Starting phenix.real_space_refine
on Tue Mar  3 13:50:23 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wus_32840/03_2026/7wus_32840.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wus_32840/03_2026/7wus_32840.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wus_32840/03_2026/7wus_32840.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wus_32840/03_2026/7wus_32840.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wus_32840/03_2026/7wus_32840.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wus_32840/03_2026/7wus_32840.cif"
  }
  resolution = 3.4
  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
-------------------------------------------------------------------------------
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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 336 atoms to isotropic.
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      42      5.16       5
     C    3446      2.51       5
     N     946      2.21       5
     O    1016      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5450
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2725
          Classifications: {'peptide': 341}
          Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 319}
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.69, per 1000 atoms: 0.31
  Number of scatterers: 5450
  At special positions: 0
  Unit cell: (105.6, 101.64, 67.32, 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      42     16.00
     O    1016      8.00
     N     946      7.00
     C    3446      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   4 " - pdb=" SG  CYS A  15 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  55 " - pdb=" SG  CYS A 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 179 " - pdb=" SG  CYS A 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 280 " - pdb=" SG  CYS A 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 313 " - pdb=" SG  CYS A 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   4 " - pdb=" SG  CYS B  15 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  55 " - pdb=" SG  CYS B 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 179 " - pdb=" SG  CYS B 223 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 280 " - pdb=" SG  CYS B 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 313 " - pdb=" SG  CYS B 316 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.44
  Conformation dependent library (CDL) restraints added in 431.5 milliseconds
  

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1264

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 11 sheets defined
      16.1% alpha, 17.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 50
      removed outlier: 4.242A  pdb=" N   LEU A  42 " --> pdb=" O   SER A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 53
      No H-bonds generated for 'chain 'A' and resid 51 through 53'
    Processing helix  chain 'A' and resid 61 through 69
      removed outlier: 3.653A  pdb=" N   LYS A  69 " --> pdb=" O   ASN A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 82
    Processing helix  chain 'A' and resid 144 through 146
      No H-bonds generated for 'chain 'A' and resid 144 through 146'
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.731A  pdb=" N   THR A 230 " --> pdb=" O   LYS A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 248
    Processing helix  chain 'A' and resid 252 through 256
      removed outlier: 3.574A  pdb=" N   ASN A 255 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 50
      removed outlier: 4.242A  pdb=" N   LEU B  42 " --> pdb=" O   SER B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 53
      No H-bonds generated for 'chain 'B' and resid 51 through 53'
    Processing helix  chain 'B' and resid 61 through 69
      removed outlier: 3.652A  pdb=" N   LYS B  69 " --> pdb=" O   ASN B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 82
    Processing helix  chain 'B' and resid 144 through 146
      No H-bonds generated for 'chain 'B' and resid 144 through 146'
    Processing helix  chain 'B' and resid 226 through 230
      removed outlier: 3.731A  pdb=" N   THR B 230 " --> pdb=" O   LYS B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 248
    Processing helix  chain 'B' and resid 252 through 256
      removed outlier: 3.575A  pdb=" N   ASN B 255 " --> pdb=" O   SER B 252 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16
      removed outlier: 3.561A  pdb=" N   GLU A  12 " --> pdb=" O   SER A   7 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   CYS A   4 " --> pdb=" O   CYS B   4 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   CYS B   4 " --> pdb=" O   CYS A   4 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLU B  12 " --> pdb=" O   SER B   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21
    Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 36
      removed outlier: 7.483A  pdb=" N   GLN A  35 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   TRP A 168 " --> pdb=" O   GLU A 156 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 89
      removed outlier: 6.267A  pdb=" N   THR A  87 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   ILE A 135 " --> pdb=" O   THR A  87 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   MET A  89 " --> pdb=" O   ILE A 135 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   GLY A  56 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 275
      removed outlier: 5.213A  pdb=" N   ILE A 212 " --> pdb=" O   ALA A 205 " (cutoff:3.500A)
      removed outlier: 5.536A  pdb=" N   ALA A 205 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   SER A 216 " --> pdb=" O   TRP A 201 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ARG A 192 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA A 186 " --> pdb=" O   ILE B 188 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA B 186 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ARG B 192 " --> pdb=" O   LYS B 189 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   SER B 216 " --> pdb=" O   TRP B 201 " (cutoff:3.500A)
      removed outlier: 5.537A  pdb=" N   ALA B 205 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
      removed outlier: 5.212A  pdb=" N   ILE B 212 " --> pdb=" O   ALA B 205 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 287
    Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 324
    Processing sheet with id=AA8, first strand: chain 'B' and resid 34 through 36
      removed outlier: 7.484A  pdb=" N   GLN B  35 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   TRP B 168 " --> pdb=" O   GLU B 156 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 87 through 89
      removed outlier: 6.267A  pdb=" N   THR B  87 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   ILE B 135 " --> pdb=" O   THR B  87 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   MET B  89 " --> pdb=" O   ILE B 135 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   GLY B  56 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 287
    Processing sheet with id=AB2, first strand: chain 'B' and resid 322 through 324

