 (t0)
REVERT: A  172 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8277 (tp30)
REVERT: F    1 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7287 (tpp)
REVERT: F  187 MET cc_start: 0.8128 (ptt) cc_final: 0.7890 (ptp)
REVERT: F  333 ARG cc_start: 0.6354 (mmm-85) cc_final: 0.5607 (mtt180)
  outliers start: 25
  outliers final: 14
  residues processed: 119
  average time/residue: 0.4438
  time to fit residues: 55.6003
Evaluate side-chains
  119 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   17 THR
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain F residue  118 GLU
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain F residue  269 LEU
Chi-restraints excluded: chain J residue   91 ILE
Chi-restraints excluded: chain J residue  101 VAL
Chi-restraints excluded: chain J residue  115 THR
Chi-restraints excluded: chain J residue  171 VAL
Chi-restraints excluded: chain J residue  222 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 68 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0570
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.6700

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS
F 122 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.193243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.145393 restraints weight = 6940.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.21
r_work: 0.3416 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3267 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6293  Z= 0.111
  Angle     :  0.483   7.350   8510  Z= 0.253
  Chirality :  0.043   0.155    963
  Planarity :  0.004   0.036   1086
  Dihedral  :  4.757  42.230    831
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 20.12 %
    Favored  : 75.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.04 (0.30), residues: 758
  helix:  1.19 (0.30), residues: 281
  sheet: -0.58 (0.53), residues: 84
  loop : -0.66 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 259 
 TYR   0.013   0.001   TYR A  46 
 PHE   0.008   0.001   PHE J 199 
 TRP   0.005   0.001   TRP F 257 
 HIS   0.002   0.000   HIS F 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6293)
  covalent geometry    : angle       0.48329 ( 8510)
  hydrogen bonds       : bond        0.03285 (  251)
  hydrogen bonds       : angle       4.33747 (  744)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8022 (mtp85) cc_final: 0.7690 (ttm-80)
REVERT: A  113 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7136 (tp30)
REVERT: A  123 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7481 (mp0)
REVERT: A  147 ASP cc_start: 0.7297 (t0) cc_final: 0.6845 (t0)
REVERT: A  172 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8357 (tp30)
REVERT: F    1 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7376 (tpp)
REVERT: F  187 MET cc_start: 0.8157 (ptt) cc_final: 0.7913 (ptp)
REVERT: F  333 ARG cc_start: 0.6363 (mmm-85) cc_final: 0.5716 (mtt180)
REVERT: J  186 GLU cc_start: 0.6985 (pm20) cc_final: 0.6255 (tm-30)
  outliers start: 30
  outliers final: 15
  residues processed: 134
  average time/residue: 0.4340
  time to fit residues: 61.3888
Evaluate side-chains
  129 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  146 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue  118 GLU
Chi-restraints excluded: chain F residue  122 ASN
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain F residue  269 LEU
Chi-restraints excluded: chain J residue   91 ILE
Chi-restraints excluded: chain J residue  101 VAL
Chi-restraints excluded: chain J residue  115 THR
Chi-restraints excluded: chain J residue  171 VAL
Chi-restraints excluded: chain J residue  222 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 15 optimal weight:    0.4980
   chunk 59 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 16 optimal weight:    0.2980
   chunk 51 optimal weight:    0.7980
   chunk 37 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.193197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.146057 restraints weight = 6867.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.11
r_work: 0.3427 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6293  Z= 0.114
  Angle     :  0.489   7.241   8510  Z= 0.257
  Chirality :  0.044   0.185    963
  Planarity :  0.004   0.036   1086
  Dihedral  :  4.544  45.346    829
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 19.39 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.30), residues: 758
  helix:  1.27 (0.30), residues: 281
  sheet: -0.56 (0.53), residues: 86
  loop : -0.64 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 111 
 TYR   0.010   0.001   TYR F 207 
 PHE   0.009   0.001   PHE J 199 
 TRP   0.005   0.001   TRP F 257 
 HIS   0.002   0.000   HIS F  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6293)
  covalent geometry    : angle       0.48893 ( 8510)
  hydrogen bonds       : bond        0.03233 (  251)
  hydrogen bonds       : angle       4.27616 (  744)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 111
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7703 (ttm-80)
REVERT: A  113 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7215 (tp30)
