Starting phenix.real_space_refine
on Thu Jul 24 08:46:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7f3t_31440/07_2025/7f3t_31440.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7f3t_31440/07_2025/7f3t_31440.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7f3t_31440/07_2025/7f3t_31440.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7f3t_31440/07_2025/7f3t_31440.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7f3t_31440/07_2025/7f3t_31440.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7f3t_31440/07_2025/7f3t_31440.cif"
  }
  resolution = 3.69
  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=   0.003 sd=   0.107
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: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      34      5.16       5
     C    3682      2.51       5
     N     934      2.21       5
     O     976      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5632
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2768
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2768
          Classifications: {'peptide': 330}
          Link IDs: {'PTRANS': 8, 'TRANS': 321}
    Chain: "A"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 48
          Unusual residues: {'COA': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.90, per 1000 atoms: 0.87
  Number of scatterers: 5632
  At special positions: 0
  Unit cell: (86.67, 118.77, 93.09, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      34     16.00
     P       6     15.00
     O     976      8.00
     N     934      7.00
     C    3682      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: 1.78
  Conformation dependent library (CDL) restraints added in 667.8 milliseconds
  

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1252

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 0 sheets defined
      85.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 69
      removed outlier: 3.558A  pdb=" N   CYS A  12 " --> pdb=" O   PRO A   8 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   THR A  29 " --> pdb=" O   ASN A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 99
      removed outlier: 5.171A  pdb=" N   ALA A  79 " --> pdb=" O   GLU A  75 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ALA A  80 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   GLU A  89 " --> pdb=" O   ASN A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 112
    Processing helix  chain 'A' and resid 123 through 154
      removed outlier: 4.440A  pdb=" N   TYR A 129 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ASP A 131 " --> pdb=" O   PHE A 127 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   GLU A 132 " --> pdb=" O   ALA A 128 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU A 154 " --> pdb=" O   THR A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 186
      removed outlier: 3.954A  pdb=" N   CYS A 173 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ASN A 184 " --> pdb=" O   SER A 180 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY A 186 " --> pdb=" O   LEU A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 209
      removed outlier: 4.289A  pdb=" N   HIS A 197 " --> pdb=" O   TRP A 193 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   THR A 209 " --> pdb=" O   GLY A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 253
      removed outlier: 3.808A  pdb=" N   TYR A 239 " --> pdb=" O   PHE A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 299
      removed outlier: 3.791A  pdb=" N   PHE A 264 " --> pdb=" O   THR A 260 " (cutoff:3.500A)
      Proline residue:  A 277  - end of helix
      removed outlier: 3.702A  pdb=" N   ASP A 299 " --> pdb=" O   ASN A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 336
      removed outlier: 3.704A  pdb=" N   MET A 309 " --> pdb=" O   TRP A 305 " (cutoff:3.500A)
      Proline residue:  A 313  - end of helix
    Processing helix  chain 'B' and resid 8 through 69
      removed outlier: 3.559A  pdb=" N   CYS B  12 " --> pdb=" O   PRO B   8 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   THR B  29 " --> pdb=" O   ASN B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 99
      removed outlier: 5.171A  pdb=" N   ALA B  79 " --> pdb=" O   GLU B  75 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ALA B  80 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   GLU B  89 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 112
    Processing helix  chain 'B' and resid 123 through 154
      removed outlier: 4.440A  pdb=" N   TYR B 129 " --> pdb=" O   ALA B 125 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ASP B 131 " --> pdb=" O   PHE B 127 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   GLU B 132 " --> pdb=" O   ALA B 128 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU B 154 " --> pdb=" O   THR B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 186
      removed outlier: 3.954A  pdb=" N   CYS B 173 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ASN B 184 " --> pdb=" O   SER B 180 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY B 186 " --> pdb=" O   LEU B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 209
      removed outlier: 4.288A  pdb=" N   HIS B 197 " --> pdb=" O   TRP B 193 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   THR B 209 " --> pdb=" O   GLY B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 253
      removed outlier: 3.808A  pdb=" N   TYR B 239 " --> pdb=" O   PHE B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 299
      removed outlier: 3.791A  pdb=" N   PHE B 264 " --> pdb=" O   THR B 260 " (cutoff:3.500A)
      Proline residue:  B 277  - end of helix
      removed outlier: 3.702A  pdb=" N   ASP B 299 " --> pdb=" O   ASN B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 336
      removed outlier: 3.704A  pdb=" N   MET B 309 " --> pdb=" O   TRP B 305 " (cutoff:3.500A)
      Proline residue:  B 313  - end of helix

