Starting phenix.real_space_refine
on Tue Feb  3 12:49:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9tbf_55769/02_2026/9tbf_55769.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9tbf_55769/02_2026/9tbf_55769.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9tbf_55769/02_2026/9tbf_55769.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9tbf_55769/02_2026/9tbf_55769.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9tbf_55769/02_2026/9tbf_55769.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9tbf_55769/02_2026/9tbf_55769.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
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      10      5.16       5
     C    1630      2.51       5
     N     351      2.21       5
     O     418      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2409
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2172
          Classifications: {'peptide': 274}
          Link IDs: {'PTRANS': 12, 'TRANS': 261}
    Chain: "A"
      Number of atoms: 237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 237
          Unusual residues: {'LFA': 10, 'LMT': 3, 'RET': 1}
          Classifications: {'undetermined': 14, 'water': 13}
          Link IDs: {None: 26}
          Unresolved non-hydrogen bonds: 102
          Unresolved non-hydrogen angles: 102
          Unresolved non-hydrogen dihedrals: 102
          Planarities with less than four sites: {'RET:plan-5': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 0.77, per 1000 atoms: 0.32
  Number of scatterers: 2409
  At special positions: 0
  Unit cell: (49.368, 58.08, 84.216, 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      10     16.00
     O     418      8.00
     N     351      7.00
     C    1630      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.23
  Conformation dependent library (CDL) restraints added in 82.2 milliseconds
  

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  510

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 1 sheets defined
      75.5% alpha, 2.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 8
      removed outlier: 3.711A  pdb=" N   PHE A   7 " --> pdb=" O   ILE A   4 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LEU A   8 " --> pdb=" O   GLU A   5 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 4 through 8'
    Processing helix  chain 'A' and resid 11 through 28
      removed outlier: 4.116A  pdb=" N   ILE A  18 " --> pdb=" O   GLN A  14 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   THR A  26 " --> pdb=" O   PHE A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 39
      removed outlier: 4.207A  pdb=" N   VAL A  34 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 47
    Processing helix  chain 'A' and resid 48 through 75
      removed outlier: 3.722A  pdb=" N   MET A  58 " --> pdb=" O   SER A  54 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   VAL A  59 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ALA A  61 " --> pdb=" O   VAL A  57 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU A  63 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   GLU A  64 " --> pdb=" O   SER A  60 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU A  68 " --> pdb=" O   GLU A  64 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   TRP A  69 " --> pdb=" O   LEU A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 106
      removed outlier: 4.221A  pdb=" N   TYR A  99 " --> pdb=" O   ASN A  95 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   LEU A 103 " --> pdb=" O   TYR A  99 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   ILE A 104 " --> pdb=" O   MET A 100 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ASP A 105 " --> pdb=" O   ASN A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 117
      removed outlier: 3.951A  pdb=" N   ALA A 110 " --> pdb=" O   VAL A 106 " (cutoff:3.500A)
      removed outlier: 5.264A  pdb=" N   GLN A 112 " --> pdb=" O   MET A 108 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   LEU A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL A 116 " --> pdb=" O   GLN A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 135
      removed outlier: 3.820A  pdb=" N   ARG A 127 " --> pdb=" O   GLU A 123 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU A 131 " --> pdb=" O   ARG A 127 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ILE A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 143
    Processing helix  chain 'A' and resid 144 through 147
    Processing helix  chain 'A' and resid 148 through 154
      removed outlier: 3.618A  pdb=" N   GLY A 154 " --> pdb=" O   PRO A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 183
      removed outlier: 4.061A  pdb=" N   PHE A 164 " --> pdb=" O   GLY A 160 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   TRP A 165 " --> pdb=" O   ALA A 161 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   SER A 171 " --> pdb=" O   TRP A 167 " (cutoff:3.500A)
      removed outlier: 4.675A  pdb=" N   PHE A 174 " --> pdb=" O   ILE A 170 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   TRP A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 210
      removed outlier: 3.620A  pdb=" N   LEU A 201 " --> pdb=" O   VAL A 197 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   LYS A 202 " --> pdb=" O   ARG A 198 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   PHE A 203 " --> pdb=" O   SER A 199 " (cutoff:3.500A)
      removed outlier: 4.808A  pdb=" N   TRP A 206 " --> pdb=" O   LYS A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 220
      removed outlier: 3.872A  pdb=" N   PHE A 217 " --> pdb=" O   SER A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 225
      removed outlier: 3.680A  pdb=" N   PHE A 224 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 237
      removed outlier: 4.800A  pdb=" N   VAL A 233 " --> pdb=" O   ASP A 229 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ARG A 234 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 261
    Processing helix  chain 'A' and resid 266 through 271
    Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79
      removed outlier: 3.605A  pdb=" N   SER A  84 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)