    118 hydrogen bonds defined for protein.
    294 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: 0.71

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1762
        1.34 -     1.46: 1309
        1.46 -     1.58: 2463
        1.58 -     1.70: 0
        1.70 -     1.81: 60
  Bond restraints: 5594
  Sorted by residual:
  bond pdb=" N   GLN B 107 "
       pdb=" CA  GLN B 107 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.83e+00
  bond pdb=" N   GLN A 107 "
       pdb=" CA  GLN A 107 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.79e+00
  bond pdb=" C   PRO A 106 "
       pdb=" N   GLN A 107 "
    ideal  model  delta    sigma   weight residual
    1.329  1.349 -0.020 1.40e-02 5.10e+03 1.95e+00
  bond pdb=" C   PRO B 106 "
       pdb=" N   GLN B 107 "
    ideal  model  delta    sigma   weight residual
    1.329  1.347 -0.018 1.40e-02 5.10e+03 1.64e+00
  bond pdb=" CA  TYR B  32 "
       pdb=" C   TYR B  32 "
    ideal  model  delta    sigma   weight residual
    1.523  1.538 -0.014 1.30e-02 5.92e+03 1.22e+00
  ... (remaining 5589 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 7441
        2.33 -     4.65: 115
        4.65 -     6.98: 12
        6.98 -     9.31: 8
        9.31 -    11.64: 4
  Bond angle restraints: 7580
  Sorted by residual:
  angle pdb=" C   PRO B 106 "
        pdb=" N   GLN B 107 "
        pdb=" CA  GLN B 107 "
      ideal   model   delta    sigma   weight residual
     121.70  133.34  -11.64 1.80e+00 3.09e-01 4.18e+01
  angle pdb=" C   PRO A 106 "
        pdb=" N   GLN A 107 "
        pdb=" CA  GLN A 107 "
      ideal   model   delta    sigma   weight residual
     121.70  133.32  -11.62 1.80e+00 3.09e-01 4.17e+01
  angle pdb=" C   TYR B  32 "
        pdb=" N   LYS B  33 "
        pdb=" CA  LYS B  33 "
      ideal   model   delta    sigma   weight residual
     121.70  131.65   -9.95 1.80e+00 3.09e-01 3.06e+01
  angle pdb=" C   TYR A  32 "
        pdb=" N   LYS A  33 "
        pdb=" CA  LYS A  33 "
      ideal   model   delta    sigma   weight residual
     121.70  131.63   -9.93 1.80e+00 3.09e-01 3.04e+01
  angle pdb=" C   LYS B 189 "
        pdb=" N   ASP B 190 "
        pdb=" CA  ASP B 190 "
      ideal   model   delta    sigma   weight residual
     121.54  128.85   -7.31 1.91e+00 2.74e-01 1.47e+01
  ... (remaining 7575 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 2734
       16.00 -    32.00: 466
       32.00 -    48.00: 124
       48.00 -    64.00: 22
       64.00 -    80.00: 10
  Dihedral angle restraints: 3356
    sinusoidal: 1396
      harmonic: 1960
  Sorted by residual:
  dihedral pdb=" CA  GLN B  31 "
           pdb=" C   GLN B  31 "
           pdb=" N   TYR B  32 "
           pdb=" CA  TYR B  32 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.44  -25.56     0      5.00e+00 4.00e-02 2.61e+01
  dihedral pdb=" CA  GLN A  31 "
           pdb=" C   GLN A  31 "
           pdb=" N   TYR A  32 "
           pdb=" CA  TYR A  32 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.47  -25.53     0      5.00e+00 4.00e-02 2.61e+01
  dihedral pdb=" CB  CYS B 291 "
           pdb=" SG  CYS B 291 "
           pdb=" SG  CYS B 312 "
           pdb=" CB  CYS B 312 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   54.60   38.40     1      1.00e+01 1.00e-02 2.08e+01
  ... (remaining 3353 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 628
       0.047 -    0.093: 129
       0.093 -    0.140: 41
       0.140 -    0.186: 6
       0.186 -    0.233: 4
  Chirality restraints: 808
  Sorted by residual:
  chirality pdb=" CA  GLN A 107 "
            pdb=" N   GLN A 107 "
            pdb=" C   GLN A 107 "
            pdb=" CB  GLN A 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CA  GLN B 107 "
            pdb=" N   GLN B 107 "
            pdb=" C   GLN B 107 "
            pdb=" CB  GLN B 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CB  ILE A 167 "
            pdb=" CA  ILE A 167 "
            pdb=" CG1 ILE A 167 "
            pdb=" CG2 ILE A 167 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 805 not shown)

