Starting phenix.real_space_refine
on Wed Mar 12 08:23:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8okd_16926/03_2025/8okd_16926.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8okd_16926/03_2025/8okd_16926.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8okd_16926/03_2025/8okd_16926.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8okd_16926/03_2025/8okd_16926.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8okd_16926/03_2025/8okd_16926.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8okd_16926/03_2025/8okd_16926.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.058
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     138      5.49       5
     S      30      5.16       5
     C    4392      2.51       5
     N    1358      2.21       5
     O    1830      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7748
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2390
          Classifications: {'peptide': 291}
          Link IDs: {'PTRANS': 11, 'TRANS': 279}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2390
          Classifications: {'peptide': 291}
          Link IDs: {'PTRANS': 11, 'TRANS': 279}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 1484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 1484
          Classifications: {'RNA': 70}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 28, 'rna3p_pyr': 31}
          Link IDs: {'rna2p': 10, 'rna3p': 59}
          Chain breaks: 1
    Chain: "X"
      Number of atoms: 1484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 1484
          Classifications: {'RNA': 70}
          Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 27, 'rna3p_pyr': 31}
          Link IDs: {'rna2p': 11, 'rna3p': 58}
          Chain breaks: 1
  Time building chain proxies: 5.44, per 1000 atoms: 0.70
  Number of scatterers: 7748
  At special positions: 0
  Unit cell: (98.9, 162.54, 66.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      30     16.00
     P     138     15.00
     O    1830      8.00
     N    1358      7.00
     C    4392      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.03
  Conformation dependent library (CDL) restraints added in 547.3 milliseconds
  

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1112

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 7 sheets defined
      37.3% alpha, 21.0% beta
      46 base pairs and 67 stacking pairs defined.
    Time for finding SS restraints: 3.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 60
      removed outlier: 3.782A  pdb=" N   ALA A  59 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 101
      removed outlier: 3.718A  pdb=" N   LYS A  92 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 109
      removed outlier: 3.954A  pdb=" N   SER A 109 " --> pdb=" O   ARG A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 164
    Processing helix  chain 'A' and resid 206 through 212
    Processing helix  chain 'A' and resid 213 through 217
      removed outlier: 3.862A  pdb=" N   VAL A 217 " --> pdb=" O   GLN A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 262
    Processing helix  chain 'A' and resid 277 through 291
      removed outlier: 3.746A  pdb=" N   CYS A 281 " --> pdb=" O   HIS A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 304
      removed outlier: 4.281A  pdb=" N   GLU A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ASN A 304 " --> pdb=" O   ASP A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 308
    Processing helix  chain 'A' and resid 337 through 369
      removed outlier: 3.842A  pdb=" N   LYS A 358 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU A 369 " --> pdb=" O   MET A 365 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 60
      removed outlier: 3.909A  pdb=" N   ALA B  59 " --> pdb=" O   ASP B  56 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   HIS B  60 " --> pdb=" O   PHE B  57 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 56 through 60'
    Processing helix  chain 'B' and resid 88 through 100
      removed outlier: 3.827A  pdb=" N   LYS B  92 " --> pdb=" O   THR B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 109
      removed outlier: 4.038A  pdb=" N   SER B 109 " --> pdb=" O   ARG B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 166
      removed outlier: 3.660A  pdb=" N   ARG B 166 " --> pdb=" O   HIS B 162 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 185 through 190
