Starting phenix.real_space_refine
on Tue Jan 14 07:36:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yqx_39509/01_2025/8yqx_39509.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yqx_39509/01_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yqx_39509/01_2025/8yqx_39509.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yqx_39509/01_2025/8yqx_39509.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yqx_39509/01_2025/8yqx_39509.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yqx_39509/01_2025/8yqx_39509.cif"
  }
  resolution = 2.97
  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=   0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 5.09, per 1000 atoms: 0.83
  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: 1.44
  Conformation dependent library (CDL) restraints added in 959.7 milliseconds
  

  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: 0.65
  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: 1.63

  Time building geometry restraints manager: 1.66 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:             2.010
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.570
  Find NCS groups from input model:        0.050
  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:13.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.550
-------------------------------------------------------------------------------
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= 0.172
  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 (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: -0.18 (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
 TRP   0.006   0.001   TRP F 327 
 HIS   0.002   0.001   HIS A  72 
 PHE   0.009   0.001   PHE F   7 
 TYR   0.011   0.001   TYR F 207 
 ARG   0.013   0.000   ARG A 111 

*********************** 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  : 0.792 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 114
  average time/residue: 1.1150
  time to fit residues: 134.2407
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  : 0.683 
-------------------------------------------------------------------------------
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 63 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 31 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 38 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    1.0384

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.183405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.141180 restraints weight = 6778.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 1.81
r_work: 0.3314 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.0818

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= 0.222
  Angle     :  0.506   7.058   8510  Z= 0.267
  Chirality :  0.044   0.170    963
  Planarity :  0.004   0.043   1086
  Dihedral  :  5.162  49.480    837
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 18.81 %
    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 (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: -0.20 (0.29), residues: 758
  helix:  0.83 (0.30), residues: 281
  sheet: -0.63 (0.51), residues: 86
  loop : -0.69 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP J 217 
 HIS   0.003   0.001   HIS J 215 
 PHE   0.011   0.001   PHE J 199 
 TYR   0.010   0.001   TYR A 112 
 ARG   0.006   0.000   ARG A 111 

*********************** 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
  131 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.717 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7663 (ttm-80)
REVERT: A  123 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7422 (mp0)
REVERT: A  147 ASP cc_start: 0.7359 (t0) cc_final: 0.6992 (t0)
REVERT: A  172 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8251 (tp30)
  outliers start: 23
  outliers final: 8
  residues processed: 121
  average time/residue: 1.0535
  time to fit residues: 134.6684
Evaluate side-chains
  113 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
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  172 GLU
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain F residue    1 MET
Chi-restraints excluded: chain F residue  132 VAL
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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
F 122 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.174184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.128262 restraints weight = 6950.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 1.85
r_work: 0.3230 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3093 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   6293  Z= 0.358
  Angle     :  0.575   7.510   8510  Z= 0.300
  Chirality :  0.047   0.167    963
  Planarity :  0.005   0.042   1086
  Dihedral  :  5.129  41.794    831
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 18.09 %
    Favored  : 77.13 %
  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: -0.45 (0.29), residues: 758
  helix:  0.70 (0.30), residues: 281
  sheet: -0.84 (0.53), residues: 82
  loop : -0.87 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 155 
 HIS   0.006   0.001   HIS J 215 
 PHE   0.017   0.002   PHE J 199 
 TYR   0.017   0.002   TYR J 207 
 ARG   0.004   0.001   ARG A 111 

