Starting phenix.real_space_refine
on Thu Mar  6 08:44:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wus_32840/03_2025/7wus_32840.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wus_32840/03_2025/7wus_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_2025/7wus_32840.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wus_32840/03_2025/7wus_32840.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wus_32840/03_2025/7wus_32840.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wus_32840/03_2025/7wus_32840.cif"
  }
  resolution = 3.4
  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
-------------------------------------------------------------------------------
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.57, per 1000 atoms: 0.84
  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: 1.14
  Conformation dependent library (CDL) restraints added in 663.1 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: 0.61
  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: 1.39

  Time building geometry restraints manager: 1.41 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: 0.03
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=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:             0.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.200
  Find NCS groups from input model:        0.090
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.680
-------------------------------------------------------------------------------
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   5594  Z= 0.170
  Angle     :  0.748  11.636   7580  Z= 0.404
  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 (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: -2.40 (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
 TRP   0.011   0.001   TRP B 225 
 HIS   0.002   0.000   HIS A 195 
 PHE   0.009   0.001   PHE B 217 
 TYR   0.012   0.001   TYR B  32 
 ARG   0.009   0.001   ARG A 324 

*********************** 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  : 0.568 
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: 0.8181 (t60)
  outliers start: 6
  outliers final: 2
  residues processed: 129
  average time/residue: 0.2172
  time to fit residues: 34.3981
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  : 0.570 
-------------------------------------------------------------------------------
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 57 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 17 optimal weight:    0.6980
   chunk 34 optimal weight:    9.9990
   chunk 27 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 39 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   overall best weight:    3.5388

-------------------------------------------------------------------------------
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**
** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  10 ASN
** B  31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.4213 r_free = 0.4213 target = 0.174306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.130615 restraints weight = 7518.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 3.82
r_work: 0.3494 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.064   5594  Z= 0.518
  Angle     :  0.888  11.988   7580  Z= 0.470
  Chirality :  0.051   0.222    808
  Planarity :  0.006   0.038    962
  Dihedral  :  6.755  51.684    728
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.62 %
    Favored  : 89.38 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 22.91 %
    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 (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: -2.59 (0.32), residues: 678
  helix: -0.72 (0.65), residues: 68
  sheet: -1.86 (0.38), residues: 170
  loop : -1.89 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 311 
 HIS   0.011   0.002   HIS A 195 
 PHE   0.021   0.003   PHE A 217 
 TYR   0.020   0.003   TYR A  32 
 ARG   0.006   0.001   ARG A 257 

*********************** 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
  111 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 75
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  272 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7605 (mmt90)
REVERT: B  232 TRP cc_start: 0.9013 (t60) cc_final: 0.8705 (t60)
REVERT: B  314 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.7837 (mtt-85)
  outliers start: 36
  outliers final: 16
  residues processed: 100
  average time/residue: 0.1648
  time to fit residues: 21.8802
Evaluate side-chains
  88 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
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 A residue  191 ASN
Chi-restraints excluded: chain A residue  272 ARG
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  131 HIS
Chi-restraints excluded: chain B residue  188 ILE
Chi-restraints excluded: chain B residue  194 VAL
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  287 VAL
Chi-restraints excluded: chain B residue  297 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 12 optimal weight:    8.9990
   chunk 34 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  31 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.181147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.131363 restraints weight = 7249.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3740 rms_B_bonded: 3.66
r_work: 0.3571 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.2712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5594  Z= 0.199
  Angle     :  0.752  11.775   7580  Z= 0.397
  Chirality :  0.047   0.230    808
  Planarity :  0.004   0.034    962
  Dihedral  :  5.738  25.741    726
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.70 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 22.41 %
    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 (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: -2.28 (0.32), residues: 678
  helix: -0.19 (0.67), residues: 68
  sheet: -1.79 (0.39), residues: 176
  loop : -1.66 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 225 
 HIS   0.005   0.001   HIS B 195 
 PHE   0.010   0.001   PHE A 133 
 TYR   0.016   0.001   TYR B  32 
 ARG   0.005   0.000   ARG B 324 