    Processing helix  chain 'B' and resid 205 through 214
    Processing helix  chain 'B' and resid 215 through 217
      No H-bonds generated for 'chain 'B' and resid 215 through 217'
    Processing helix  chain 'B' and resid 259 through 263
    Processing helix  chain 'B' and resid 277 through 291
      removed outlier: 3.731A  pdb=" N   CYS B 281 " --> pdb=" O   HIS B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 304
      removed outlier: 4.333A  pdb=" N   GLU B 301 " --> pdb=" O   GLU B 297 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ASN B 304 " --> pdb=" O   ASP B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 369
      removed outlier: 3.801A  pdb=" N   LYS B 358 " --> pdb=" O   ASN B 354 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   LEU B 369 " --> pdb=" O   MET B 365 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113
      removed outlier: 3.762A  pdb=" N   SER A 129 " --> pdb=" O   HIS A 112 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ILE A 128 " --> pdb=" O   LEU A  67 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113
      removed outlier: 3.762A  pdb=" N   SER A 129 " --> pdb=" O   HIS A 112 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ILE A 128 " --> pdb=" O   LEU A  67 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 123
      removed outlier: 7.098A  pdb=" N   SER A 122 " --> pdb=" O   LEU A 324 " (cutoff:3.500A)
      removed outlier: 8.216A  pdb=" N   ASP A 326 " --> pdb=" O   SER A 122 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   THR A 194 " --> pdb=" O   TYR A 325 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER A 243 " --> pdb=" O   THR A 270 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 221
      removed outlier: 3.531A  pdb=" N   GLY A 218 " --> pdb=" O   ILE A 241 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ILE A 241 " --> pdb=" O   GLY A 218 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   HIS A 220 " --> pdb=" O   ARG A 239 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   ARG A 239 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 126 through 134
      removed outlier: 7.798A  pdb=" N   HIS B  64 " --> pdb=" O   PRO B 179 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ALA B  66 " --> pdb=" O   TRP B 177 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   TRP B 177 " --> pdb=" O   ALA B  66 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ARG B  68 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 122 through 123
      removed outlier: 6.824A  pdb=" N   SER B 122 " --> pdb=" O   LEU B 324 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   ASP B 326 " --> pdb=" O   SER B 122 " (cutoff:3.500A)
      removed outlier: 7.257A  pdb=" N   THR B 194 " --> pdb=" O   TYR B 325 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL B 269 " --> pdb=" O   TYR B 195 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 220 through 221

    190 hydrogen bonds defined for protein.
    507 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      120 hydrogen bonds
      212 hydrogen bond angles
      0 basepair planarities
      46 basepair parallelities
      67 stacking parallelities
  Total time for adding SS restraints: 2.54

  Time building geometry restraints manager: 2.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1941
        1.34 -     1.46: 2451
        1.46 -     1.57: 3492
        1.57 -     1.69: 274
        1.69 -     1.81: 48
  Bond restraints: 8206
  Sorted by residual:
  bond pdb=" C   GLU A 260 "
       pdb=" N   PRO A 261 "
    ideal  model  delta    sigma   weight residual
    1.334  1.345 -0.011 8.40e-03 1.42e+04 1.75e+00
  bond pdb=" C   GLU B 260 "
       pdb=" N   PRO B 261 "
    ideal  model  delta    sigma   weight residual
    1.334  1.344 -0.011 8.40e-03 1.42e+04 1.68e+00
  bond pdb=" CB  LYS A 307 "
       pdb=" CG  LYS A 307 "
    ideal  model  delta    sigma   weight residual
    1.520  1.544 -0.024 3.00e-02 1.11e+03 6.35e-01
  bond pdb=" CG1 ILE A  69 "
       pdb=" CD1 ILE A  69 "
    ideal  model  delta    sigma   weight residual
    1.513  1.485  0.028 3.90e-02 6.57e+02 5.31e-01
  bond pdb=" C3'   U X  20 "
       pdb=" O3'   U X  20 "
    ideal  model  delta    sigma   weight residual
    1.417  1.428 -0.011 1.50e-02 4.44e+03 5.18e-01
  ... (remaining 8201 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 11572
        1.66 -     3.31: 167
        3.31 -     4.97: 21
        4.97 -     6.63: 3