    444 hydrogen bonds defined for protein.
    1320 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: 1.40

  Time building geometry restraints manager: 2.05 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1595
        1.33 -     1.45: 1148
        1.45 -     1.57: 2989
        1.57 -     1.69: 10
        1.69 -     1.81: 50
  Bond restraints: 5792
  Sorted by residual:
  bond pdb=" O3B COA B1000 "
       pdb=" P3B COA B1000 "
    ideal  model  delta    sigma   weight residual
    1.683  1.600  0.083 2.00e-02 2.50e+03 1.70e+01
  bond pdb=" O3B COA A1000 "
       pdb=" P3B COA A1000 "
    ideal  model  delta    sigma   weight residual
    1.683  1.601  0.082 2.00e-02 2.50e+03 1.69e+01
  bond pdb=" C4A COA A1000 "
       pdb=" C5A COA A1000 "
    ideal  model  delta    sigma   weight residual
    1.395  1.468 -0.073 2.00e-02 2.50e+03 1.32e+01
  bond pdb=" C4A COA B1000 "
       pdb=" C5A COA B1000 "
    ideal  model  delta    sigma   weight residual
    1.395  1.467 -0.072 2.00e-02 2.50e+03 1.31e+01
  bond pdb=" C4A COA A1000 "
       pdb=" N9A COA A1000 "
    ideal  model  delta    sigma   weight residual
    1.381  1.317  0.064 2.00e-02 2.50e+03 1.03e+01
  ... (remaining 5787 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.84: 7533
        2.84 -     5.68: 259
        5.68 -     8.52: 38
        8.52 -    11.36: 10
       11.36 -    14.20: 2
  Bond angle restraints: 7842
  Sorted by residual:
  angle pdb=" C   GLN A  81 "
        pdb=" N   GLU A  82 "
        pdb=" CA  GLU A  82 "
      ideal   model   delta    sigma   weight residual
     120.72  110.57   10.15 1.67e+00 3.59e-01 3.69e+01
  angle pdb=" C   GLN B  81 "
        pdb=" N   GLU B  82 "
        pdb=" CA  GLU B  82 "
      ideal   model   delta    sigma   weight residual
     120.72  110.59   10.13 1.67e+00 3.59e-01 3.68e+01
  angle pdb=" C   LEU A 154 "
        pdb=" N   LEU A 155 "
        pdb=" CA  LEU A 155 "
      ideal   model   delta    sigma   weight residual
     121.54  131.46   -9.92 1.91e+00 2.74e-01 2.70e+01
  angle pdb=" C   LEU B 154 "
        pdb=" N   LEU B 155 "
        pdb=" CA  LEU B 155 "
      ideal   model   delta    sigma   weight residual
     121.54  131.40   -9.86 1.91e+00 2.74e-01 2.66e+01
  angle pdb=" P1A COA A1000 "
        pdb=" O3A COA A1000 "
        pdb=" P2A COA A1000 "
      ideal   model   delta    sigma   weight residual
     135.11  120.91   14.20 3.00e+00 1.11e-01 2.24e+01
  ... (remaining 7837 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.34: 2930
       17.34 -    34.68: 364
       34.68 -    52.02: 106
       52.02 -    69.36: 22
       69.36 -    86.70: 6
  Dihedral angle restraints: 3428
    sinusoidal: 1488
      harmonic: 1940
  Sorted by residual:
  dihedral pdb=" CA  ILE A 189 "
           pdb=" C   ILE A 189 "
           pdb=" N   LYS A 190 "
           pdb=" CA  LYS A 190 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.91   19.09     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  ILE B 189 "
           pdb=" C   ILE B 189 "
           pdb=" N   LYS B 190 "
           pdb=" CA  LYS B 190 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.95   19.05     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  LEU A 154 "
           pdb=" C   LEU A 154 "
           pdb=" N   LEU A 155 "
           pdb=" CA  LEU A 155 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.65   18.35     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 3425 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 591
       0.057 -    0.114: 182
       0.114 -    0.171: 41
       0.171 -    0.228: 12
       0.228 -    0.284: 2
  Chirality restraints: 828
  Sorted by residual:
  chirality pdb=" C2B COA B1000 "
            pdb=" C1B COA B1000 "
            pdb=" C3B COA B1000 "
            pdb=" O2B COA B1000 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.69    0.28 2.00e-01 2.50e+01 2.02e+00
  chirality pdb=" C2B COA A1000 "
            pdb=" C1B COA A1000 "
            pdb=" C3B COA A1000 "
            pdb=" O2B COA A1000 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.68    0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CA  ARG A  14 "
            pdb=" N   ARG A  14 "
            pdb=" C   ARG A  14 "
            pdb=" CB  ARG A  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 825 not shown)