*********************** 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
  111 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 84
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.8386 (pp30) cc_final: 0.8028 (pp30)
REVERT: A  333 MET cc_start: 0.7879 (ttm) cc_final: 0.7551 (ttm)
REVERT: B   62 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7492 (ttt-90)
REVERT: B   67 MET cc_start: 0.8980 (tmm) cc_final: 0.8765 (tmm)
REVERT: B  232 TRP cc_start: 0.8879 (t60) cc_final: 0.8533 (t60)
REVERT: B  324 ARG cc_start: 0.8185 (mtt-85) cc_final: 0.7927 (mtt90)
  outliers start: 27
  outliers final: 13
  residues processed: 100
  average time/residue: 0.1636
  time to fit residues: 21.7265
Evaluate side-chains
  95 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
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 B residue   62 ARG
Chi-restraints excluded: chain B residue   84 VAL
Chi-restraints excluded: chain B residue  131 HIS
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  180 ASP
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 20 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 67 optimal weight:    4.9990
   chunk 1 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 57 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4238 r_free = 0.4238 target = 0.177154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.127369 restraints weight = 7411.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 3.69
r_work: 0.3521 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5594  Z= 0.308
  Angle     :  0.785  11.803   7580  Z= 0.410
  Chirality :  0.049   0.233    808
  Planarity :  0.004   0.035    962
  Dihedral  :  5.880  28.250    726
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.44 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 23.75 %
    Favored  : 72.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.54 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.26 (0.33), residues: 678
  helix: -0.12 (0.67), residues: 68
  sheet: -1.71 (0.40), residues: 176
  loop : -1.69 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  28 
 HIS   0.007   0.001   HIS B 195 
 PHE   0.022   0.002   PHE A 133 
 TYR   0.017   0.002   TYR B  32 
 ARG   0.004   0.001   ARG A 257 

*********************** 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
  106 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 81
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.8393 (pp30) cc_final: 0.8032 (pp30)
REVERT: A  333 MET cc_start: 0.8057 (ttm) cc_final: 0.7778 (ttp)
REVERT: B   34 PHE cc_start: 0.8380 (m-80) cc_final: 0.7939 (m-80)
REVERT: B   62 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7618 (ttt-90)
REVERT: B   83 GLU cc_start: 0.8184 (mp0) cc_final: 0.7729 (tm-30)
REVERT: B  232 TRP cc_start: 0.8947 (t60) cc_final: 0.8618 (t60)
REVERT: B  289 GLU cc_start: 0.7126 (tp30) cc_final: 0.6924 (tp30)
REVERT: B  321 LEU cc_start: 0.9209 (tp) cc_final: 0.8996 (tp)
  outliers start: 25
  outliers final: 19
  residues processed: 93
  average time/residue: 0.1668
  time to fit residues: 20.6024
Evaluate side-chains
  98 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
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   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  216 SER
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   84 VAL
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  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
Chi-restraints excluded: chain B residue  276 ASP
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 51 optimal weight:    6.9990
   chunk 63 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 17 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 62 optimal weight:    0.1980
   chunk 33 optimal weight:    0.7980
   chunk 10 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  70 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.182636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.131675 restraints weight = 7338.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 3.72
r_work: 0.3587 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.3115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5594  Z= 0.176
  Angle     :  0.720  11.778   7580  Z= 0.376
  Chirality :  0.047   0.234    808
  Planarity :  0.004   0.032    962
  Dihedral  :  5.541  26.718    726
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 24.25 %
    Favored  : 72.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.54 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.08 (0.33), residues: 678
  helix:  0.16 (0.67), residues: 68
  sheet: -1.57 (0.41), residues: 164
  loop : -1.61 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 225 
 HIS   0.004   0.001   HIS B 195 
 PHE   0.016   0.002   PHE A 133 
 TYR   0.018   0.001   TYR B  32 
 ARG   0.003   0.000   ARG B 322 