    104 hydrogen bonds defined for protein.
    306 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.31

  Time building geometry restraints manager: 0.28 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 335
        1.30 -     1.43: 714
        1.43 -     1.55: 1389
        1.55 -     1.68: 0
        1.68 -     1.80: 18
  Bond restraints: 2456
  Sorted by residual:
  bond pdb=" CA  TYR A  99 "
       pdb=" C   TYR A  99 "
    ideal  model  delta    sigma   weight residual
    1.522  1.454  0.068 1.39e-02 5.18e+03 2.38e+01
  bond pdb=" CA  TYR A 238 "
       pdb=" C   TYR A 238 "
    ideal  model  delta    sigma   weight residual
    1.522  1.465  0.056 1.31e-02 5.83e+03 1.85e+01
  bond pdb=" C   ARG A 234 "
       pdb=" O   ARG A 234 "
    ideal  model  delta    sigma   weight residual
    1.236  1.179  0.057 1.32e-02 5.74e+03 1.85e+01
  bond pdb=" C   TYR A 219 "
       pdb=" O   TYR A 219 "
    ideal  model  delta    sigma   weight residual
    1.234  1.180  0.055 1.35e-02 5.49e+03 1.63e+01
  bond pdb=" C8  RET A 314 "
       pdb=" C9  RET A 314 "
    ideal  model  delta    sigma   weight residual
    1.450  1.373  0.077 2.00e-02 2.50e+03 1.48e+01
  ... (remaining 2451 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.71: 3212
        2.71 -     5.43: 73
        5.43 -     8.14: 17
        8.14 -    10.85: 3
       10.85 -    13.56: 2
  Bond angle restraints: 3307
  Sorted by residual:
  angle pdb=" N   TYR A 238 "
        pdb=" CA  TYR A 238 "
        pdb=" C   TYR A 238 "
      ideal   model   delta    sigma   weight residual
     113.30  102.84   10.46 1.34e+00 5.57e-01 6.09e+01
  angle pdb=" N   TYR A 219 "
        pdb=" CA  TYR A 219 "
        pdb=" C   TYR A 219 "
      ideal   model   delta    sigma   weight residual
     112.68  103.02    9.66 1.33e+00 5.65e-01 5.28e+01
  angle pdb=" C   TYR A 219 "
        pdb=" CA  TYR A 219 "
        pdb=" CB  TYR A 219 "
      ideal   model   delta    sigma   weight residual
     110.24  121.15  -10.91 1.67e+00 3.59e-01 4.27e+01
  angle pdb=" C   ARG A 234 "
        pdb=" CA  ARG A 234 "
        pdb=" CB  ARG A 234 "
      ideal   model   delta    sigma   weight residual
     109.99   96.43   13.56 2.09e+00 2.29e-01 4.21e+01
  angle pdb=" CA  TYR A 238 "
        pdb=" CB  TYR A 238 "
        pdb=" CG  TYR A 238 "
      ideal   model   delta    sigma   weight residual
     113.90  124.62  -10.72 1.80e+00 3.09e-01 3.55e+01
  ... (remaining 3302 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.33: 1407
       25.33 -    50.65: 114
       50.65 -    75.97: 6
       75.97 -   101.29: 3
      101.29 -   126.62: 1
  Dihedral angle restraints: 1531
    sinusoidal: 736
      harmonic: 795
  Sorted by residual:
  dihedral pdb=" C   ARG A 234 "
           pdb=" N   ARG A 234 "
           pdb=" CA  ARG A 234 "
           pdb=" CB  ARG A 234 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.16  -13.44     0      2.50e+00 1.60e-01 2.89e+01
  dihedral pdb=" CA  SER A  25 "
           pdb=" C   SER A  25 "
           pdb=" N   THR A  26 "
           pdb=" CA  THR A  26 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.89   23.11     0      5.00e+00 4.00e-02 2.14e+01
  dihedral pdb=" C1  RET A 314 "
           pdb=" C2  RET A 314 "
           pdb=" C3  RET A 314 "
           pdb=" C4  RET A 314 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.54   64.08 -126.62     1      3.00e+01 1.11e-03 1.70e+01
  ... (remaining 1528 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 281
       0.052 -    0.104: 80
       0.104 -    0.155: 5
       0.155 -    0.207: 1
       0.207 -    0.258: 1
  Chirality restraints: 368
  Sorted by residual:
  chirality pdb=" CA  TYR A 219 "
            pdb=" N   TYR A 219 "
            pdb=" C   TYR A 219 "
            pdb=" CB  TYR A 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" CA  GLN A 146 "
            pdb=" N   GLN A 146 "
            pdb=" C   GLN A 146 "
            pdb=" CB  GLN A 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 6.89e-01
  chirality pdb=" CA  VAL A 155 "
            pdb=" N   VAL A 155 "
            pdb=" C   VAL A 155 "
            pdb=" CB  VAL A 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.54e-01
  ... (remaining 365 not shown)

