Starting phenix.real_space_refine
on Tue Mar 11 14:31:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yqx_39509/03_2025/8yqx_39509.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yqx_39509/03_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_39509/03_2025/8yqx_39509.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yqx_39509/03_2025/8yqx_39509.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yqx_39509/03_2025/8yqx_39509.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yqx_39509/03_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-5624/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: 4.31, per 1000 atoms: 0.70
  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: 1.43
  Conformation dependent library (CDL) restraints added in 825.7 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: 0.68
  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: 1.54

  Time building geometry restraints manager: 1.73 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:             1.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.710
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:14.520
  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  : 0.706 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 114
  average time/residue: 1.0554
  time to fit residues: 126.9786
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  : 0.633 
-------------------------------------------------------------------------------
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 = 0.141154 restraints weight = 6778.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 1.81
r_work: 0.3322 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
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  : 0.704 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8032 (mtp85) cc_final: 0.7644 (ttm-80)
REVERT: A  123 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7426 (mp0)
REVERT: A  147 ASP cc_start: 0.7360 (t0) cc_final: 0.6994 (t0)
REVERT: A  172 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8257 (tp30)
  outliers start: 23
  outliers final: 8
  residues processed: 121
  average time/residue: 1.0168
  time to fit residues: 129.9831
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  : 0.644 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 52 optimal weight:    0.1980
   chunk 66 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   overall best weight:    2.3986

-------------------------------------------------------------------------------
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 = 0.3857 r_free = 0.3857 target = 0.173196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.128231 restraints weight = 6958.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 1.90
r_work: 0.3242 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3101 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.1345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.045   6293  Z= 0.428
  Angle     :  0.610   7.795   8510  Z= 0.317
  Chirality :  0.048   0.170    963
  Planarity :  0.005   0.042   1086
  Dihedral  :  5.243  41.593    831
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 18.52 %
    Favored  : 76.70 %
  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: -0.59 (0.29), residues: 758
  helix:  0.56 (0.30), residues: 281
  sheet: -0.93 (0.52), residues: 82
  loop : -0.94 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP A 155 
 HIS   0.007   0.001   HIS J 215 
 PHE   0.018   0.002   PHE J 199 
 TYR   0.019   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  : 0.645 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8076 (mtp85) cc_final: 0.7708 (ttm-80)
REVERT: A  123 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7577 (mp0)
REVERT: A  147 ASP cc_start: 0.7528 (t0) cc_final: 0.6994 (t0)
REVERT: F  187 MET cc_start: 0.8121 (ptt) cc_final: 0.7856 (ptp)
REVERT: F  333 ARG cc_start: 0.6401 (mmm-85) cc_final: 0.5708 (mtt180)
REVERT: J  181 TRP cc_start: 0.8240 (OUTLIER) cc_final: 0.7929 (t60)
  outliers start: 33
  outliers final: 20
  residues processed: 126
  average time/residue: 1.0849
  time to fit residues: 143.9773
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  : 0.691 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
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 = 0.3926 r_free = 0.3926 target = 0.178791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.136195 restraints weight = 7062.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 1.82
r_work: 0.3289 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3152 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.1362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6293  Z= 0.270
  Angle     :  0.539   7.836   8510  Z= 0.282
  Chirality :  0.045   0.164    963
  Planarity :  0.004   0.040   1086
  Dihedral  :  5.095  42.070    831
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 20.26 %
    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 (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: -0.46 (0.29), residues: 758
  helix:  0.70 (0.30), residues: 281
  sheet: -0.87 (0.52), residues: 82
  loop : -0.89 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP F 257 
 HIS   0.004   0.001   HIS J 215 
 PHE   0.012   0.001   PHE J 199 
 TYR   0.015   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
  127 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 97
  time to evaluate  : 0.702 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8104 (mtp85) cc_final: 0.7769 (ttm-80)
REVERT: A  123 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7512 (mp0)
REVERT: A  147 ASP cc_start: 0.7495 (t0) cc_final: 0.6954 (t0)
REVERT: A  172 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8345 (tp30)
REVERT: F  187 MET cc_start: 0.8161 (ptt) cc_final: 0.7893 (ptp)
REVERT: F  312 ASP cc_start: 0.7827 (m-30) cc_final: 0.7613 (OUTLIER)
REVERT: F  333 ARG cc_start: 0.6445 (mmm-85) cc_final: 0.5742 (mtt180)
REVERT: J  181 TRP cc_start: 0.8224 (OUTLIER) cc_final: 0.7959 (t60)
  outliers start: 30
  outliers final: 18
  residues processed: 117
  average time/residue: 1.0520
  time to fit residues: 129.8307
Evaluate side-chains
  118 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
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  208 ILE
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  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 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
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:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 71 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 61 optimal weight:   10.0000
   chunk 73 optimal weight:    3.9990
   chunk 41 optimal weight:    0.0870
   chunk 29 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.7760