REVERT: A  122 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.7872 (mp)
REVERT: A  123 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7488 (mp0)
REVERT: A  147 ASP cc_start: 0.7258 (t0) cc_final: 0.6817 (t0)
REVERT: A  172 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8335 (tp30)
REVERT: F    1 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7392 (tpp)
REVERT: F  187 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7918 (ptp)
REVERT: F  244 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.7267 (m-10)
REVERT: F  333 ARG cc_start: 0.6391 (mmm-85) cc_final: 0.5788 (mtt180)
REVERT: J  186 GLU cc_start: 0.7007 (pm20) cc_final: 0.6383 (tm-30)
  outliers start: 32
  outliers final: 15
  residues processed: 133
  average time/residue: 0.4657
  time to fit residues: 65.3428
Evaluate side-chains
  130 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  146 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   17 THR
Chi-restraints excluded: chain F residue  118 GLU
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain F residue  187 MET
Chi-restraints excluded: chain F residue  244 TYR
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain F residue  269 LEU
Chi-restraints excluded: chain J residue   91 ILE
Chi-restraints excluded: chain J residue  101 VAL
Chi-restraints excluded: chain J residue  171 VAL
Chi-restraints excluded: chain J residue  222 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0370
   chunk 27 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   chunk 74 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS
F 122 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.193716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.147126 restraints weight = 6825.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.16
r_work: 0.3437 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6293  Z= 0.109
  Angle     :  0.484   7.223   8510  Z= 0.253
  Chirality :  0.044   0.169    963
  Planarity :  0.004   0.034   1086
  Dihedral  :  4.556  49.170    829
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 20.69 %
    Favored  : 75.40 %
  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 aren not related in a simple way.
  whole:  0.17 (0.30), residues: 758
  helix:  1.31 (0.30), residues: 282
  sheet: -0.43 (0.51), residues: 90
  loop : -0.63 (0.31), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 259 
 TYR   0.010   0.001   TYR J 207 
 PHE   0.008   0.001   PHE J 199 
 TRP   0.005   0.001   TRP F 257 
 HIS   0.002   0.000   HIS F  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 6293)
  covalent geometry    : angle       0.48420 ( 8510)
  hydrogen bonds       : bond        0.03175 (  251)
  hydrogen bonds       : angle       4.22997 (  744)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.7918 (mtp85) cc_final: 0.7636 (ttm-80)
REVERT: A  113 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7041 (tp30)
REVERT: A  122 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7883 (mp)
REVERT: A  123 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7552 (mp0)
REVERT: A  147 ASP cc_start: 0.7241 (t0) cc_final: 0.6786 (t0)
REVERT: A  172 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8297 (tp30)
REVERT: F    1 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7376 (tpp)
REVERT: F  187 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7885 (ptp)
REVERT: F  219 ASP cc_start: 0.7056 (t0) cc_final: 0.6455 (p0)
REVERT: F  244 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.7196 (m-80)
REVERT: F  333 ARG cc_start: 0.6366 (mmm-85) cc_final: 0.5712 (mtt180)
REVERT: J  186 GLU cc_start: 0.6955 (pm20) cc_final: 0.6389 (tm-30)
  outliers start: 27
  outliers final: 15
  residues processed: 129
  average time/residue: 0.4820
  time to fit residues: 65.7548
Evaluate side-chains
  128 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  146 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   17 THR
Chi-restraints excluded: chain F residue   85 ASP
Chi-restraints excluded: chain F residue  118 GLU
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain F residue  187 MET
Chi-restraints excluded: chain F residue  244 TYR
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain J residue   91 ILE
Chi-restraints excluded: chain J residue  101 VAL
Chi-restraints excluded: chain J residue  171 VAL
Chi-restraints excluded: chain J residue  222 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.189896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.145212 restraints weight = 6903.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 2.17
r_work: 0.3385 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.1551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6293  Z= 0.194
  Angle     :  0.561   7.765   8510  Z= 0.289
  Chirality :  0.046   0.173    963
  Planarity :  0.004   0.033   1086
  Dihedral  :  4.942  49.066    829
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 21.13 %
    Favored  : 74.67 %
  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 aren not related in a simple way.