  Planarity restraints: 386
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C6  RET A 314 "    0.157 2.00e-02 2.50e+03   1.55e-01 2.41e+02
        pdb=" C7  RET A 314 "   -0.175 2.00e-02 2.50e+03
        pdb=" C8  RET A 314 "   -0.135 2.00e-02 2.50e+03
        pdb=" C9  RET A 314 "    0.152 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 RET A 314 "   -0.159 2.00e-02 2.50e+03   9.69e-02 1.17e+02
        pdb=" C11 RET A 314 "    0.118 2.00e-02 2.50e+03
        pdb=" C19 RET A 314 "   -0.016 2.00e-02 2.50e+03
        pdb=" C8  RET A 314 "    0.083 2.00e-02 2.50e+03
        pdb=" C9  RET A 314 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C12 RET A 314 "    0.048 2.00e-02 2.50e+03   4.72e-02 2.78e+01
        pdb=" C13 RET A 314 "   -0.022 2.00e-02 2.50e+03
        pdb=" C14 RET A 314 "   -0.070 2.00e-02 2.50e+03
        pdb=" C15 RET A 314 "    0.057 2.00e-02 2.50e+03
        pdb=" C20 RET A 314 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 383 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 812
        2.85 -     3.36: 2078
        3.36 -     3.87: 3825
        3.87 -     4.39: 4949
        4.39 -     4.90: 8301
  Nonbonded interactions: 19965
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 149 "
            pdb=" O   HOH A 401 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" ND2 ASN A  95 "
            pdb=" O   HOH A 401 "
     model   vdw
     2.434 3.120
  nonbonded pdb=" N   GLY A 230 "
            pdb=" N   VAL A 231 "
     model   vdw
     2.491 2.560
  nonbonded pdb=" N   TYR A 238 "
            pdb=" N   THR A 239 "
     model   vdw
     2.503 2.560
  nonbonded pdb=" O5' LMT A 311 "
            pdb=" O6' LMT A 311 "
     model   vdw
     2.543 2.432
  ... (remaining 19960 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.810
  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:          0.050
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     4.400
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
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      :  0.006   0.077   2457  Z= 0.383
  Angle     :  1.070  13.565   3307  Z= 0.661
  Chirality :  0.046   0.258    368
  Planarity :  0.012   0.155    386
  Dihedral  : 16.583 126.618   1021
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 22.97 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.78 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.02 (0.39), residues: 272
  helix: -3.65 (0.25), residues: 207
  sheet:  None (None), residues: 0
  loop : -1.08 (0.68), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  98 
 TYR   0.029   0.003   TYR A 238 
 PHE   0.010   0.001   PHE A 119 
 TRP   0.012   0.001   TRP A  13 
 HIS   0.001   0.001   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00635 ( 2456)
  covalent geometry    : angle       1.06953 ( 3307)
  hydrogen bonds       : bond        0.24730 (  104)
  hydrogen bonds       : angle       8.64120 (  306)
  Misc. bond           : bond        0.02392 (    1)