  Planarity restraints: 966
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C7P COA B1000 "   -0.308 2.00e-02 2.50e+03   2.56e-01 8.19e+02
        pdb=" C9P COA B1000 "    0.094 2.00e-02 2.50e+03
        pdb=" CAP COA B1000 "   -0.201 2.00e-02 2.50e+03
        pdb=" N8P COA B1000 "    0.428 2.00e-02 2.50e+03
        pdb=" O9P COA B1000 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C7P COA A1000 "    0.308 2.00e-02 2.50e+03   2.56e-01 8.18e+02
        pdb=" C9P COA A1000 "   -0.094 2.00e-02 2.50e+03
        pdb=" CAP COA A1000 "    0.201 2.00e-02 2.50e+03
        pdb=" N8P COA A1000 "   -0.428 2.00e-02 2.50e+03
        pdb=" O9P COA A1000 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C3P COA B1000 "   -0.038 2.00e-02 2.50e+03   3.07e-02 1.18e+01
        pdb=" C5P COA B1000 "    0.009 2.00e-02 2.50e+03
        pdb=" C6P COA B1000 "   -0.028 2.00e-02 2.50e+03
        pdb=" N4P COA B1000 "    0.049 2.00e-02 2.50e+03
        pdb=" O5P COA B1000 "    0.008 2.00e-02 2.50e+03
  ... (remaining 963 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 185
        2.68 -     3.23: 5977
        3.23 -     3.79: 8941
        3.79 -     4.34: 10341
        4.34 -     4.90: 17071
  Nonbonded interactions: 42515
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A  54 "
            pdb=" OD2 ASP B  22 "
     model   vdw
     2.124 3.120
  nonbonded pdb=" OD2 ASP A  22 "
            pdb=" NE2 GLN B  54 "
     model   vdw
     2.155 3.120
  nonbonded pdb=" NH1 ARG B  57 "
            pdb=" OE2 GLU B  60 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" NH1 ARG A  57 "
            pdb=" OE2 GLU A  60 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" O   LEU B  83 "
            pdb=" NE2 GLN B  86 "
     model   vdw
     2.235 3.120
  ... (remaining 42510 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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=0.00 max=1.00 mean=0.89
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             1.630
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.400
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
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      :  0.011   0.083   5792  Z= 0.476
  Angle     :  1.227  14.197   7842  Z= 0.637
  Chirality :  0.060   0.284    828
  Planarity :  0.013   0.256    966
  Dihedral  : 16.921  86.699   2176
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.18 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  2.51 %
    Favored  : 97.16 %
  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:  0.40 (0.32), residues: 656
  helix:  0.98 (0.22), residues: 522
  sheet:  None (None), residues: 0
  loop : -2.50 (0.56), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 192 
 HIS   0.007   0.002   HIS B 196 
 PHE   0.019   0.002   PHE A 274 
 TYR   0.024   0.002   TYR B 171 
 ARG   0.015   0.002   ARG B  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11462 (  444)
  hydrogen bonds       : angle       5.71364 ( 1320)
  covalent geometry    : bond        0.01100 ( 5792)
  covalent geometry    : angle       1.22744 ( 7842)