*********************** 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
  106 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 GLN cc_start: 0.5114 (OUTLIER) cc_final: 0.4831 (tt0)
REVERT: A  175 GLN cc_start: 0.8352 (pp30) cc_final: 0.8046 (pp30)
REVERT: A  272 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7439 (mmt90)
REVERT: A  333 MET cc_start: 0.7877 (ttm) cc_final: 0.7623 (ttm)
REVERT: B   34 PHE cc_start: 0.8285 (m-80) cc_final: 0.7440 (m-80)
REVERT: B   62 ARG cc_start: 0.8177 (ptp-110) cc_final: 0.7495 (ttt-90)
REVERT: B  123 MET cc_start: 0.1944 (ttp) cc_final: 0.1733 (tmm)
REVERT: B  232 TRP cc_start: 0.8851 (t60) cc_final: 0.8489 (t60)
  outliers start: 22
  outliers final: 18
  residues processed: 96
  average time/residue: 0.1670
  time to fit residues: 21.1371
Evaluate side-chains
  98 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 GLN
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  167 ILE
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   84 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  180 ASP
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  329 CYS
Chi-restraints excluded: chain B residue  333 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 44 optimal weight:    0.3980
   chunk 51 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 36 optimal weight:    9.9990
   chunk 59 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  70 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.192487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.138545 restraints weight = 7402.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3864 rms_B_bonded: 3.89
r_work: 0.3699 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.3202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5594  Z= 0.176
  Angle     :  0.702  11.793   7580  Z= 0.368
  Chirality :  0.046   0.232    808
  Planarity :  0.004   0.031    962
  Dihedral  :  5.341  26.432    726
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 23.58 %
    Favored  : 72.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.54 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.99 (0.33), residues: 678
  helix:  0.14 (0.66), residues: 68
  sheet: -1.43 (0.41), residues: 162
  loop : -1.57 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 225 
 HIS   0.003   0.001   HIS B 195 
 PHE   0.013   0.001   PHE A 133 
 TYR   0.018   0.001   TYR B  32 
 ARG   0.004   0.000   ARG B 324 

*********************** 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
  106 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 80
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 ASP cc_start: 0.5372 (OUTLIER) cc_final: 0.5107 (t0)
REVERT: A  175 GLN cc_start: 0.8357 (pp30) cc_final: 0.7983 (pp30)
REVERT: A  272 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7543 (mmt90)
REVERT: B   32 TYR cc_start: 0.6715 (OUTLIER) cc_final: 0.5911 (p90)
REVERT: B   34 PHE cc_start: 0.8225 (m-80) cc_final: 0.7485 (m-80)
REVERT: B   62 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7501 (ttt-90)
REVERT: B  232 TRP cc_start: 0.8850 (t60) cc_final: 0.8503 (t60)
  outliers start: 26
  outliers final: 13
  residues processed: 97
  average time/residue: 0.1620
  time to fit residues: 21.0108
Evaluate side-chains
  94 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASP
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  252 SER
Chi-restraints excluded: chain A residue  272 ARG
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   32 TYR
Chi-restraints excluded: chain B residue   62 ARG
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  329 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   chunk 45 optimal weight:    8.9990
   chunk 16 optimal weight:    0.8980
   chunk 64 optimal weight:    0.2980
   chunk 20 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 30 optimal weight:    9.9990
   chunk 27 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B  70 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.192601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.139527 restraints weight = 7332.405|
|-----------------------------------------------------------------------------|
r_work (start): 0.3871 rms_B_bonded: 3.79
r_work: 0.3712 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.3331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5594  Z= 0.186
  Angle     :  0.707  11.729   7580  Z= 0.370
  Chirality :  0.046   0.232    808
  Planarity :  0.003   0.031    962
  Dihedral  :  5.317  26.329    726
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 23.75 %
    Favored  : 71.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.54 %
    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: -1.95 (0.32), residues: 678
  helix:  0.14 (0.66), residues: 68
  sheet: -1.27 (0.41), residues: 154
  loop : -1.60 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 225 
 HIS   0.004   0.001   HIS B 195 
 PHE   0.017   0.002   PHE A 133 
 TYR   0.018   0.001   TYR B  32 
 ARG   0.004   0.000   ARG B 324 