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

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

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 28
  time to evaluate  : 0.047 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 GLN cc_start: 0.8554 (mt0) cc_final: 0.8274 (mt0)
REVERT: A  162 GLU cc_start: 0.7668 (tt0) cc_final: 0.6883 (pm20)
REVERT: A  184 ASN cc_start: 0.8710 (m-40) cc_final: 0.8418 (m-40)
REVERT: A  187 ARG cc_start: 0.7655 (mtp180) cc_final: 0.6825 (mpt180)
REVERT: A  234 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7658 (ttm170)
REVERT: A  235 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7134 (mp10)
  outliers start: 10
  outliers final: 7
  residues processed: 35
  average time/residue: 0.0497
  time to fit residues: 2.0397
Evaluate side-chains
  36 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 27
  time to evaluate  : 0.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   95 ASN
Chi-restraints excluded: chain A residue   99 TYR
Chi-restraints excluded: chain A residue  186 VAL
Chi-restraints excluded: chain A residue  219 TYR
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  234 ARG
Chi-restraints excluded: chain A residue  235 GLN
Chi-restraints excluded: chain A residue  246 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 13 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0980
   chunk 8 optimal weight:    0.4980
   chunk 16 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0980
   overall best weight:    0.4380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.157558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.148459 restraints weight = 2849.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 1.01
r_work: 0.3479 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.3372 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.0816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2457  Z= 0.134
  Angle     :  0.632   7.132   3307  Z= 0.313
  Chirality :  0.037   0.127    368
  Planarity :  0.004   0.034    386
  Dihedral  : 13.079 107.064    583
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 22.97 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.11 (0.42), residues: 272
  helix: -2.89 (0.29), residues: 209
  sheet:  None (None), residues: 0
  loop : -1.08 (0.70), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  98 
 TYR   0.011   0.001   TYR A  99 
 PHE   0.011   0.001   PHE A 175 
 TRP   0.010   0.001   TRP A  13 
 HIS   0.001   0.000   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 2456)
  covalent geometry    : angle       0.63182 ( 3307)
  hydrogen bonds       : bond        0.04421 (  104)
  hydrogen bonds       : angle       4.86656 (  306)
  Misc. bond           : bond        0.00034 (    1)

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

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

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.077 
Fit side-chains
REVERT: A  162 GLU cc_start: 0.7798 (tt0) cc_final: 0.7160 (pm20)
REVERT: A  184 ASN cc_start: 0.8753 (m-40) cc_final: 0.8549 (m-40)
REVERT: A  187 ARG cc_start: 0.7850 (mtp180) cc_final: 0.6915 (mpt180)
  outliers start: 7
  outliers final: 3
  residues processed: 31
  average time/residue: 0.0821
  time to fit residues: 2.9808
Evaluate side-chains
  29 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue  229 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0170
   chunk 19 optimal weight:    0.2980
   chunk 4 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.4818

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.134510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.125119 restraints weight = 3069.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3733 rms_B_bonded: 0.88
r_work: 0.3608 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3497 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.1127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2457  Z= 0.131
  Angle     :  0.600   6.877   3307  Z= 0.295
  Chirality :  0.037   0.123    368
  Planarity :  0.004   0.034    386
  Dihedral  : 12.366 108.280    561
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 22.07 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.26 (0.45), residues: 272
  helix: -2.25 (0.32), residues: 208
  sheet:  None (None), residues: 0
  loop : -0.92 (0.70), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  98 
 TYR   0.011   0.001   TYR A 143 
 PHE   0.009   0.001   PHE A 175 
 TRP   0.008   0.001   TRP A  13 
 HIS   0.001   0.001   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 2456)
  covalent geometry    : angle       0.60038 ( 3307)
  hydrogen bonds       : bond        0.03647 (  104)
  hydrogen bonds       : angle       4.43352 (  306)
  Misc. bond           : bond        0.00039 (    1)

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

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

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 26
  time to evaluate  : 0.077 
Fit side-chains
REVERT: A  162 GLU cc_start: 0.7798 (tt0) cc_final: 0.7278 (pm20)
REVERT: A  187 ARG cc_start: 0.7994 (mtp180) cc_final: 0.7075 (mpt180)
REVERT: A  235 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.6618 (mp10)
  outliers start: 9
  outliers final: 6
  residues processed: 32
  average time/residue: 0.0679
  time to fit residues: 2.5654
Evaluate side-chains
  32 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   58 MET
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  235 GLN
Chi-restraints excluded: chain A residue  238 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 17 optimal weight:    0.1980
   chunk 10 optimal weight:    0.2980
   chunk 12 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0010
   chunk 22 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0370
   overall best weight:    0.2264