  Planarity restraints: 962
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 189 "    0.007 2.00e-02 2.50e+03   1.45e-02 2.09e+00
        pdb=" C   LYS A 189 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   LYS A 189 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASP A 190 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 189 "   -0.007 2.00e-02 2.50e+03   1.44e-02 2.07e+00
        pdb=" C   LYS B 189 "    0.025 2.00e-02 2.50e+03
        pdb=" O   LYS B 189 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASP B 190 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 277 "    0.005 2.00e-02 2.50e+03   1.08e-02 1.17e+00
        pdb=" C   PHE A 277 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   PHE A 277 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ASP A 278 "    0.006 2.00e-02 2.50e+03
  ... (remaining 959 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1513
        2.80 -     3.33: 4826
        3.33 -     3.85: 8758
        3.85 -     4.38: 9812
        4.38 -     4.90: 16744
  Nonbonded interactions: 41653
  Sorted by model distance:
  nonbonded pdb=" O   THR B 164 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   THR A 164 "
            pdb=" OG1 THR A 165 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   ARG A 105 "
            pdb=" NE2 GLN A 107 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" O   ARG B 105 "
            pdb=" NE2 GLN B 107 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" OD1 ASP A 176 "
            pdb=" N   PHE A 178 "
     model   vdw
     2.295 3.120
  ... (remaining 41648 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: 0.01
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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.290
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5606  Z= 0.129
  Angle     :  0.747  11.636   7604  Z= 0.403
  Chirality :  0.046   0.233    808
  Planarity :  0.004   0.038    962
  Dihedral  : 17.105  79.998   2056
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 24.08 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.54 %
    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: -2.40 (0.32), residues: 678
  helix: -0.05 (0.70), residues: 64
  sheet: -1.82 (0.40), residues: 156
  loop : -1.82 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 324 
 TYR   0.012   0.001   TYR B  32 
 PHE   0.009   0.001   PHE B 217 
 TRP   0.011   0.001   TRP B 225 
 HIS   0.002   0.000   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 5594)
  covalent geometry    : angle       0.74839 ( 7580)
  SS BOND              : bond        0.00135 (   12)
  SS BOND              : angle       0.34122 (   24)
  hydrogen bonds       : bond        0.21900 (  118)
  hydrogen bonds       : angle      11.00360 (  294)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 127
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   34 PHE cc_start: 0.7575 (m-80) cc_final: 0.7175 (m-80)
REVERT: B   35 GLN cc_start: 0.7206 (pt0) cc_final: 0.6988 (pt0)
REVERT: B   62 ARG cc_start: 0.7403 (ptp-110) cc_final: 0.7115 (ttt-90)
REVERT: B  232 TRP cc_start: 0.8435 (t60) cc_final: 0.8182 (t60)
  outliers start: 6
  outliers final: 2
  residues processed: 129
  average time/residue: 0.0953
  time to fit residues: 15.0696
Evaluate side-chains
  88 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 THR
Chi-restraints excluded: chain B residue  165 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.0050
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:   20.0000
   chunk 27 optimal weight:    4.9990
   overall best weight:    1.7800