  whole: -0.11 (0.29), residues: 758
  helix:  1.04 (0.30), residues: 281
  sheet: -0.68 (0.54), residues: 86
  loop : -0.72 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 209 
 TYR   0.015   0.002   TYR J 207 
 PHE   0.016   0.002   PHE J 199 
 TRP   0.006   0.001   TRP A 155 
 HIS   0.004   0.001   HIS J 215 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 6293)
  covalent geometry    : angle       0.56130 ( 8510)
  hydrogen bonds       : bond        0.03852 (  251)
  hydrogen bonds       : angle       4.43070 (  744)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 94
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7754 (ttm-80)
REVERT: A  113 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7207 (tp30)
REVERT: A  122 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.7905 (mp)
REVERT: A  123 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7532 (mp0)
REVERT: A  147 ASP cc_start: 0.7366 (t0) cc_final: 0.6929 (t0)
REVERT: F    1 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7426 (tpp)
REVERT: F  187 MET cc_start: 0.8140 (ptt) cc_final: 0.7819 (ptp)
REVERT: F  244 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.7240 (m-80)
REVERT: F  333 ARG cc_start: 0.6459 (mmm-85) cc_final: 0.5795 (mtt180)
REVERT: J  186 GLU cc_start: 0.7063 (pm20) cc_final: 0.6523 (tm-30)
  outliers start: 29
  outliers final: 15
  residues processed: 114
  average time/residue: 0.4484
  time to fit residues: 54.2181
Evaluate side-chains
  115 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  146 LYS
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   17 THR
Chi-restraints excluded: chain F residue  116 SER
Chi-restraints excluded: chain F residue  118 GLU
Chi-restraints excluded: chain F residue  122 ASN
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain F residue  244 TYR
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain J residue  101 VAL
Chi-restraints excluded: chain J residue  171 VAL
Chi-restraints excluded: chain J residue  222 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 47 optimal weight:    8.9990
   chunk 43 optimal weight:    0.6980
   chunk 30 optimal weight:    0.3980
   chunk 49 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0270
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS
F 122 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.193022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.145872 restraints weight = 6866.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 2.18
r_work: 0.3428 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3280 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.1560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6293  Z= 0.105
  Angle     :  0.490   7.815   8510  Z= 0.255
  Chirality :  0.044   0.175    963
  Planarity :  0.004   0.033   1086
  Dihedral  :  4.115  18.025    827
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 22.58 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.30), residues: 758
  helix:  1.31 (0.30), residues: 281
  sheet: -0.56 (0.54), residues: 86
  loop : -0.57 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  23 
 TYR   0.010   0.001   TYR J 207 
 PHE   0.008   0.001   PHE F  58 
 TRP   0.005   0.001   TRP J 181 
 HIS   0.002   0.000   HIS F 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 6293)
  covalent geometry    : angle       0.49048 ( 8510)
  hydrogen bonds       : bond        0.03137 (  251)
  hydrogen bonds       : angle       4.25888 (  744)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.7994 (mtp85) cc_final: 0.7703 (ttm-80)
REVERT: A  113 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7086 (tp30)
REVERT: A  122 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.7840 (mp)
REVERT: A  123 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7533 (mp0)
REVERT: A  147 ASP cc_start: 0.7301 (t0) cc_final: 0.6844 (t0)
REVERT: A  172 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8334 (tp30)
REVERT: F    1 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7385 (tpp)
REVERT: F  118 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7567 (mt-10)
REVERT: F  187 MET cc_start: 0.8074 (ptt) cc_final: 0.7831 (ptp)
REVERT: F  219 ASP cc_start: 0.6975 (t0) cc_final: 0.6367 (p0)
REVERT: F  244 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.7219 (m-80)
REVERT: F  333 ARG cc_start: 0.6250 (mmm-85) cc_final: 0.5663 (mtt180)
REVERT: J  143 MET cc_start: 0.7669 (mpp) cc_final: 0.7467 (mmm)
REVERT: J  186 GLU cc_start: 0.7080 (pm20) cc_final: 0.6550 (tm-30)
  outliers start: 21
  outliers final: 11
  residues processed: 123
  average time/residue: 0.4455
  time to fit residues: 57.9916
Evaluate side-chains
  123 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  146 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   17 THR
Chi-restraints excluded: chain F residue  118 GLU
Chi-restraints excluded: chain F residue  122 ASN
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain F residue  244 TYR
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain J residue  101 VAL
Chi-restraints excluded: chain J residue  171 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0870
   chunk 17 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 56 optimal weight:    4.9990
   chunk 48 optimal weight:   10.0000
   chunk 3 optimal weight:    0.0040
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.7372

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS
F 122 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.192724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.145881 restraints weight = 6885.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 2.12
r_work: 0.3372 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.1591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6293  Z= 0.118
  Angle     :  0.506  10.608   8510  Z= 0.260
  Chirality :  0.044   0.168    963
  Planarity :  0.004   0.034   1086
  Dihedral  :  4.113  17.925    827
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 22.87 %
    Favored  : 74.24 %
  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 aren not related in a simple way.