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

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

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.607 
Fit side-chains
REVERT: A  309 MET cc_start: 0.8572 (mmm) cc_final: 0.8286 (mmt)
REVERT: B  309 MET cc_start: 0.8570 (mmm) cc_final: 0.8309 (mmt)
  outliers start: 2
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1484
  time to fit residues: 14.7625
Evaluate side-chains
  61 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 237 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.149552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.114606 restraints weight = 7772.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.114560 restraints weight = 9361.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.115227 restraints weight = 8290.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.1603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5792  Z= 0.170
  Angle     :  0.744   9.010   7842  Z= 0.388
  Chirality :  0.042   0.143    828
  Planarity :  0.004   0.029    966
  Dihedral  : 10.532  54.907    840
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 11.20 %
    Favored  : 85.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.34), residues: 656
  helix:  1.90 (0.23), residues: 510
  sheet:  None (None), residues: 0
  loop : -1.45 (0.53), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 192 
 HIS   0.004   0.001   HIS B 283 
 PHE   0.011   0.001   PHE A 127 
 TYR   0.015   0.001   TYR A 238 
 ARG   0.004   0.001   ARG A  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07184 (  444)
  hydrogen bonds       : angle       4.30379 ( 1320)
  covalent geometry    : bond        0.00346 ( 5792)
  covalent geometry    : angle       0.74426 ( 7842)

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

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

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.546 
Fit side-chains
REVERT: A  142 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8588 (mt)
  outliers start: 18
  outliers final: 7
  residues processed: 92
  average time/residue: 0.1856
  time to fit residues: 23.0738
Evaluate side-chains
  71 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  302 CYS
Chi-restraints excluded: chain B residue   96 ASP
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  302 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 2 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 58 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 39 optimal weight:    9.9990
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3848 r_free = 0.3848 target = 0.148577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.113799 restraints weight = 7848.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.114041 restraints weight = 9412.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.114656 restraints weight = 8495.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5792  Z= 0.163
  Angle     :  0.700   9.566   7842  Z= 0.362
  Chirality :  0.041   0.136    828
  Planarity :  0.004   0.028    966
  Dihedral  :  9.229  54.091    840
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 14.88 %
    Favored  : 81.61 %
  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:  2.42 (0.34), residues: 656
  helix:  2.50 (0.23), residues: 496
  sheet:  None (None), residues: 0
  loop : -1.41 (0.52), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 192 
 HIS   0.004   0.001   HIS A 283 
 PHE   0.008   0.001   PHE A 127 
 TYR   0.014   0.001   TYR A 171 
 ARG   0.003   0.000   ARG A  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06722 (  444)
  hydrogen bonds       : angle       4.04680 ( 1320)
  covalent geometry    : bond        0.00335 ( 5792)
  covalent geometry    : angle       0.70038 ( 7842)