        6.63 -     8.28: 3
  Bond angle restraints: 11766
  Sorted by residual:
  angle pdb=" N   GLY A 233 "
        pdb=" CA  GLY A 233 "
        pdb=" C   GLY A 233 "
      ideal   model   delta    sigma   weight residual
     113.18  121.06   -7.88 2.37e+00 1.78e-01 1.10e+01
  angle pdb=" CB  MET B 283 "
        pdb=" CG  MET B 283 "
        pdb=" SD  MET B 283 "
      ideal   model   delta    sigma   weight residual
     112.70  120.98   -8.28 3.00e+00 1.11e-01 7.63e+00
  angle pdb=" CA  LYS A 307 "
        pdb=" CB  LYS A 307 "
        pdb=" CG  LYS A 307 "
      ideal   model   delta    sigma   weight residual
     114.10  119.38   -5.28 2.00e+00 2.50e-01 6.98e+00
  angle pdb=" C   ALA B 118 "
        pdb=" N   LYS B 119 "
        pdb=" CA  LYS B 119 "
      ideal   model   delta    sigma   weight residual
     120.90  124.51   -3.61 1.41e+00 5.03e-01 6.55e+00
  angle pdb=" CA  LEU B 303 "
        pdb=" CB  LEU B 303 "
        pdb=" CG  LEU B 303 "
      ideal   model   delta    sigma   weight residual
     116.30  124.17   -7.87 3.50e+00 8.16e-02 5.05e+00
  ... (remaining 11761 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.81: 4606
       32.81 -    65.63: 431
       65.63 -    98.44: 58
       98.44 -   131.25: 2
      131.25 -   164.07: 1
  Dihedral angle restraints: 5098
    sinusoidal: 3384
      harmonic: 1714
  Sorted by residual:
  dihedral pdb=" O4'   C X  48 "
           pdb=" C1'   C X  48 "
           pdb=" N1    C X  48 "
           pdb=" C2    C X  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -54.00 -106.00     1      1.50e+01 4.44e-03 5.44e+01
  dihedral pdb=" O4'   C C  48 "
           pdb=" C1'   C C  48 "
           pdb=" N1    C C  48 "
           pdb=" C2    C C  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -57.34 -102.66     1      1.50e+01 4.44e-03 5.20e+01
  dihedral pdb=" O4'   U X  20 "
           pdb=" C1'   U X  20 "
           pdb=" N1    U X  20 "
           pdb=" C2    U X  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -78.93  -81.07     1      1.50e+01 4.44e-03 3.60e+01
  ... (remaining 5095 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1177
       0.042 -    0.083: 169
       0.083 -    0.125: 54
       0.125 -    0.167: 5
       0.167 -    0.208: 1
  Chirality restraints: 1406
  Sorted by residual:
  chirality pdb=" C1'   U C  39 "
            pdb=" O4'   U C  39 "
            pdb=" C2'   U C  39 "
            pdb=" N1    U C  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.26    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  ILE A 128 "
            pdb=" N   ILE A 128 "
            pdb=" C   ILE A 128 "
            pdb=" CB  ILE A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 6.00e-01
  chirality pdb=" CA  PHE A 320 "
            pdb=" N   PHE A 320 "
            pdb=" C   PHE A 320 "
            pdb=" CB  PHE A 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.07e-01
  ... (remaining 1403 not shown)

  Planarity restraints: 996
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 267 "   -0.010 2.00e-02 2.50e+03   1.50e-02 3.94e+00
        pdb=" CG  PHE A 267 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 267 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 267 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 267 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 267 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 267 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 295 "   -0.024 5.00e-02 4.00e+02   3.65e-02 2.13e+00
        pdb=" N   PRO B 296 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B 296 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 296 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 124 "    0.007 2.00e-02 2.50e+03   1.04e-02 1.88e+00
        pdb=" CG  PHE A 124 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 124 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 124 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 124 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 124 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 124 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 993 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 947
        2.75 -     3.28: 7297
        3.28 -     3.82: 13914
        3.82 -     4.36: 16028
        4.36 -     4.90: 24623
  Nonbonded interactions: 62809
  Sorted by model distance:
  nonbonded pdb=" O2'   A C   7 "