  whole:  0.20 (0.30), residues: 758
  helix:  1.32 (0.30), residues: 281
  sheet: -0.53 (0.55), residues: 86
  loop : -0.55 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 259 
 TYR   0.011   0.001   TYR F 207 
 PHE   0.008   0.001   PHE F   7 
 TRP   0.005   0.001   TRP J 181 
 HIS   0.002   0.001   HIS F  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6293)
  covalent geometry    : angle       0.50630 ( 8510)
  hydrogen bonds       : bond        0.03205 (  251)
  hydrogen bonds       : angle       4.23036 (  744)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.7976 (mtp85) cc_final: 0.7702 (ttm-80)
REVERT: A  113 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7149 (tp30)
REVERT: A  122 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.7875 (mp)
REVERT: A  123 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7571 (mp0)
REVERT: A  147 ASP cc_start: 0.7293 (t0) cc_final: 0.6833 (t0)
REVERT: A  172 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8344 (tp30)
REVERT: F    1 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7386 (tpp)
REVERT: F  118 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7587 (mt-10)
REVERT: F  187 MET cc_start: 0.8123 (ptt) cc_final: 0.7878 (ptp)
REVERT: F  219 ASP cc_start: 0.6996 (t0) cc_final: 0.6481 (p0)
REVERT: F  244 TYR cc_start: 0.7705 (OUTLIER) cc_final: 0.7242 (m-80)
REVERT: F  333 ARG cc_start: 0.6297 (mmm-85) cc_final: 0.5719 (mtt180)
REVERT: J  143 MET cc_start: 0.7695 (mpp) cc_final: 0.7476 (mmm)
REVERT: J  186 GLU cc_start: 0.7142 (pm20) cc_final: 0.6631 (tm-30)
  outliers start: 20
  outliers final: 12
  residues processed: 117
  average time/residue: 0.4733
  time to fit residues: 58.4923
Evaluate side-chains
  122 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  113 GLU
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  146 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue   17 THR
Chi-restraints excluded: chain F residue  118 GLU
Chi-restraints excluded: chain F residue  122 ASN
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain F residue  244 TYR
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain J residue   91 ILE
Chi-restraints excluded: chain J residue  101 VAL
Chi-restraints excluded: chain J residue  171 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0050
   chunk 65 optimal weight:    0.7980
   chunk 71 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0170
   overall best weight:    0.7034

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.192874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.154338 restraints weight = 6798.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3728 rms_B_bonded: 2.63
r_work: 0.3456 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6293  Z= 0.115
  Angle     :  0.518  10.225   8510  Z= 0.262
  Chirality :  0.044   0.167    963
  Planarity :  0.004   0.034   1086
  Dihedral  :  4.078  17.887    827
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 23.15 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.30), residues: 758
  helix:  1.35 (0.30), residues: 281
  sheet: -0.56 (0.54), residues: 86
  loop : -0.54 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 259 
 TYR   0.010   0.001   TYR J 207 
 PHE   0.008   0.001   PHE J 199 
 TRP   0.005   0.001   TRP F 257 
 HIS   0.002   0.000   HIS F  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6293)
  covalent geometry    : angle       0.51809 ( 8510)
  hydrogen bonds       : bond        0.03168 (  251)
  hydrogen bonds       : angle       4.21017 (  744)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2446.58 seconds
wall clock time: 42 minutes 20.82 seconds (2540.82 seconds total)