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

Flipped N/Q/H residues before XYZ refinement:
A  10 ASN
A  31 GLN
** A  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  10 ASN
B  70 GLN
B 151 ASN
** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.180506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.136967 restraints weight = 7382.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3800 rms_B_bonded: 3.87
r_work: 0.3573 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5606  Z= 0.198
  Angle     :  0.780  11.805   7604  Z= 0.411
  Chirality :  0.047   0.218    808
  Planarity :  0.005   0.033    962
  Dihedral  :  6.164  46.644    728
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 21.57 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.54 %
    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: -2.32 (0.32), residues: 678
  helix: -0.19 (0.68), residues: 68
  sheet: -1.74 (0.39), residues: 158
  loop : -1.75 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 324 
 TYR   0.017   0.002   TYR A  32 
 PHE   0.013   0.002   PHE A 217 
 TRP   0.013   0.001   TRP A  28 
 HIS   0.005   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 5594)
  covalent geometry    : angle       0.78048 ( 7580)
  SS BOND              : bond        0.00224 (   12)
  SS BOND              : angle       0.56345 (   24)
  hydrogen bonds       : bond        0.03868 (  118)
  hydrogen bonds       : angle       7.84756 (  294)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 95
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.8289 (pp30) cc_final: 0.7994 (pp30)
REVERT: B   34 PHE cc_start: 0.8220 (m-80) cc_final: 0.7723 (m-80)
REVERT: B   62 ARG cc_start: 0.8248 (ptp-110) cc_final: 0.7640 (ttt-90)
REVERT: B  232 TRP cc_start: 0.8913 (t60) cc_final: 0.8581 (t60)
REVERT: B  278 ASP cc_start: 0.7675 (m-30) cc_final: 0.7345 (m-30)
REVERT: B  314 ARG cc_start: 0.8117 (ttm-80) cc_final: 0.7759 (mtt-85)
  outliers start: 29
  outliers final: 11
  residues processed: 111
  average time/residue: 0.0662
  time to fit residues: 9.8295
Evaluate side-chains
  94 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 GLU
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain B residue  237 LEU
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  275 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0050
   chunk 33 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 12 optimal weight:    9.9990
   chunk 56 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 42 optimal weight:    8.9990
   overall best weight:    1.1196

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

Flipped N/Q/H residues before XYZ refinement:
A  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.182416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.130754 restraints weight = 7257.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3850 rms_B_bonded: 3.84
r_work: 0.3692 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5606  Z= 0.150
  Angle     :  0.744  11.777   7604  Z= 0.393
  Chirality :  0.047   0.229    808
  Planarity :  0.004   0.033    962
  Dihedral  :  5.489  25.266    726
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 21.91 %
    Favored  : 73.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.54 %
    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: -2.21 (0.32), residues: 678
  helix: -0.06 (0.68), residues: 68
  sheet: -1.72 (0.39), residues: 176
  loop : -1.63 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 324 
 TYR   0.015   0.001   TYR A  32 
 PHE   0.009   0.002   PHE A 217 
 TRP   0.014   0.001   TRP B 225 
 HIS   0.006   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 5594)
  covalent geometry    : angle       0.74454 ( 7580)
  SS BOND              : bond        0.00177 (   12)
  SS BOND              : angle       0.49067 (   24)
  hydrogen bonds       : bond        0.03373 (  118)
  hydrogen bonds       : angle       7.33132 (  294)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 84
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.8344 (pp30) cc_final: 0.8089 (pp30)
REVERT: B   34 PHE cc_start: 0.8396 (m-80) cc_final: 0.7635 (m-80)
REVERT: B   62 ARG cc_start: 0.8217 (ptp-110) cc_final: 0.7423 (ttt-90)
REVERT: B   67 MET cc_start: 0.8965 (tmm) cc_final: 0.8704 (tmm)
REVERT: B  232 TRP cc_start: 0.8827 (t60) cc_final: 0.8434 (t60)
REVERT: B  314 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7771 (mtt-85)
  outliers start: 30
  outliers final: 17
  residues processed: 102
  average time/residue: 0.0534
  time to fit residues: 7.4824
Evaluate side-chains
  96 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 79
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   64 GLU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  131 HIS
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  276 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 60 optimal weight:    0.0170
   chunk 62 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 47 optimal weight:    6.9990
   chunk 61 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.7818