*********************** 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
  135 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 102
  time to evaluate  : 0.832 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8065 (mtp85) cc_final: 0.7700 (ttm-80)
REVERT: A  123 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7461 (mp0)
REVERT: A  147 ASP cc_start: 0.7444 (t0) cc_final: 0.6899 (t0)
REVERT: F  187 MET cc_start: 0.8065 (ptt) cc_final: 0.7809 (ptp)
REVERT: F  333 ARG cc_start: 0.6378 (mmm-85) cc_final: 0.5680 (mtt180)
REVERT: J  181 TRP cc_start: 0.8180 (OUTLIER) cc_final: 0.7938 (t60)
  outliers start: 33
  outliers final: 20
  residues processed: 126
  average time/residue: 1.1111
  time to fit residues: 147.5715
Evaluate side-chains
  120 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
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  162 ILE
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain F residue   17 THR
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue  118 GLU
Chi-restraints excluded: chain F residue  122 ASN
Chi-restraints excluded: chain F residue  123 VAL
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  247 LEU
Chi-restraints excluded: chain F residue  269 LEU
Chi-restraints excluded: chain F residue  283 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  181 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 54 optimal weight:    0.3980
   chunk 24 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3894 r_free = 0.3894 target = 0.176895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.131554 restraints weight = 7044.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 1.89
r_work: 0.3259 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.1234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6293  Z= 0.183
  Angle     :  0.500   7.497   8510  Z= 0.263
  Chirality :  0.044   0.158    963
  Planarity :  0.004   0.039   1086
  Dihedral  :  4.885  42.406    831
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 20.26 %
    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 (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: -0.18 (0.29), residues: 758
  helix:  0.95 (0.30), residues: 282
  sheet: -0.74 (0.53), residues: 82
  loop : -0.72 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP F 257 
 HIS   0.002   0.001   HIS J 215 
 PHE   0.009   0.001   PHE J 199 
 TYR   0.012   0.001   TYR J 207 
 ARG   0.002   0.000   ARG A 111 

*********************** 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
  132 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 106
  time to evaluate  : 0.698 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8026 (mtp85) cc_final: 0.7686 (ttm-80)
REVERT: A  123 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7410 (mp0)
REVERT: A  147 ASP cc_start: 0.7350 (t0) cc_final: 0.6888 (t0)
REVERT: A  172 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8291 (tp30)
REVERT: A  254 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7559 (mp)
REVERT: F    1 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7219 (tpp)
REVERT: F  187 MET cc_start: 0.8108 (ptt) cc_final: 0.7868 (ptp)
REVERT: F  219 ASP cc_start: 0.7116 (t0) cc_final: 0.6547 (p0)
REVERT: F  333 ARG cc_start: 0.6301 (mmm-85) cc_final: 0.5637 (mtt180)
  outliers start: 26
  outliers final: 13
  residues processed: 125
  average time/residue: 1.0701
  time to fit residues: 141.5484
Evaluate side-chains
  120 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
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  118 GLU
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  237 CYS
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 72 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 71 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 61 optimal weight:   20.0000
   chunk 73 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 = 0.4093 r_free = 0.4093 target = 0.191174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.144001 restraints weight = 6868.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 2.12
r_work: 0.3397 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
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   0.030   6293  Z= 0.222
  Angle     :  0.519  10.261   8510  Z= 0.267
  Chirality :  0.045   0.164    963
  Planarity :  0.004   0.037   1086
  Dihedral  :  4.899  41.945    831
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 19.25 %
    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 (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: -0.12 (0.29), residues: 758
  helix:  1.02 (0.30), residues: 281
  sheet: -0.61 (0.52), residues: 86
  loop : -0.73 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 155 
 HIS   0.003   0.001   HIS J 215 
 PHE   0.011   0.001   PHE J 199 
 TYR   0.013   0.001   TYR J 207 
 ARG   0.004   0.000   ARG F 259 

*********************** 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
  135 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 102
  time to evaluate  : 0.748 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7785 (ttm-80)
REVERT: A  122 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.7876 (mp)
REVERT: A  123 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7498 (mp0)
REVERT: A  147 ASP cc_start: 0.7344 (t0) cc_final: 0.6899 (t0)
REVERT: A  172 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8389 (tp30)
REVERT: F    1 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7362 (tpp)
REVERT: F  187 MET cc_start: 0.8167 (ptt) cc_final: 0.7909 (ptp)
REVERT: F  333 ARG cc_start: 0.6366 (mmm-85) cc_final: 0.5718 (mtt180)
REVERT: J  186 GLU cc_start: 0.6927 (pm20) cc_final: 0.6202 (tm-30)
  outliers start: 33
  outliers final: 18
  residues processed: 126
  average time/residue: 1.0582
  time to fit residues: 140.8368
Evaluate side-chains
  124 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
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  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   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  237 CYS
Chi-restraints excluded: chain F residue  240 LEU
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 58 optimal weight:   10.0000
   chunk 36 optimal weight:    0.3980
   chunk 69 optimal weight:    0.0870
   chunk 48 optimal weight:    0.2980
   chunk 15 optimal weight:    0.5980
   chunk 72 optimal weight:    5.9990
   chunk 10 optimal weight:    0.6980
   chunk 65 optimal weight:    0.3980
   chunk 32 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.3558