-------------------------------------------------------------------------------
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 = 0.4102 r_free = 0.4102 target = 0.192160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.144643 restraints weight = 6862.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 2.15
r_work: 0.3390 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.1322

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= 0.188
  Angle     :  0.508  10.003   8510  Z= 0.262
  Chirality :  0.044   0.157    963
  Planarity :  0.004   0.038   1086
  Dihedral  :  4.880  42.332    831
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  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: -0.17 (0.29), residues: 758
  helix:  0.98 (0.30), residues: 281
  sheet: -0.62 (0.52), residues: 86
  loop : -0.77 (0.31), residues: 391

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   0.009   0.001   PHE F  58 
 TYR   0.012   0.001   TYR J 207 
 ARG   0.008   0.000   ARG J  80 

*********************** 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
  142 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 109
  time to evaluate  : 0.703 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8113 (mtp85) cc_final: 0.7800 (ttm-80)
REVERT: A  123 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7545 (mp0)
REVERT: A  147 ASP cc_start: 0.7413 (t0) cc_final: 0.6940 (t0)
REVERT: F    1 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7389 (tpp)
REVERT: F  187 MET cc_start: 0.8180 (ptt) cc_final: 0.7923 (ptp)
REVERT: F  219 ASP cc_start: 0.7032 (t0) cc_final: 0.6331 (p0)
REVERT: F  244 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7220 (m-80)
REVERT: F  312 ASP cc_start: 0.7829 (m-30) cc_final: 0.7610 (OUTLIER)
REVERT: F  333 ARG cc_start: 0.6369 (mmm-85) cc_final: 0.5707 (mtt180)
REVERT: J  186 GLU cc_start: 0.6991 (pm20) cc_final: 0.6247 (tm-30)
  outliers start: 33
  outliers final: 14
  residues processed: 130
  average time/residue: 1.0130
  time to fit residues: 139.3324
Evaluate side-chains
  119 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 103
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 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  179 THR
Chi-restraints excluded: chain F residue  237 CYS
Chi-restraints excluded: chain F residue  240 LEU
Chi-restraints excluded: chain F residue  244 TYR
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:    9.9990
   chunk 36 optimal weight:    5.9990
   chunk 69 optimal weight:    0.7980
   chunk 48 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0970
   chunk 3 optimal weight:    0.0170
   overall best weight:    0.9818

-------------------------------------------------------------------------------
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 = 0.4094 r_free = 0.4094 target = 0.191291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.143368 restraints weight = 6733.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3574 rms_B_bonded: 2.21
r_work: 0.3405 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.1408

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= 0.214
  Angle     :  0.522   8.854   8510  Z= 0.270
  Chirality :  0.045   0.191    963
  Planarity :  0.004   0.036   1086
  Dihedral  :  4.645  38.882    829
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 20.84 %
    Favored  : 74.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.04 (0.30), residues: 279
  sheet: -0.68 (0.53), residues: 86
  loop : -0.77 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 155 
 HIS   0.002   0.001   HIS F  71 
 PHE   0.010   0.001   PHE J 199 
 TYR   0.013   0.001   TYR J 207 
 ARG   0.004   0.000   ARG J  80 

*********************** 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
  132 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.653 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8145 (mtp85) cc_final: 0.7819 (ttm-80)
REVERT: A  122 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.7889 (mp)
REVERT: A  123 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7510 (mp0)
REVERT: A  147 ASP cc_start: 0.7340 (t0) cc_final: 0.6912 (t0)
REVERT: A  172 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8396 (tp30)
REVERT: F    1 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7366 (tpp)
REVERT: F  187 MET cc_start: 0.8210 (ptt) cc_final: 0.7941 (ptp)
REVERT: F  244 TYR cc_start: 0.7703 (OUTLIER) cc_final: 0.7256 (m-10)
REVERT: F  312 ASP cc_start: 0.7833 (m-30) cc_final: 0.7611 (OUTLIER)
REVERT: F  333 ARG cc_start: 0.6342 (mmm-85) cc_final: 0.5679 (mtt180)
REVERT: J  186 GLU cc_start: 0.7022 (pm20) cc_final: 0.6329 (tm-30)
  outliers start: 30
  outliers final: 19
  residues processed: 119
  average time/residue: 0.9426
  time to fit residues: 119.1622
Evaluate side-chains
  125 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
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   17 THR
Chi-restraints excluded: chain F residue   85 ASP
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  160 THR
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain F residue  237 CYS
Chi-restraints excluded: chain F residue  244 TYR
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 19 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.4088 r_free = 0.4088 target = 0.190871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.144268 restraints weight = 6836.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.24
r_work: 0.3316 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3168 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.1466