-------------------------------------------------------------------------------
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 = 0.4348 r_free = 0.4348 target = 0.184270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.132640 restraints weight = 7267.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3886 rms_B_bonded: 3.87
r_work: 0.3726 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5606  Z= 0.129
  Angle     :  0.731  11.768   7604  Z= 0.381
  Chirality :  0.047   0.230    808
  Planarity :  0.004   0.030    962
  Dihedral  :  5.305  24.972    726
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 21.91 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.54 %
    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: -2.09 (0.32), residues: 678
  helix:  0.05 (0.68), residues: 68
  sheet: -1.50 (0.40), residues: 168
  loop : -1.63 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 324 
 TYR   0.016   0.001   TYR B  32 
 PHE   0.013   0.001   PHE A 133 
 TRP   0.009   0.001   TRP B 225 
 HIS   0.004   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 5594)
  covalent geometry    : angle       0.73140 ( 7580)
  SS BOND              : bond        0.00153 (   12)
  SS BOND              : angle       0.51888 (   24)
  hydrogen bonds       : bond        0.02964 (  118)
  hydrogen bonds       : angle       6.88858 (  294)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 92
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.8329 (pp30) cc_final: 0.7997 (pp30)
REVERT: B   34 PHE cc_start: 0.8221 (m-80) cc_final: 0.7675 (m-80)
REVERT: B   62 ARG cc_start: 0.8194 (ptp-110) cc_final: 0.7464 (ttt-90)
REVERT: B  232 TRP cc_start: 0.8829 (t60) cc_final: 0.8476 (t60)
REVERT: B  321 LEU cc_start: 0.9150 (tp) cc_final: 0.8908 (tp)
REVERT: B  333 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7857 (mtp)
  outliers start: 29
  outliers final: 18
  residues processed: 109
  average time/residue: 0.0622
  time to fit residues: 9.2616
Evaluate side-chains
  102 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   64 GLU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   71 ILE
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  276 ASP
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  333 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 11 optimal weight:   20.0000
   chunk 14 optimal weight:   10.0000
   chunk 25 optimal weight:    0.5980
   chunk 53 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 63 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.4392 r_free = 0.4392 target = 0.186433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.135326 restraints weight = 7434.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3887 rms_B_bonded: 3.87
r_work: 0.3727 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5606  Z= 0.126
  Angle     :  0.713  11.741   7604  Z= 0.371
  Chirality :  0.047   0.231    808
  Planarity :  0.004   0.030    962
  Dihedral  :  5.207  25.500    726
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 22.24 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.54 %
    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: -2.01 (0.32), residues: 678
  helix:  0.10 (0.68), residues: 68
  sheet: -1.23 (0.42), residues: 154
  loop : -1.68 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 322 
 TYR   0.017   0.001   TYR B  32 
 PHE   0.010   0.001   PHE A 133 
 TRP   0.008   0.001   TRP B 225 
 HIS   0.004   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 5594)
  covalent geometry    : angle       0.71333 ( 7580)
  SS BOND              : bond        0.00142 (   12)
  SS BOND              : angle       0.46969 (   24)
  hydrogen bonds       : bond        0.02833 (  118)
  hydrogen bonds       : angle       6.62249 (  294)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 85
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.8309 (pp30) cc_final: 0.7965 (pp30)
REVERT: A  272 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7474 (mmt90)
REVERT: B   34 PHE cc_start: 0.8283 (m-80) cc_final: 0.7304 (m-80)
REVERT: B   62 ARG cc_start: 0.8166 (ptp-110) cc_final: 0.7507 (ttt-90)
REVERT: B  123 MET cc_start: 0.1918 (ttp) cc_final: 0.1426 (tmm)
REVERT: B  232 TRP cc_start: 0.8829 (t60) cc_final: 0.8454 (t60)
REVERT: B  278 ASP cc_start: 0.7849 (m-30) cc_final: 0.7199 (m-30)
REVERT: B  321 LEU cc_start: 0.9235 (tp) cc_final: 0.9017 (tp)
  outliers start: 25
  outliers final: 19
  residues processed: 100
  average time/residue: 0.0661
  time to fit residues: 8.9549
Evaluate side-chains
  100 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 GLU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  272 ARG
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  146 THR
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  276 ASP
Chi-restraints excluded: chain B residue  287 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 29 optimal weight:    0.0770
   chunk 51 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    1.4144