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

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

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
REVERT: B  120 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6839 (tt)
  outliers start: 21
  outliers final: 11
  residues processed: 90
  average time/residue: 0.1881
  time to fit residues: 22.7130
Evaluate side-chains
  83 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 GLU
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain B residue   96 ASP
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain B residue  328 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 6 optimal weight:    8.9990
   chunk 27 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 38 optimal weight:   10.0000
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3853 r_free = 0.3853 target = 0.149386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.114327 restraints weight = 7998.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.114439 restraints weight = 9320.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.115199 restraints weight = 8140.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5792  Z= 0.156
  Angle     :  0.685  10.248   7842  Z= 0.352
  Chirality :  0.039   0.144    828
  Planarity :  0.004   0.026    966
  Dihedral  :  8.355  45.855    840
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 16.72 %
    Favored  : 78.93 %
  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:  2.66 (0.34), residues: 656
  helix:  2.68 (0.23), residues: 496
  sheet:  None (None), residues: 0
  loop : -1.37 (0.50), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 192 
 HIS   0.004   0.001   HIS A 283 
 PHE   0.008   0.001   PHE B 136 
 TYR   0.013   0.001   TYR A 171 
 ARG   0.002   0.000   ARG A  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06369 (  444)
  hydrogen bonds       : angle       3.97838 ( 1320)
  covalent geometry    : bond        0.00319 ( 5792)
  covalent geometry    : angle       0.68520 ( 7842)

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

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

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 76
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 CYS cc_start: 0.7614 (m) cc_final: 0.7265 (m)
REVERT: A  212 ASP cc_start: 0.8256 (p0) cc_final: 0.8047 (p0)
REVERT: B  212 ASP cc_start: 0.8316 (p0) cc_final: 0.8073 (p0)
  outliers start: 26
  outliers final: 17
  residues processed: 93
  average time/residue: 0.1822
  time to fit residues: 24.4269
Evaluate side-chains
  89 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  274 PHE
Chi-restraints excluded: chain A residue  302 CYS
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain B residue   96 ASP
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  274 PHE
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain B residue  328 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0570
   chunk 35 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.6298

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.151120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.116138 restraints weight = 7886.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.116613 restraints weight = 8886.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.117009 restraints weight = 8014.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5792  Z= 0.143
  Angle     :  0.659  10.804   7842  Z= 0.334
  Chirality :  0.038   0.142    828
  Planarity :  0.003   0.025    966
  Dihedral  :  8.068  50.487    840
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 19.90 %
    Favored  : 76.59 %
  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:  2.82 (0.34), residues: 656
  helix:  2.69 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.87 (0.57), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 192 
 HIS   0.004   0.001   HIS A 283 
 PHE   0.007   0.001   PHE B 136 
 TYR   0.012   0.001   TYR B 171 
 ARG   0.002   0.000   ARG B  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05880 (  444)
  hydrogen bonds       : angle       3.83446 ( 1320)
  covalent geometry    : bond        0.00286 ( 5792)
  covalent geometry    : angle       0.65934 ( 7842)

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

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

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
REVERT: A  276 LEU cc_start: 0.8559 (tp) cc_final: 0.8213 (tp)
REVERT: A  285 TRP cc_start: 0.8644 (t-100) cc_final: 0.8311 (t60)
REVERT: B  269 TRP cc_start: 0.8015 (m100) cc_final: 0.7628 (m100)
REVERT: B  285 TRP cc_start: 0.8648 (t-100) cc_final: 0.8333 (t60)
  outliers start: 21
  outliers final: 16
  residues processed: 85
  average time/residue: 0.1661
  time to fit residues: 21.0321
Evaluate side-chains
  88 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  274 PHE
Chi-restraints excluded: chain A residue  302 CYS
Chi-restraints excluded: chain A residue  309 MET
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue   96 ASP
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  274 PHE
Chi-restraints excluded: chain B residue  302 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 51 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0020
   chunk 3 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 61 optimal weight:    0.3980
   overall best weight:    0.4788