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.137994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.129167 restraints weight = 2984.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3787 rms_B_bonded: 0.80
r_work: 0.3671 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3566 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   2457  Z= 0.094
  Angle     :  0.564   6.968   3307  Z= 0.273
  Chirality :  0.035   0.124    368
  Planarity :  0.003   0.031    386
  Dihedral  : 11.939 100.083    561
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 22.52 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.65 (0.48), residues: 272
  helix: -1.78 (0.34), residues: 210
  sheet:  None (None), residues: 0
  loop : -0.77 (0.74), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  98 
 TYR   0.008   0.001   TYR A 143 
 PHE   0.007   0.001   PHE A 175 
 TRP   0.007   0.001   TRP A  13 
 HIS   0.000   0.000   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 ( 2456)
  covalent geometry    : angle       0.56360 ( 3307)
  hydrogen bonds       : bond        0.03146 (  104)
  hydrogen bonds       : angle       4.09416 (  306)
  Misc. bond           : bond        0.00009 (    1)

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

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

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.082 
Fit side-chains
REVERT: A  162 GLU cc_start: 0.7643 (tt0) cc_final: 0.7250 (pm20)
REVERT: A  187 ARG cc_start: 0.7907 (mtp180) cc_final: 0.7010 (mpt180)
REVERT: A  235 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.6638 (mp10)
  outliers start: 7
  outliers final: 4
  residues processed: 29
  average time/residue: 0.0788
  time to fit residues: 2.7048
Evaluate side-chains
  30 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 25
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  235 GLN
Chi-restraints excluded: chain A residue  238 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 24 optimal weight:    0.0970
   chunk 10 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 13 optimal weight:    0.3980
   chunk 19 optimal weight:    0.0470
   overall best weight:    0.3476

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.137214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.128047 restraints weight = 2991.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 0.87
r_work: 0.3599 rms_B_bonded: 1.85 restraints_weight: 0.5000
r_work: 0.3491 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2457  Z= 0.107
  Angle     :  0.562   6.946   3307  Z= 0.271
  Chirality :  0.036   0.123    368
  Planarity :  0.003   0.032    386
  Dihedral  : 11.910 100.902    561
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 22.07 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.19 (0.49), residues: 272
  helix: -1.44 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -0.71 (0.74), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  98 
 TYR   0.010   0.001   TYR A 143 
 PHE   0.008   0.001   PHE A 175 
 TRP   0.007   0.001   TRP A  13 
 HIS   0.001   0.000   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 2456)
  covalent geometry    : angle       0.56228 ( 3307)
  hydrogen bonds       : bond        0.03130 (  104)
  hydrogen bonds       : angle       4.00188 (  306)
  Misc. bond           : bond        0.00027 (    1)

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

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

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 26
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A  162 GLU cc_start: 0.7609 (tt0) cc_final: 0.7192 (pm20)
REVERT: A  187 ARG cc_start: 0.7953 (mtp180) cc_final: 0.7020 (mpt180)
REVERT: A  235 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.6552 (mp10)
  outliers start: 7
  outliers final: 4
  residues processed: 31
  average time/residue: 0.0921
  time to fit residues: 3.2818
Evaluate side-chains
  31 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 26
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  235 GLN
Chi-restraints excluded: chain A residue  238 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 1 optimal weight:    0.2980
   chunk 0 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0970
   chunk 26 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0980
   chunk 18 optimal weight:    0.4980
   overall best weight:    0.3378

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.137177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.128278 restraints weight = 2985.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3783 rms_B_bonded: 0.81
r_work: 0.3665 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3556 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.1633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2457  Z= 0.103
  Angle     :  0.558   7.120   3307  Z= 0.267
  Chirality :  0.036   0.123    368
  Planarity :  0.003   0.031    386
  Dihedral  : 11.712  95.999    561
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 22.52 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.78 (0.51), residues: 272
  helix: -1.14 (0.37), residues: 203
  sheet:  None (None), residues: 0
  loop : -0.64 (0.72), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  98 
 TYR   0.010   0.001   TYR A 143 
 PHE   0.007   0.001   PHE A 175 
 TRP   0.006   0.001   TRP A  13 
 HIS   0.001   0.000   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 2456)
  covalent geometry    : angle       0.55813 ( 3307)
  hydrogen bonds       : bond        0.03078 (  104)
  hydrogen bonds       : angle       3.93545 (  306)
  Misc. bond           : bond        0.00026 (    1)