-------------------------------------------------------------------------------
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 = 0.4125 r_free = 0.4125 target = 0.194604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.155112 restraints weight = 6738.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 2.69
r_work: 0.3456 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6293  Z= 0.144
  Angle     :  0.488   9.095   8510  Z= 0.253
  Chirality :  0.043   0.195    963
  Planarity :  0.004   0.035   1086
  Dihedral  :  4.689  44.384    831
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 20.26 %
    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 (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 (0.30), residues: 758
  helix:  1.36 (0.30), residues: 281
  sheet: -0.44 (0.51), residues: 90
  loop : -0.61 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F 257 
 HIS   0.002   0.000   HIS F 165 
 PHE   0.008   0.001   PHE F  58 
 TYR   0.013   0.001   TYR A  46 
 ARG   0.002   0.000   ARG A 111 

*********************** 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
  140 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.743 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.7914 (mtp85) cc_final: 0.7677 (ttm-80)
REVERT: A  122 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7845 (mp)
REVERT: A  123 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7312 (mp0)
REVERT: A  147 ASP cc_start: 0.7089 (t0) cc_final: 0.6781 (t0)
REVERT: A  172 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8118 (tp30)
REVERT: F    1 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7415 (tpp)
REVERT: F  187 MET cc_start: 0.8215 (ptt) cc_final: 0.7947 (ptp)
REVERT: F  219 ASP cc_start: 0.7039 (t0) cc_final: 0.6458 (p0)
REVERT: F  333 ARG cc_start: 0.6321 (mmm-85) cc_final: 0.5760 (mtt180)
REVERT: J  186 GLU cc_start: 0.7049 (pm20) cc_final: 0.6505 (tm-30)
  outliers start: 26
  outliers final: 11
  residues processed: 131
  average time/residue: 1.1376
  time to fit residues: 157.0420
Evaluate side-chains
  121 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  118 GLU
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain F residue  237 CYS
Chi-restraints excluded: chain F residue  240 LEU
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 35 optimal weight:    7.9990
   chunk 44 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.4097 r_free = 0.4097 target = 0.191637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.146005 restraints weight = 6815.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 2.09
r_work: 0.3382 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.1502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6293  Z= 0.234
  Angle     :  0.523   8.481   8510  Z= 0.268
  Chirality :  0.045   0.166    963
  Planarity :  0.004   0.034   1086
  Dihedral  :  4.682  47.830    829
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 21.56 %
    Favored  : 75.11 %
  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:  0.07 (0.30), residues: 758
  helix:  1.22 (0.30), residues: 281
  sheet: -0.60 (0.53), residues: 86
  loop : -0.63 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 155 
 HIS   0.003   0.001   HIS J 215 
 PHE   0.012   0.001   PHE J 199 
 TYR   0.012   0.001   TYR J 207 
 ARG   0.002   0.000   ARG F 259 