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

Flipped N/Q/H residues before XYZ refinement:
** A 107 GLN ** 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 = 0.4316 r_free = 0.4316 target = 0.180825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.130095 restraints weight = 7365.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3844 rms_B_bonded: 3.81
r_work: 0.3685 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5606  Z= 0.164
  Angle     :  0.732  11.720   7604  Z= 0.383
  Chirality :  0.047   0.231    808
  Planarity :  0.004   0.031    962
  Dihedral  :  5.411  26.808    726
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 22.91 %
    Favored  : 72.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.54 %
    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: -2.05 (0.33), residues: 678
  helix:  0.01 (0.66), residues: 68
  sheet: -1.46 (0.41), residues: 174
  loop : -1.58 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 322 
 TYR   0.017   0.002   TYR B  32 
 PHE   0.010   0.002   PHE A 217 
 TRP   0.008   0.001   TRP A  28 
 HIS   0.006   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 5594)
  covalent geometry    : angle       0.73259 ( 7580)
  SS BOND              : bond        0.00185 (   12)
  SS BOND              : angle       0.50023 (   24)
  hydrogen bonds       : bond        0.02902 (  118)
  hydrogen bonds       : angle       6.60752 (  294)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 78
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.8340 (pp30) cc_final: 0.7988 (pp30)
REVERT: A  198 MET cc_start: 0.8517 (mmp) cc_final: 0.8267 (mmp)
REVERT: A  272 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7517 (mmt90)
REVERT: B   34 PHE cc_start: 0.8261 (m-80) cc_final: 0.7952 (m-80)
REVERT: B   62 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7549 (ttt-90)
REVERT: B  123 MET cc_start: 0.2015 (ttp) cc_final: 0.1735 (tmm)
REVERT: B  232 TRP cc_start: 0.8877 (t60) cc_final: 0.8512 (t60)
REVERT: B  321 LEU cc_start: 0.9233 (tp) cc_final: 0.8988 (tp)
  outliers start: 25
  outliers final: 18
  residues processed: 94
  average time/residue: 0.0615
  time to fit residues: 7.9478
Evaluate side-chains
  97 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 GLU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  191 ASN
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  272 ARG
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  131 HIS
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  276 ASP
Chi-restraints excluded: chain B residue  287 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 24 optimal weight:    0.3980
   chunk 46 optimal weight:   20.0000
   chunk 57 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0370
   chunk 61 optimal weight:    4.9990
   overall best weight:    1.0460