            pdb=" O2    C C  48 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O2'   A X   7 "
            pdb=" O2    C X  48 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O2'   A C  57 "
            pdb=" OP2   U C  59 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" ND2 ASN B 224 "
            pdb=" O   LEU B 302 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" O   GLY A 115 "
            pdb=" NE2 GLN A 126 "
     model   vdw
     2.306 3.120
  ... (remaining 62804 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'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'X'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     23.440
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5958
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   0.028   8206  Z= 0.180
  Angle     :  0.509   8.284  11766  Z= 0.267
  Chirality :  0.034   0.208   1406
  Planarity :  0.003   0.036    996
  Dihedral  : 21.865 164.067   3986
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 35.94 %
    Favored  : 63.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.35), residues: 570
  helix:  1.83 (0.43), residues: 146
  sheet: -0.83 (0.51), residues: 100
  loop : -1.57 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 352 
 HIS   0.002   0.001   HIS A 360 
 PHE   0.034   0.002   PHE A 267 
 TYR   0.007   0.001   TYR A 160 
 ARG   0.002   0.000   ARG B 193 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.566 
Fit side-chains
REVERT: A  119 LYS cc_start: 0.6643 (pttt) cc_final: 0.6378 (ptmm)
REVERT: A  228 MET cc_start: 0.6839 (mtm) cc_final: 0.6537 (mtp)
REVERT: A  313 GLN cc_start: 0.5796 (tp-100) cc_final: 0.5578 (mt0)
REVERT: A  316 MET cc_start: 0.5871 (ptp) cc_final: 0.5106 (ptt)
REVERT: A  320 PHE cc_start: 0.6789 (p90) cc_final: 0.5657 (p90)
REVERT: A  328 LYS cc_start: 0.5720 (ttmm) cc_final: 0.5416 (ttpt)
REVERT: A  331 ASN cc_start: 0.7059 (m-40) cc_final: 0.6816 (m-40)
REVERT: B  210 ASP cc_start: 0.6151 (t0) cc_final: 0.5945 (t0)
REVERT: B  247 GLN cc_start: 0.6086 (pt0) cc_final: 0.5367 (pm20)
REVERT: B  282 MET cc_start: 0.5447 (tpp) cc_final: 0.5172 (mtt)
REVERT: B  347 HIS cc_start: 0.5805 (t70) cc_final: 0.5526 (t-170)
  outliers start: 2
  outliers final: 1
  residues processed: 100
  average time/residue: 0.2438
  time to fit residues: 31.3901
Evaluate side-chains
  65 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  361 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    7.9990
   chunk 54 optimal weight:    0.4980
   chunk 30 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 29 optimal weight:    7.9990
   chunk 56 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 65 optimal weight:   10.0000
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 126 GLN
A 238 GLN
A 247 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.197158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.162491 restraints weight = 8731.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.4033 rms_B_bonded: 1.44
r_work: 0.3819 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7527
moved from start:          0.1528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8206  Z= 0.175
  Angle     :  0.532   8.542  11766  Z= 0.276
  Chirality :  0.035   0.194   1406
  Planarity :  0.004   0.034    996
  Dihedral  : 21.066 162.652   2821
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 32.81 %
    Favored  : 64.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.35), residues: 570
  helix:  1.83 (0.42), residues: 146
  sheet: -0.48 (0.50), residues: 90
  loop : -1.49 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 352 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.021   0.002   PHE A 320 
 TYR   0.008   0.001   TYR A 197 
 ARG   0.004   0.001   ARG B 133 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.665 
Fit side-chains
REVERT: A  304 ASN cc_start: 0.6875 (m-40) cc_final: 0.6034 (t0)
REVERT: A  316 MET cc_start: 0.5795 (ptp) cc_final: 0.5529 (ptt)
REVERT: B  282 MET cc_start: 0.5977 (tpp) cc_final: 0.5753 (mtt)
REVERT: B  303 LEU cc_start: 0.7442 (pp) cc_final: 0.6850 (mt)
  outliers start: 16
  outliers final: 9
  residues processed: 76
  average time/residue: 0.1912
  time to fit residues: 20.2918
Evaluate side-chains
  65 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  361 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 52 optimal weight:    0.0060
   chunk 0 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0670