*********************** 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
  128 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.853 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.7983 (mtp85) cc_final: 0.7678 (ttm-80)
REVERT: A  113 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7134 (tp30)
REVERT: A  122 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.7883 (mp)
REVERT: A  123 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7586 (mp0)
REVERT: A  147 ASP cc_start: 0.7262 (t0) cc_final: 0.6801 (t0)
REVERT: A  172 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8378 (tp30)
REVERT: F    1 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7332 (tpp)
REVERT: F  187 MET cc_start: 0.8162 (ptt) cc_final: 0.7888 (ptp)
REVERT: F  219 ASP cc_start: 0.7123 (t0) cc_final: 0.6518 (p0)
REVERT: F  333 ARG cc_start: 0.6291 (mmm-85) cc_final: 0.5652 (mtt180)
REVERT: J  186 GLU cc_start: 0.7111 (pm20) cc_final: 0.6464 (tm-30)
  outliers start: 23
  outliers final: 14
  residues processed: 119
  average time/residue: 1.0662
  time to fit residues: 134.1176
Evaluate side-chains
  118 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   85 ASP
Chi-restraints excluded: chain F residue  118 GLU
Chi-restraints excluded: chain F residue  123 VAL
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain F residue  237 CYS
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 67 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.4100 r_free = 0.4100 target = 0.191988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.144526 restraints weight = 6757.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 2.16
r_work: 0.3389 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6293  Z= 0.206
  Angle     :  0.517   8.169   8510  Z= 0.265
  Chirality :  0.044   0.163    963
  Planarity :  0.004   0.035   1086
  Dihedral  :  4.701  51.527    829
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 20.98 %
    Favored  : 75.25 %
  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:  0.10 (0.30), residues: 758
  helix:  1.23 (0.30), residues: 280
  sheet: -0.57 (0.53), residues: 86
  loop : -0.61 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 155 
 HIS   0.002   0.001   HIS F  71 
 PHE   0.011   0.001   PHE J 199 
 TYR   0.014   0.001   TYR A  46 
 ARG   0.002   0.000   ARG F 259 

*********************** 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
  128 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.750 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.7979 (mtp85) cc_final: 0.7700 (ttm-80)
REVERT: A  113 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7148 (tp30)
REVERT: A  122 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.7861 (mp)
REVERT: A  123 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7548 (mp0)
REVERT: A  147 ASP cc_start: 0.7260 (t0) cc_final: 0.6812 (t0)
REVERT: A  172 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8384 (tp30)
REVERT: F    1 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7327 (tpp)
REVERT: F  187 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7890 (ptp)
REVERT: F  333 ARG cc_start: 0.6264 (mmm-85) cc_final: 0.5641 (mtt180)
REVERT: J  186 GLU cc_start: 0.7119 (pm20) cc_final: 0.6546 (tm-30)
  outliers start: 26
  outliers final: 16
  residues processed: 118
  average time/residue: 0.9905
  time to fit residues: 124.0022
Evaluate side-chains
  123 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
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   85 ASP
Chi-restraints excluded: chain F residue  118 GLU
Chi-restraints excluded: chain F residue  123 VAL
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  231 MET
Chi-restraints excluded: chain F residue  237 CYS
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 44 optimal weight:    6.9990
   chunk 58 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
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 = 0.4078 r_free = 0.4078 target = 0.189605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.142281 restraints weight = 6794.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 2.16
r_work: 0.3331 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6293  Z= 0.292
  Angle     :  0.558   7.953   8510  Z= 0.286
  Chirality :  0.046   0.167    963
  Planarity :  0.004   0.034   1086
  Dihedral  :  4.970  50.978    829
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 21.56 %
    Favored  : 74.53 %
  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: -0.09 (0.29), residues: 758
  helix:  1.00 (0.30), residues: 281
  sheet: -0.66 (0.54), residues: 86
  loop : -0.67 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 155 
 HIS   0.004   0.001   HIS J 215 
 PHE   0.015   0.001   PHE J 199 
 TYR   0.015   0.002   TYR J 207 
 ARG   0.002   0.000   ARG F 259 