-------------------------------------------------------------------------------
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 = 0.4326 r_free = 0.4326 target = 0.181967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.131531 restraints weight = 7394.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3850 rms_B_bonded: 3.82
r_work: 0.3687 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.3287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5606  Z= 0.138
  Angle     :  0.718  11.714   7604  Z= 0.376
  Chirality :  0.046   0.232    808
  Planarity :  0.004   0.031    962
  Dihedral  :  5.377  26.545    726
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 23.91 %
    Favored  : 72.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.54 %
    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: -1.99 (0.33), residues: 678
  helix:  0.13 (0.67), residues: 68
  sheet: -1.24 (0.42), residues: 154
  loop : -1.65 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 322 
 TYR   0.016   0.001   TYR B  32 
 PHE   0.008   0.002   PHE A 217 
 TRP   0.009   0.001   TRP B 225 
 HIS   0.005   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 5594)
  covalent geometry    : angle       0.71777 ( 7580)
  SS BOND              : bond        0.00158 (   12)
  SS BOND              : angle       0.84911 (   24)
  hydrogen bonds       : bond        0.02814 (  118)
  hydrogen bonds       : angle       6.46866 (  294)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 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: 21
    poor density    : 81
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.8294 (pp30) cc_final: 0.7929 (pp30)
REVERT: A  198 MET cc_start: 0.8496 (mmp) cc_final: 0.8293 (mmp)
REVERT: A  272 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7456 (mmt90)
REVERT: B   62 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7436 (ttt-90)
REVERT: B  232 TRP cc_start: 0.8850 (t60) cc_final: 0.8462 (t60)
REVERT: B  321 LEU cc_start: 0.9227 (tp) cc_final: 0.9025 (tp)
  outliers start: 21
  outliers final: 17
  residues processed: 93
  average time/residue: 0.0606
  time to fit residues: 7.7118
Evaluate side-chains
  102 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 GLU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  272 ARG
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  131 HIS
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  276 ASP
Chi-restraints excluded: chain B residue  287 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 3 optimal weight:    0.0870
   chunk 66 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0980
   chunk 23 optimal weight:    0.6980
   chunk 35 optimal weight:    8.9990
   chunk 14 optimal weight:    9.9990
   chunk 61 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 = 0.4409 r_free = 0.4409 target = 0.187735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.136516 restraints weight = 7231.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3894 rms_B_bonded: 3.87
r_work: 0.3734 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.3383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5606  Z= 0.117
  Angle     :  0.701  11.718   7604  Z= 0.365
  Chirality :  0.046   0.230    808
  Planarity :  0.004   0.032    962
  Dihedral  :  5.128  25.469    726
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 25.25 %
    Favored  : 71.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.54 %
    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 (0.33), residues: 678
  helix:  0.24 (0.68), residues: 68
  sheet: -0.90 (0.44), residues: 142
  loop : -1.62 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 322 
 TYR   0.017   0.001   TYR B  32 
 PHE   0.023   0.002   PHE A 133 
 TRP   0.011   0.001   TRP A 225 
 HIS   0.003   0.000   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 5594)
  covalent geometry    : angle       0.70150 ( 7580)
  SS BOND              : bond        0.00122 (   12)
  SS BOND              : angle       0.54080 (   24)
  hydrogen bonds       : bond        0.02669 (  118)
  hydrogen bonds       : angle       6.20284 (  294)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.8284 (pp30) cc_final: 0.7928 (pp30)
REVERT: A  272 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7507 (mmt90)
REVERT: B   62 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7449 (ttt-90)
REVERT: B  232 TRP cc_start: 0.8790 (t60) cc_final: 0.8384 (t60)
  outliers start: 19
  outliers final: 14
  residues processed: 95
  average time/residue: 0.0645
  time to fit residues: 8.3516
Evaluate side-chains
  94 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  272 ARG
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  276 ASP
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  329 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 48 optimal weight:    0.1980
   chunk 61 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 35 optimal weight:    8.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.4388 r_free = 0.4388 target = 0.185475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.134253 restraints weight = 7350.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 3.87
r_work: 0.3689 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.3508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5606  Z= 0.135
  Angle     :  0.708  11.683   7604  Z= 0.369
  Chirality :  0.046   0.231    808
  Planarity :  0.004   0.031    962
  Dihedral  :  5.220  26.074    726
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.96 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 25.75 %
    Favored  : 70.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.54 %
    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: -1.81 (0.33), residues: 678
  helix:  0.31 (0.68), residues: 68
  sheet: -1.03 (0.44), residues: 150
  loop : -1.58 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 322 
 TYR   0.017   0.001   TYR B  32 
 PHE   0.019   0.002   PHE A 133 
 TRP   0.008   0.001   TRP A 225 
 HIS   0.005   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 5594)
  covalent geometry    : angle       0.70846 ( 7580)
  SS BOND              : bond        0.00146 (   12)
  SS BOND              : angle       0.54500 (   24)
  hydrogen bonds       : bond        0.02771 (  118)
  hydrogen bonds       : angle       6.21960 (  294)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.8350 (pp30) cc_final: 0.7940 (pp30)
REVERT: A  272 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7512 (mmt90)
REVERT: B   62 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7476 (ttt-90)
REVERT: B  232 TRP cc_start: 0.8851 (t60) cc_final: 0.8453 (t60)
  outliers start: 20
  outliers final: 17
  residues processed: 89
  average time/residue: 0.0629
  time to fit residues: 7.6843
Evaluate side-chains
  101 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   97 MET
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  272 ARG
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue   97 MET
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  275 MET
Chi-restraints excluded: chain B residue  276 ASP
Chi-restraints excluded: chain B residue  329 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 25 optimal weight:    0.5980
   chunk 31 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 28 optimal weight:    9.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    2.7188