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= 0.244
  Angle     :  0.525   8.448   8510  Z= 0.272
  Chirality :  0.045   0.158    963
  Planarity :  0.004   0.036   1086
  Dihedral  :  4.706  38.142    829
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 20.84 %
    Favored  : 74.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.29), residues: 758
  helix:  0.95 (0.30), residues: 279
  sheet: -0.72 (0.53), residues: 86
  loop : -0.79 (0.30), residues: 393

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   0.014   0.001   TYR J 207 
 ARG   0.002   0.000   ARG J  80 

*********************** 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
  133 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.706 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8136 (mtp85) cc_final: 0.7792 (ttm-80)
REVERT: A  113 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7192 (tp30)
REVERT: A  122 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.7908 (mp)
REVERT: A  123 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7568 (mp0)
REVERT: A  147 ASP cc_start: 0.7344 (t0) cc_final: 0.6884 (t0)
REVERT: F    1 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7381 (tpp)
REVERT: F  187 MET cc_start: 0.8202 (ptt) cc_final: 0.7933 (ptp)
REVERT: F  219 ASP cc_start: 0.7018 (t0) cc_final: 0.6353 (p0)
REVERT: F  244 TYR cc_start: 0.7718 (OUTLIER) cc_final: 0.7313 (m-10)
REVERT: F  312 ASP cc_start: 0.7826 (m-30) cc_final: 0.7603 (OUTLIER)
REVERT: F  333 ARG cc_start: 0.6327 (mmm-85) cc_final: 0.5669 (mtt180)
REVERT: J  186 GLU cc_start: 0.7075 (pm20) cc_final: 0.6416 (tm-30)
  outliers start: 29
  outliers final: 18
  residues processed: 122
  average time/residue: 1.1108
  time to fit residues: 142.7629
Evaluate side-chains
  122 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
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  162 ILE
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  237 CYS
Chi-restraints excluded: chain F residue  244 TYR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4098 r_free = 0.4098 target = 0.191852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.144248 restraints weight = 6762.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 2.22
r_work: 0.3352 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.1463

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= 0.195
  Angle     :  0.512   8.117   8510  Z= 0.265
  Chirality :  0.044   0.154    963
  Planarity :  0.004   0.035   1086
  Dihedral  :  4.599  37.470    829
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 21.13 %
    Favored  : 74.96 %
  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:  1.07 (0.30), residues: 279
  sheet: -0.67 (0.53), residues: 86
  loop : -0.72 (0.31), residues: 393

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   0.013   0.001   TYR A  46 
 ARG   0.002   0.000   ARG J  80 

*********************** 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
  133 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.717 
Fit side-chains
REVERT: A  111 ARG cc_start: 0.8039 (mtp85) cc_final: 0.7708 (ttm-80)
REVERT: A  113 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7149 (tp30)
REVERT: A  122 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.7868 (mp)
REVERT: A  123 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7599 (mp0)
REVERT: A  147 ASP cc_start: 0.7302 (t0) cc_final: 0.6829 (t0)
REVERT: A  172 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8393 (tp30)
REVERT: F    1 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7393 (tpp)
REVERT: F  187 MET cc_start: 0.8159 (ptt) cc_final: 0.7890 (ptp)
REVERT: F  219 ASP cc_start: 0.7058 (t0) cc_final: 0.6352 (p0)
REVERT: F  244 TYR cc_start: 0.7700 (OUTLIER) cc_final: 0.7229 (m-80)
REVERT: F  333 ARG cc_start: 0.6282 (mmm-85) cc_final: 0.5677 (mtt180)
REVERT: J  186 GLU cc_start: 0.7111 (pm20) cc_final: 0.6531 (tm-30)
  outliers start: 27
  outliers final: 14
  residues processed: 123
  average time/residue: 0.9577
  time to fit residues: 125.1608
Evaluate side-chains
  118 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
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  160 THR
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain F residue  237 CYS
Chi-restraints excluded: chain F residue  244 TYR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 41 optimal weight:    0.0070
   chunk 44 optimal weight:    6.9990
   chunk 58 optimal weight:   10.0000
   chunk 62 optimal weight:    0.0050
   chunk 57 optimal weight:    0.2980
   chunk 24 optimal weight:    0.0170
   chunk 38 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.2450