*********************** 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
  122 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 95
  time to evaluate  : 0.743 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8126 (mtp85) cc_final: 0.7769 (ttm-80)
REVERT: A  113 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7229 (tp30)
REVERT: A  122 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.7913 (mp)
REVERT: A  123 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7567 (mp0)
REVERT: A  147 ASP cc_start: 0.7374 (t0) cc_final: 0.6902 (t0)
REVERT: F    1 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7347 (tpp)
REVERT: F  187 MET cc_start: 0.8167 (ptt) cc_final: 0.7833 (ptp)
REVERT: F  219 ASP cc_start: 0.7055 (t0) cc_final: 0.6411 (p0)
REVERT: F  333 ARG cc_start: 0.6284 (mmm-85) cc_final: 0.5650 (mtt180)
REVERT: J  186 GLU cc_start: 0.7143 (pm20) cc_final: 0.6574 (tm-30)
  outliers start: 27
  outliers final: 13
  residues processed: 113
  average time/residue: 1.0039
  time to fit residues: 120.2834
Evaluate side-chains
  111 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
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  118 GLU
Chi-restraints excluded: chain F residue  123 VAL
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  231 MET
Chi-restraints excluded: chain F residue  237 CYS
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 65 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0570
   chunk 27 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.7500

-------------------------------------------------------------------------------
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 = 0.4100 r_free = 0.4100 target = 0.191797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.145504 restraints weight = 6873.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 2.10
r_work: 0.3341 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.1610

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= 0.187
  Angle     :  0.520   9.048   8510  Z= 0.268
  Chirality :  0.044   0.163    963
  Planarity :  0.004   0.034   1086
  Dihedral  :  4.235  18.103    827
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 23.01 %
    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 (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:  0.06 (0.30), residues: 758
  helix:  1.13 (0.30), residues: 282
  sheet: -0.58 (0.54), residues: 86
  loop : -0.58 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP F 257 
 HIS   0.002   0.001   HIS F  71 
 PHE   0.009   0.001   PHE J 199 
 TYR   0.012   0.001   TYR J 207 
 ARG   0.002   0.000   ARG F 259 

********************** 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
  121 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8053 (mtp85) cc_final: 0.7735 (ttm-80)
REVERT: A  113 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7160 (tp30)
REVERT: A  122 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7861 (mp)
REVERT: A  123 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7564 (mp0)
REVERT: A  147 ASP cc_start: 0.7277 (t0) cc_final: 0.6819 (t0)
REVERT: A  172 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8377 (tp30)
REVERT: F    1 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7314 (tpp)
REVERT: F  187 MET cc_start: 0.8125 (ptt) cc_final: 0.7861 (ptp)
REVERT: F  219 ASP cc_start: 0.6968 (t0) cc_final: 0.6379 (p0)
REVERT: F  312 ASP cc_start: 0.7850 (m-30) cc_final: 0.7626 (OUTLIER)
REVERT: F  333 ARG cc_start: 0.6244 (mmm-85) cc_final: 0.5659 (mtt180)
REVERT: J  186 GLU cc_start: 0.7184 (pm20) cc_final: 0.6629 (tm-30)
  outliers start: 21
  outliers final: 17
  residues processed: 113
  average time/residue: 0.9694
  time to fit residues: 116.4501
Evaluate side-chains
  121 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
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  123 VAL
Chi-restraints excluded: chain F residue  160 THR
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain F residue  231 MET
Chi-restraints excluded: chain F residue  237 CYS
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 5 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   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 = 0.4076 r_free = 0.4076 target = 0.189384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.141011 restraints weight = 6927.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 2.07
r_work: 0.3258 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6293  Z= 0.306
  Angle     :  0.567   8.558   8510  Z= 0.291
  Chirality :  0.046   0.165    963
  Planarity :  0.004   0.033   1086
  Dihedral  :  4.496  18.651    827
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 22.87 %
    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 (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: -0.15 (0.29), residues: 758
  helix:  0.95 (0.30), residues: 281
  sheet: -0.72 (0.54), residues: 86
  loop : -0.69 (0.30), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 155 
 HIS   0.004   0.001   HIS J 215 
 PHE   0.015   0.002   PHE J 199 
 TYR   0.015   0.002   TYR J 207 
 ARG   0.002   0.000   ARG A 235 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5040.62 seconds
wall clock time: 90 minutes 5.37 seconds (5405.37 seconds total)