-------------------------------------------------------------------------------
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 = 0.3840 r_free = 0.3840 target = 0.150532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.115808 restraints weight = 7839.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.115143 restraints weight = 7413.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.116443 restraints weight = 6596.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.3200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5792  Z= 0.136
  Angle     :  0.658  11.198   7842  Z= 0.334
  Chirality :  0.038   0.171    828
  Planarity :  0.003   0.025    966
  Dihedral  :  7.765  53.140    840
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 20.90 %
    Favored  : 75.92 %
  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:  3.06 (0.34), residues: 656
  helix:  2.82 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.63 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 192 
 HIS   0.004   0.001   HIS A 283 
 PHE   0.012   0.001   PHE B 127 
 TYR   0.010   0.001   TYR A 171 
 ARG   0.001   0.000   ARG A 158 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05416 (  444)
  hydrogen bonds       : angle       3.73439 ( 1320)
  covalent geometry    : bond        0.00266 ( 5792)
  covalent geometry    : angle       0.65762 ( 7842)

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

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

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 LEU cc_start: 0.8573 (tp) cc_final: 0.8245 (tp)
REVERT: A  285 TRP cc_start: 0.8633 (t-100) cc_final: 0.8347 (t60)
REVERT: B   23 PHE cc_start: 0.8207 (t80) cc_final: 0.7984 (t80)
REVERT: B  276 LEU cc_start: 0.8611 (tp) cc_final: 0.8279 (tp)
REVERT: B  285 TRP cc_start: 0.8637 (t-100) cc_final: 0.8376 (t60)
  outliers start: 19
  outliers final: 11
  residues processed: 83
  average time/residue: 0.1685
  time to fit residues: 20.3263
Evaluate side-chains
  80 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  274 PHE
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue   96 ASP
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  274 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 6 optimal weight:   20.0000
   chunk 30 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3805 r_free = 0.3805 target = 0.147431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.112331 restraints weight = 7931.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.108461 restraints weight = 8911.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.110542 restraints weight = 7274.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.3117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5792  Z= 0.162
  Angle     :  0.723  14.824   7842  Z= 0.365
  Chirality :  0.040   0.200    828
  Planarity :  0.003   0.023    966
  Dihedral  :  7.789  53.712    840
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 21.57 %
    Favored  : 75.08 %
  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:  2.95 (0.34), residues: 656
  helix:  2.72 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.59 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 192 
 HIS   0.004   0.001   HIS A 283 
 PHE   0.010   0.001   PHE A 136 
 TYR   0.015   0.001   TYR A 171 
 ARG   0.001   0.000   ARG B 178 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05898 (  444)
  hydrogen bonds       : angle       3.90591 ( 1320)
  covalent geometry    : bond        0.00347 ( 5792)
  covalent geometry    : angle       0.72297 ( 7842)

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

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

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 LEU cc_start: 0.8676 (tp) cc_final: 0.8342 (tp)
REVERT: A  285 TRP cc_start: 0.8646 (t-100) cc_final: 0.8336 (t60)
REVERT: B   23 PHE cc_start: 0.8166 (t80) cc_final: 0.7960 (t80)
REVERT: B  215 MET cc_start: 0.8253 (ppp) cc_final: 0.8022 (tmm)
REVERT: B  276 LEU cc_start: 0.8677 (tp) cc_final: 0.8337 (tp)
REVERT: B  285 TRP cc_start: 0.8648 (t-100) cc_final: 0.8344 (t60)
  outliers start: 20
  outliers final: 17
  residues processed: 83
  average time/residue: 0.1848
  time to fit residues: 22.4423
Evaluate side-chains
  83 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  274 PHE
Chi-restraints excluded: chain A residue  302 CYS
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue   96 ASP
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  274 PHE
Chi-restraints excluded: chain B residue  302 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0770
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0470
   chunk 54 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.4836