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

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

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.054 
Fit side-chains
REVERT: A  162 GLU cc_start: 0.7609 (tt0) cc_final: 0.7214 (pm20)
REVERT: A  187 ARG cc_start: 0.7969 (mtp180) cc_final: 0.7037 (mpt180)
REVERT: A  235 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.6493 (mp10)
  outliers start: 7
  outliers final: 4
  residues processed: 31
  average time/residue: 0.0604
  time to fit residues: 2.2015
Evaluate side-chains
  32 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 27
  time to evaluate  : 0.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 THR
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  235 GLN
Chi-restraints excluded: chain A residue  238 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0060
   chunk 0 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 22 optimal weight:    0.1980
   chunk 11 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.4196

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.136430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.127280 restraints weight = 3037.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 0.84
r_work: 0.3646 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3535 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2457  Z= 0.118
  Angle     :  0.564   7.167   3307  Z= 0.273
  Chirality :  0.036   0.123    368
  Planarity :  0.003   0.032    386
  Dihedral  : 10.489  88.258    561
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 22.52 %
    Favored  : 73.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.63 (0.51), residues: 272
  helix: -1.01 (0.37), residues: 203
  sheet:  None (None), residues: 0
  loop : -0.70 (0.71), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  98 
 TYR   0.012   0.001   TYR A 143 
 PHE   0.008   0.001   PHE A 175 
 TRP   0.006   0.001   TRP A  78 
 HIS   0.001   0.001   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 2456)
  covalent geometry    : angle       0.56425 ( 3307)
  hydrogen bonds       : bond        0.03175 (  104)
  hydrogen bonds       : angle       3.98903 (  306)
  Misc. bond           : bond        0.00029 (    1)

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

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

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.076 
Fit side-chains
REVERT: A  162 GLU cc_start: 0.7618 (tt0) cc_final: 0.7200 (pm20)
REVERT: A  187 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7031 (mpt180)
REVERT: A  235 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.6498 (mp10)
  outliers start: 8
  outliers final: 3
  residues processed: 30
  average time/residue: 0.0777
  time to fit residues: 2.7444
Evaluate side-chains
  28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 24
  time to evaluate  : 0.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 SER
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  235 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.7984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.133205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.124313 restraints weight = 3035.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 0.80
r_work: 0.3518 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3411 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2457  Z= 0.183
  Angle     :  0.608   7.468   3307  Z= 0.297
  Chirality :  0.039   0.122    368
  Planarity :  0.004   0.036    386
  Dihedral  : 10.669  84.999    561
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 21.17 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.82 (0.50), residues: 272
  helix: -1.20 (0.36), residues: 204
  sheet:  None (None), residues: 0
  loop : -0.55 (0.72), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  98 
 TYR   0.016   0.002   TYR A 143 
 PHE   0.011   0.001   PHE A 175 
 TRP   0.007   0.001   TRP A  78 
 HIS   0.001   0.001   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 2456)
  covalent geometry    : angle       0.60773 ( 3307)
  hydrogen bonds       : bond        0.03654 (  104)
  hydrogen bonds       : angle       4.26479 (  306)
  Misc. bond           : bond        0.00059 (    1)

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

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

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 22
  time to evaluate  : 0.049 
Fit side-chains
REVERT: A  162 GLU cc_start: 0.7627 (tt0) cc_final: 0.7170 (pm20)
REVERT: A  187 ARG cc_start: 0.8041 (mtp180) cc_final: 0.7084 (mpt180)
REVERT: A  235 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.6619 (mp10)
  outliers start: 9
  outliers final: 5
  residues processed: 28
  average time/residue: 0.0664
  time to fit residues: 2.1547
Evaluate side-chains
  28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 22
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   60 SER
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  235 GLN
Chi-restraints excluded: chain A residue  238 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 8 optimal weight:    0.0670
   chunk 7 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0050
   chunk 21 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0010
   chunk 1 optimal weight:    0.0980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.1538