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS
A 255 ASN
J 116 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.195793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.157321 restraints weight = 6765.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 2.62
r_work: 0.3456 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.1771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6293  Z= 0.133
  Angle     :  0.484   8.006   8510  Z= 0.251
  Chirality :  0.043   0.158    963
  Planarity :  0.004   0.036   1086
  Dihedral  :  4.261  36.038    829
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 22.87 %
    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:  0.21 (0.30), residues: 758
  helix:  1.30 (0.30), residues: 282
  sheet: -0.47 (0.52), residues: 88
  loop : -0.53 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP F 257 
 HIS   0.002   0.000   HIS A 114 
 PHE   0.009   0.001   PHE F  58 
 TYR   0.008   0.001   TYR F 207 
 ARG   0.003   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
  130 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.733 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.8223 (tt0) cc_final: 0.7983 (tt0)
REVERT: A  147 ASP cc_start: 0.7051 (t0) cc_final: 0.6702 (t0)
REVERT: A  172 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8038 (tp30)
REVERT: F    1 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7373 (tpp)
REVERT: F  182 VAL cc_start: 0.8473 (t) cc_final: 0.8207 (p)
REVERT: F  244 TYR cc_start: 0.7579 (OUTLIER) cc_final: 0.7124 (m-80)
REVERT: F  333 ARG cc_start: 0.6172 (mmm-85) cc_final: 0.5572 (mtt180)
REVERT: J  186 GLU cc_start: 0.7112 (pm20) cc_final: 0.6663 (tm-30)
  outliers start: 18
  outliers final: 11
  residues processed: 124
  average time/residue: 0.9433
  time to fit residues: 124.3460
Evaluate side-chains
  117 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ILE
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  179 THR
Chi-restraints excluded: chain F residue  237 CYS
Chi-restraints excluded: chain F residue  244 TYR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 36 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 31 optimal weight:    0.3980
   chunk 60 optimal weight:    0.8980
   chunk 1 optimal weight:    0.1980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS
F 262 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.194564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.146180 restraints weight = 6848.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 2.08
r_work: 0.3431 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3288 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.1656

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= 0.169
  Angle     :  0.506   8.906   8510  Z= 0.260
  Chirality :  0.043   0.173    963
  Planarity :  0.004   0.044   1086
  Dihedral  :  4.358  37.939    829
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 23.88 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.30), residues: 758
  helix:  1.33 (0.30), residues: 281
  sheet: -0.50 (0.52), residues: 88
  loop : -0.54 (0.32), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP F 327 
 HIS   0.002   0.000   HIS F  71 
 PHE   0.009   0.001   PHE F  58 
 TYR   0.010   0.001   TYR F 207 
 ARG   0.011   0.000   ARG A 111 

********************** 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
  125 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.723 
Fit side-chains
REVERT: A   28 GLU cc_start: 0.8476 (tt0) cc_final: 0.8207 (tt0)
REVERT: A  147 ASP cc_start: 0.7096 (t0) cc_final: 0.6635 (t0)
REVERT: A  172 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8292 (tp30)
REVERT: F    1 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7375 (tpp)
REVERT: F  187 MET cc_start: 0.8083 (ptt) cc_final: 0.7828 (ptp)
REVERT: F  217 ILE cc_start: 0.7190 (mp) cc_final: 0.6900 (tp)
REVERT: F  244 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.7202 (m-80)
REVERT: F  271 TYR cc_start: 0.8030 (m-80) cc_final: 0.7762 (m-80)
REVERT: J  186 GLU cc_start: 0.7158 (pm20) cc_final: 0.6661 (tm-30)
  outliers start: 20
  outliers final: 13
  residues processed: 118
  average time/residue: 0.9335
  time to fit residues: 117.1679
Evaluate side-chains
  122 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
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 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  123 VAL
Chi-restraints excluded: chain F residue  179 THR
Chi-restraints excluded: chain F residue  237 CYS
Chi-restraints excluded: chain F residue  244 TYR
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=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:    0.0770
   chunk 16 optimal weight:    2.9990
   chunk 38 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 60 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9980
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS
F 262 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.194820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.149096 restraints weight = 6881.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.11
r_work: 0.3367 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6293  Z= 0.163
  Angle     :  0.506   8.889   8510  Z= 0.259
  Chirality :  0.043   0.180    963
  Planarity :  0.004   0.036   1086
  Dihedral  :  4.452  44.035    829
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 24.17 %
    Favored  : 73.08 %
  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:  0.31 (0.30), residues: 758
  helix:  1.37 (0.30), residues: 281
  sheet: -0.29 (0.51), residues: 98
  loop : -0.50 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP F 327 
 HIS   0.002   0.000   HIS J 228 
 PHE   0.008   0.001   PHE F  58 
 TYR   0.009   0.001   TYR J 207 
 ARG   0.009   0.000   ARG A 111 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5217.69 seconds
wall clock time: 89 minutes 25.08 seconds (5365.08 seconds total)