*********************** 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
  105 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 78
  time to evaluate  : 0.617 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   23 ASP cc_start: 0.5174 (OUTLIER) cc_final: 0.4920 (t0)
REVERT: A  175 GLN cc_start: 0.8360 (pp30) cc_final: 0.7973 (pp30)
REVERT: A  272 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7589 (mmt90)
REVERT: B   32 TYR cc_start: 0.6596 (OUTLIER) cc_final: 0.5746 (p90)
REVERT: B   34 PHE cc_start: 0.8202 (m-80) cc_final: 0.7442 (m-80)
REVERT: B   62 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7423 (ttt-90)
REVERT: B  232 TRP cc_start: 0.8837 (t60) cc_final: 0.8453 (t60)
  outliers start: 27
  outliers final: 17
  residues processed: 97
  average time/residue: 0.1600
  time to fit residues: 20.7713
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  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ASP
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   97 MET
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  152 SER
Chi-restraints excluded: chain A residue  157 ASP
Chi-restraints excluded: chain A residue  167 ILE
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   32 TYR
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  329 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 46 optimal weight:    8.9990
   chunk 16 optimal weight:    0.5980
   chunk 49 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 8 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  70 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.185120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.134332 restraints weight = 7236.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3865 rms_B_bonded: 3.81
r_work: 0.3705 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.3426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5594  Z= 0.190
  Angle     :  0.709  11.698   7580  Z= 0.368
  Chirality :  0.046   0.232    808
  Planarity :  0.003   0.031    962
  Dihedral  :  5.256  26.357    726
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 23.58 %
    Favored  : 72.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.54 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.90 (0.33), residues: 678
  helix:  0.25 (0.67), residues: 68
  sheet: -1.23 (0.40), residues: 154
  loop : -1.57 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 225 
 HIS   0.004   0.001   HIS B 195 
 PHE   0.009   0.001   PHE A 133 
 TYR   0.018   0.001   TYR B  32 
 ARG   0.004   0.000   ARG B 324 

*********************** 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
  100 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.8356 (pp30) cc_final: 0.7976 (pp30)
REVERT: A  198 MET cc_start: 0.8436 (mmp) cc_final: 0.8214 (mmp)
REVERT: A  272 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7599 (mmt90)
REVERT: B   32 TYR cc_start: 0.6530 (OUTLIER) cc_final: 0.5683 (p90)
REVERT: B   34 PHE cc_start: 0.8215 (m-80) cc_final: 0.7470 (m-80)
REVERT: B   62 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7332 (ttt-90)
REVERT: B  232 TRP cc_start: 0.8850 (t60) cc_final: 0.8506 (t60)
  outliers start: 25
  outliers final: 16
  residues processed: 93
  average time/residue: 0.1582
  time to fit residues: 19.6751
Evaluate side-chains
  97 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
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  103 SER
Chi-restraints excluded: chain A residue  152 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 B residue   32 TYR
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  209 THR
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  252 SER
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 10 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:    7.9990
   chunk 33 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B  70 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 = 0.4381 r_free = 0.4381 target = 0.190864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.137410 restraints weight = 7401.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3858 rms_B_bonded: 3.82
r_work: 0.3697 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5594  Z= 0.219
  Angle     :  0.720  11.711   7580  Z= 0.374
  Chirality :  0.047   0.232    808
  Planarity :  0.004   0.035    962
  Dihedral  :  5.368  26.963    726
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 24.08 %
    Favored  : 72.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.54 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.89 (0.33), residues: 678
  helix:  0.23 (0.67), residues: 68
  sheet: -1.22 (0.41), residues: 154
  loop : -1.57 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 225 
 HIS   0.005   0.001   HIS B 195 
 PHE   0.009   0.002   PHE A 163 
 TYR   0.018   0.001   TYR B  32 
 ARG   0.004   0.000   ARG B 324 