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

Flipped N/Q/H residues before XYZ refinement:
B 107 GLN
B 129 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.184877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.131341 restraints weight = 7581.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3780 rms_B_bonded: 3.81
r_work: 0.3614 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.3876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   5606  Z= 0.268
  Angle     :  0.801  11.499   7604  Z= 0.422
  Chirality :  0.049   0.239    808
  Planarity :  0.004   0.038    962
  Dihedral  :  6.010  29.725    726
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.88 %
    Favored  : 90.12 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 24.58 %
    Favored  : 71.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.54 %
    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: -2.03 (0.34), residues: 678
  helix:  0.10 (0.69), residues: 68
  sheet: -1.53 (0.41), residues: 176
  loop : -1.55 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 322 
 TYR   0.018   0.002   TYR B  32 
 PHE   0.034   0.003   PHE A 133 
 TRP   0.017   0.002   TRP B 225 
 HIS   0.007   0.002   HIS A 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00614 ( 5594)
  covalent geometry    : angle       0.80099 ( 7580)
  SS BOND              : bond        0.00285 (   12)
  SS BOND              : angle       0.89985 (   24)
  hydrogen bonds       : bond        0.03401 (  118)
  hydrogen bonds       : angle       6.71382 (  294)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 77
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.8400 (pp30) cc_final: 0.7997 (pp30)
REVERT: A  272 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7574 (mmt90)
REVERT: B   62 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7475 (ttt-90)
REVERT: B  232 TRP cc_start: 0.8954 (t60) cc_final: 0.8627 (t60)
  outliers start: 26
  outliers final: 16
  residues processed: 95
  average time/residue: 0.0606
  time to fit residues: 7.8020
Evaluate side-chains
  94 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 THR
Chi-restraints excluded: chain A residue   64 GLU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  185 SER
Chi-restraints excluded: chain A residue  191 ASN
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  272 ARG
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  252 SER
Chi-restraints excluded: chain B residue  275 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 16 optimal weight:    0.0470
   chunk 49 optimal weight:    4.9990
   chunk 47 optimal weight:    0.0570
   chunk 53 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 37 optimal weight:    8.9990
   chunk 17 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
** B 263 GLN ** 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 = 0.4379 r_free = 0.4379 target = 0.184930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.134607 restraints weight = 7333.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3864 rms_B_bonded: 3.85
r_work: 0.3705 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.3790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5606  Z= 0.124
  Angle     :  0.729  11.617   7604  Z= 0.382
  Chirality :  0.047   0.246    808
  Planarity :  0.004   0.034    962
  Dihedral  :  5.439  27.461    726
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.41 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 25.25 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.54 %
    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: -1.77 (0.33), residues: 678
  helix:  0.33 (0.68), residues: 68
  sheet: -0.98 (0.44), residues: 154
  loop : -1.55 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 322 
 TYR   0.017   0.001   TYR B  32 
 PHE   0.021   0.002   PHE A 133 
 TRP   0.013   0.001   TRP A 225 
 HIS   0.003   0.001   HIS B 195 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 5594)
  covalent geometry    : angle       0.72945 ( 7580)
  SS BOND              : bond        0.00172 (   12)
  SS BOND              : angle       0.59348 (   24)
  hydrogen bonds       : bond        0.02805 (  118)
  hydrogen bonds       : angle       6.27969 (  294)

===============================================================================
Job complete
usr+sys time: 1414.98 seconds
wall clock time: 24 minutes 50.38 seconds (1490.38 seconds total)