-------------------------------------------------------------------------------
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 = 0.3838 r_free = 0.3838 target = 0.150617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.114792 restraints weight = 7852.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.110530 restraints weight = 6751.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.112062 restraints weight = 6853.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.3482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5792  Z= 0.142
  Angle     :  0.703  13.892   7842  Z= 0.354
  Chirality :  0.038   0.178    828
  Planarity :  0.003   0.024    966
  Dihedral  :  7.597  55.124    840
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 21.91 %
    Favored  : 74.58 %
  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:  3.11 (0.34), residues: 656
  helix:  2.87 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.71 (0.56), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 192 
 HIS   0.004   0.001   HIS A 283 
 PHE   0.009   0.001   PHE B 127 
 TYR   0.013   0.001   TYR B 239 
 ARG   0.001   0.000   ARG B  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05298 (  444)
  hydrogen bonds       : angle       3.79304 ( 1320)
  covalent geometry    : bond        0.00287 ( 5792)
  covalent geometry    : angle       0.70288 ( 7842)

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

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

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 LEU cc_start: 0.8602 (tp) cc_final: 0.8278 (tp)
REVERT: A  285 TRP cc_start: 0.8639 (t-100) cc_final: 0.8366 (t60)
REVERT: B   23 PHE cc_start: 0.8167 (t80) cc_final: 0.7933 (t80)
REVERT: B  276 LEU cc_start: 0.8636 (tp) cc_final: 0.8312 (tp)
REVERT: B  285 TRP cc_start: 0.8655 (t-100) cc_final: 0.8346 (t60)
  outliers start: 21
  outliers final: 20
  residues processed: 86
  average time/residue: 0.1466
  time to fit residues: 18.2805
Evaluate side-chains
  89 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  274 PHE
Chi-restraints excluded: chain A residue  302 CYS
Chi-restraints excluded: chain A residue  309 MET
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue   96 ASP
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  274 PHE
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain B residue  334 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    0.3980
   chunk 23 optimal weight:    0.9990
   chunk 58 optimal weight:   20.0000
   chunk 59 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 33 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3815 r_free = 0.3815 target = 0.148146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.112099 restraints weight = 7931.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.109225 restraints weight = 7163.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.110586 restraints weight = 6988.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   5792  Z= 0.160
  Angle     :  0.726  12.079   7842  Z= 0.368
  Chirality :  0.040   0.183    828
  Planarity :  0.004   0.052    966
  Dihedral  :  7.651  55.062    840
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 22.58 %
    Favored  : 73.75 %
  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:  3.01 (0.34), residues: 656
  helix:  2.77 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.62 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 192 
 HIS   0.004   0.001   HIS A 283 
 PHE   0.009   0.001   PHE A  23 
 TYR   0.014   0.001   TYR A 171 
 ARG   0.017   0.000   ARG A  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05728 (  444)
  hydrogen bonds       : angle       3.86839 ( 1320)
  covalent geometry    : bond        0.00345 ( 5792)
  covalent geometry    : angle       0.72567 ( 7842)