*********************** 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
  102 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.8369 (pp30) cc_final: 0.8006 (pp30)
REVERT: A  272 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7533 (mmt90)
REVERT: A  278 ASP cc_start: 0.7995 (m-30) cc_final: 0.7678 (m-30)
REVERT: B   32 TYR cc_start: 0.6682 (OUTLIER) cc_final: 0.5936 (p90)
REVERT: B   62 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7444 (ttt-90)
REVERT: B  232 TRP cc_start: 0.8893 (t60) cc_final: 0.8565 (t60)
  outliers start: 23
  outliers final: 18
  residues processed: 94
  average time/residue: 0.1589
  time to fit residues: 19.9745
Evaluate side-chains
  95 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
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  103 SER
Chi-restraints excluded: chain A residue  152 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   32 TYR
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  209 THR
Chi-restraints excluded: chain B residue  238 GLU
Chi-restraints excluded: chain B residue  252 SER
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 41 optimal weight:    0.0970
   chunk 51 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 44 optimal weight:    8.9990
   chunk 15 optimal weight:    0.4980
   chunk 13 optimal weight:    0.0170
   chunk 36 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.4216

-------------------------------------------------------------------------------
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 = 0.4399 r_free = 0.4399 target = 0.187085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.136765 restraints weight = 7363.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3894 rms_B_bonded: 3.86
r_work: 0.3739 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.3670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5594  Z= 0.165
  Angle     :  0.714  11.757   7580  Z= 0.371
  Chirality :  0.046   0.229    808
  Planarity :  0.003   0.032    962
  Dihedral  :  5.193  25.795    726
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 24.58 %
    Favored  : 72.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 1.54 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.80 (0.33), residues: 678
  helix:  0.23 (0.67), residues: 68
  sheet: -1.16 (0.41), residues: 154
  loop : -1.49 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 225 
 HIS   0.003   0.000   HIS B 195 
 PHE   0.010   0.001   PHE A 163 
 TYR   0.018   0.001   TYR B  32 
 ARG   0.004   0.000   ARG B 324 

********************** 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
  97 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 GLN cc_start: 0.8396 (pp30) cc_final: 0.7960 (pp30)
REVERT: A  198 MET cc_start: 0.8384 (mmp) cc_final: 0.7754 (mmt)
REVERT: A  272 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7482 (mmt90)
REVERT: A  278 ASP cc_start: 0.8041 (m-30) cc_final: 0.7642 (m-30)
REVERT: A  331 TYR cc_start: 0.8709 (m-80) cc_final: 0.7978 (t80)
REVERT: B   32 TYR cc_start: 0.6172 (OUTLIER) cc_final: 0.5452 (p90)
REVERT: B   62 ARG cc_start: 0.8002 (ptp-110) cc_final: 0.7271 (ttt-90)
REVERT: B  232 TRP cc_start: 0.8796 (t60) cc_final: 0.8423 (t60)
  outliers start: 20
  outliers final: 16
  residues processed: 90
  average time/residue: 0.1658
  time to fit residues: 19.8298
Evaluate side-chains
  92 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
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   97 MET
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  152 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 B residue   21 ILE
Chi-restraints excluded: chain B residue   32 TYR
Chi-restraints excluded: chain B residue   84 VAL
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  287 VAL
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 56 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0070
   chunk 32 optimal weight:    0.9980
   chunk 43 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 66 optimal weight:    1.9990
   chunk 16 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 19 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.8600

-------------------------------------------------------------------------------
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 = 0.4380 r_free = 0.4380 target = 0.185134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.135283 restraints weight = 7312.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 3.81
r_work: 0.3716 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.3705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5594  Z= 0.198
  Angle     :  0.721  11.714   7580  Z= 0.375
  Chirality :  0.046   0.230    808
  Planarity :  0.004   0.035    962
  Dihedral  :  5.187  26.221    726
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 24.92 %
    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 (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: -1.80 (0.33), residues: 678
  helix:  0.51 (0.69), residues: 66
  sheet: -1.15 (0.41), residues: 154
  loop : -1.54 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 225 
 HIS   0.005   0.001   HIS B 195 
 PHE   0.012   0.002   PHE A 163 
 TYR   0.018   0.001   TYR B  32 
 ARG   0.004   0.000   ARG B 324 

===============================================================================
Job complete
usr+sys time: 3002.33 seconds
wall clock time: 52 minutes 9.47 seconds (3129.47 seconds total)