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.138336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.129454 restraints weight = 3011.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3756 rms_B_bonded: 0.82
r_work: 0.3644 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3534 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.1898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   2457  Z= 0.093
  Angle     :  0.541   6.995   3307  Z= 0.265
  Chirality :  0.035   0.123    368
  Planarity :  0.004   0.031    386
  Dihedral  :  9.793  77.201    561
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 22.97 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.51), residues: 272
  helix: -0.86 (0.38), residues: 204
  sheet:  None (None), residues: 0
  loop : -0.43 (0.73), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 259 
 TYR   0.009   0.001   TYR A 143 
 PHE   0.006   0.001   PHE A 164 
 TRP   0.008   0.001   TRP A  13 
 HIS   0.000   0.000   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 2456)
  covalent geometry    : angle       0.54082 ( 3307)
  hydrogen bonds       : bond        0.03025 (  104)
  hydrogen bonds       : angle       3.93071 (  306)
  Misc. bond           : bond        0.00031 (    1)

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

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

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.055 
Fit side-chains
REVERT: A  162 GLU cc_start: 0.7536 (tt0) cc_final: 0.7179 (pm20)
REVERT: A  187 ARG cc_start: 0.7965 (mtp180) cc_final: 0.7049 (mpt180)
REVERT: A  235 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.6546 (mp10)
  outliers start: 4
  outliers final: 3
  residues processed: 26
  average time/residue: 0.0906
  time to fit residues: 2.7546
Evaluate side-chains
  27 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  235 GLN
Chi-restraints excluded: chain A residue  238 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 26 optimal weight:    0.4980
   chunk 24 optimal weight:    3.9990
   chunk 25 optimal weight:    0.5980
   chunk 17 optimal weight:    0.2980
   chunk 6 optimal weight:    0.9990
   chunk 14 optimal weight:    0.2980
   chunk 4 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.4580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.150453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.140465 restraints weight = 3081.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 1.14
r_work: 0.3405 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2457  Z= 0.124
  Angle     :  0.558   7.253   3307  Z= 0.273
  Chirality :  0.036   0.122    368
  Planarity :  0.003   0.033    386
  Dihedral  :  9.917  80.479    561
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 22.52 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.51), residues: 272
  helix: -0.81 (0.38), residues: 201
  sheet:  None (None), residues: 0
  loop : -0.58 (0.71), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  98 
 TYR   0.012   0.001   TYR A 143 
 PHE   0.008   0.001   PHE A 175 
 TRP   0.007   0.001   TRP A  13 
 HIS   0.001   0.001   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 2456)
  covalent geometry    : angle       0.55813 ( 3307)
  hydrogen bonds       : bond        0.03196 (  104)
  hydrogen bonds       : angle       3.97635 (  306)
  Misc. bond           : bond        0.00034 (    1)

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

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

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  544 Ramachandran restraints generated.
    272 Oldfield, 0 Emsley, 272 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.048 
Fit side-chains
REVERT: A  162 GLU cc_start: 0.7479 (tt0) cc_final: 0.7032 (pm20)
REVERT: A  187 ARG cc_start: 0.7901 (mtp180) cc_final: 0.6848 (mpt180)
REVERT: A  235 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.6336 (mp10)
  outliers start: 5
  outliers final: 4
  residues processed: 27
  average time/residue: 0.0659
  time to fit residues: 2.1565
Evaluate side-chains
  28 residues out of total 222 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 23
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 SER
Chi-restraints excluded: chain A residue   73 ASN
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  235 GLN
Chi-restraints excluded: chain A residue  238 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 27
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 19 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0970
   chunk 11 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0020
   chunk 12 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.3586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.151178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.141266 restraints weight = 3051.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.11
r_work: 0.3413 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3301 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2457  Z= 0.110
  Angle     :  0.550   7.116   3307  Z= 0.269
  Chirality :  0.036   0.122    368
  Planarity :  0.003   0.032    386
  Dihedral  :  9.815  80.889    561
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 22.97 %
    Favored  : 74.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.21 (0.51), residues: 272
  helix: -0.74 (0.38), residues: 202
  sheet:  None (None), residues: 0
  loop : -0.40 (0.71), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  98 
 TYR   0.011   0.001   TYR A 143 
 PHE   0.007   0.001   PHE A 164 
 TRP   0.007   0.001   TRP A  13 
 HIS   0.001   0.000   HIS A  20 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 2456)
  covalent geometry    : angle       0.54960 ( 3307)
  hydrogen bonds       : bond        0.03095 (  104)
  hydrogen bonds       : angle       3.91265 (  306)
  Misc. bond           : bond        0.00030 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 751.84 seconds
wall clock time: 13 minutes 33.91 seconds (813.91 seconds total)