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

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

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 67
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 PHE cc_start: 0.7967 (t80) cc_final: 0.7418 (m-80)
REVERT: A  276 LEU cc_start: 0.8659 (tp) cc_final: 0.8326 (tp)
REVERT: A  285 TRP cc_start: 0.8633 (t-100) cc_final: 0.8338 (t60)
REVERT: B   23 PHE cc_start: 0.8146 (t80) cc_final: 0.7943 (t80)
REVERT: B  228 MET cc_start: 0.7739 (ttm) cc_final: 0.7343 (mtt)
REVERT: B  276 LEU cc_start: 0.8652 (tp) cc_final: 0.8319 (tp)
REVERT: B  285 TRP cc_start: 0.8632 (t-100) cc_final: 0.8340 (t60)
  outliers start: 22
  outliers final: 21
  residues processed: 79
  average time/residue: 0.1306
  time to fit residues: 15.3750
Evaluate side-chains
  87 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  274 PHE
Chi-restraints excluded: chain A residue  302 CYS
Chi-restraints excluded: chain A residue  309 MET
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue   96 ASP
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  274 PHE
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain B residue  309 MET
Chi-restraints excluded: chain B residue  334 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 7 optimal weight:   10.0000
   chunk 24 optimal weight:    0.4980
   chunk 54 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 5 optimal weight:    6.9990
   chunk 37 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.152976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.120091 restraints weight = 7834.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.118848 restraints weight = 9576.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.117052 restraints weight = 7586.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.3481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   5792  Z= 0.166
  Angle     :  0.745  12.133   7842  Z= 0.383
  Chirality :  0.040   0.170    828
  Planarity :  0.004   0.057    966
  Dihedral  :  7.665  55.803    840
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 23.24 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.01 (0.34), residues: 656
  helix:  2.76 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.56 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 192 
 HIS   0.004   0.001   HIS A 283 
 PHE   0.010   0.001   PHE A  23 
 TYR   0.014   0.001   TYR A 171 
 ARG   0.014   0.000   ARG A  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05759 (  444)
  hydrogen bonds       : angle       3.89208 ( 1320)
  covalent geometry    : bond        0.00363 ( 5792)
  covalent geometry    : angle       0.74549 ( 7842)

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

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

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1312 Ramachandran restraints generated.
    656 Oldfield, 0 Emsley, 656 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 PHE cc_start: 0.7934 (t80) cc_final: 0.7447 (m-80)
REVERT: A  276 LEU cc_start: 0.8606 (tp) cc_final: 0.8290 (tp)
REVERT: A  285 TRP cc_start: 0.8614 (t-100) cc_final: 0.8320 (t60)
REVERT: B  228 MET cc_start: 0.7566 (ttm) cc_final: 0.7126 (mtt)
REVERT: B  276 LEU cc_start: 0.8595 (tp) cc_final: 0.8280 (tp)
REVERT: B  285 TRP cc_start: 0.8603 (t-100) cc_final: 0.8328 (t60)
  outliers start: 21
  outliers final: 21
  residues processed: 77
  average time/residue: 0.2105
  time to fit residues: 24.8165
Evaluate side-chains
  85 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue   96 ASP
Chi-restraints excluded: chain A residue  142 ILE
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  274 PHE
Chi-restraints excluded: chain A residue  302 CYS
Chi-restraints excluded: chain A residue  309 MET
Chi-restraints excluded: chain A residue  334 HIS
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue   84 GLU
Chi-restraints excluded: chain B residue   96 ASP
Chi-restraints excluded: chain B residue  153 PHE
Chi-restraints excluded: chain B residue  154 LEU
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  274 PHE
Chi-restraints excluded: chain B residue  302 CYS
Chi-restraints excluded: chain B residue  309 MET
Chi-restraints excluded: chain B residue  334 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 7 optimal weight:    8.9990
   chunk 32 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 63 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.151923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.119272 restraints weight = 7825.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.118241 restraints weight = 8963.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.118440 restraints weight = 7980.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.3441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   5792  Z= 0.173
  Angle     :  0.749  12.401   7842  Z= 0.385
  Chirality :  0.040   0.170    828
  Planarity :  0.004   0.052    966
  Dihedral  :  7.745  56.458    840
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 22.74 %
    Favored  : 73.58 %
  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:  2.98 (0.34), residues: 656
  helix:  2.74 (0.22), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.53 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 285 
 HIS   0.005   0.001   HIS A 283 
 PHE   0.022   0.001   PHE B  23 
 TYR   0.015   0.001   TYR B 171 
 ARG   0.012   0.000   ARG A  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05957 (  444)
  hydrogen bonds       : angle       3.93546 ( 1320)
  covalent geometry    : bond        0.00384 ( 5792)
  covalent geometry    : angle       0.74914 ( 7842)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2369.96 seconds
wall clock time: 44 minutes 12.56 seconds (2652.56 seconds total)