   chunk 43 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    2.0140

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

Flipped N/Q/H residues before XYZ refinement:
A 126 GLN
A 247 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.191222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.155708 restraints weight = 8861.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 1.29
r_work: 0.3765 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3619 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.2548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8206  Z= 0.262
  Angle     :  0.604   8.304  11766  Z= 0.313
  Chirality :  0.039   0.248   1406
  Planarity :  0.004   0.037    996
  Dihedral  : 21.090 157.449   2818
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 29.30 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.34), residues: 570
  helix:  1.07 (0.40), residues: 158
  sheet: -0.54 (0.50), residues: 90
  loop : -1.61 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 352 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.028   0.002   PHE A 320 
 TYR   0.013   0.002   TYR B 276 
 ARG   0.006   0.001   ARG B 133 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 58
  time to evaluate  : 0.603 
Fit side-chains
REVERT: A  304 ASN cc_start: 0.6714 (m-40) cc_final: 0.6086 (t0)
REVERT: A  316 MET cc_start: 0.6799 (ptp) cc_final: 0.6439 (ptt)
REVERT: B   82 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7345 (mt0)
REVERT: B  156 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6581 (pt0)
REVERT: B  260 GLU cc_start: 0.6759 (tm-30) cc_final: 0.6534 (tp30)
REVERT: B  279 VAL cc_start: 0.6827 (OUTLIER) cc_final: 0.6614 (m)
REVERT: B  303 LEU cc_start: 0.7398 (pp) cc_final: 0.6641 (mt)
REVERT: B  350 GLN cc_start: 0.6696 (OUTLIER) cc_final: 0.6273 (mt0)
  outliers start: 26
  outliers final: 13
  residues processed: 76
  average time/residue: 0.1623
  time to fit residues: 17.7356
Evaluate side-chains
  66 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 49
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain A residue  365 MET
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  350 GLN
Chi-restraints excluded: chain B residue  361 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 47 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 126 GLN
B  64 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.192173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.156556 restraints weight = 8861.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3987 rms_B_bonded: 1.47
r_work: 0.3780 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3628 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8206  Z= 0.212
  Angle     :  0.549   8.233  11766  Z= 0.286
  Chirality :  0.037   0.228   1406
  Planarity :  0.004   0.036    996
  Dihedral  : 20.938 156.263   2818
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 27.15 %
    Favored  : 67.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.34), residues: 570
  helix:  1.33 (0.41), residues: 146
  sheet: -0.55 (0.49), residues: 90
  loop : -1.52 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 352 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.025   0.002   PHE A 320 
 TYR   0.010   0.001   TYR A 195 
 ARG   0.006   0.000   ARG B 280 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 50
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.6422 (mp10)
REVERT: A  304 ASN cc_start: 0.6495 (m-40) cc_final: 0.5769 (t0)
REVERT: A  316 MET cc_start: 0.6740 (ptp) cc_final: 0.6469 (ptt)
REVERT: B   64 HIS cc_start: 0.6805 (OUTLIER) cc_final: 0.6202 (t-90)
REVERT: B   82 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7335 (mt0)
REVERT: B  156 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6501 (pt0)
REVERT: B  282 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.5921 (mtt)
REVERT: B  303 LEU cc_start: 0.7247 (pp) cc_final: 0.6476 (mt)
  outliers start: 27
  outliers final: 17
  residues processed: 68
  average time/residue: 0.1729
  time to fit residues: 16.9353
Evaluate side-chains
  70 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 48
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 GLN
Chi-restraints excluded: chain A residue   84 ASN
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  333 LYS
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  362 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 16 optimal weight:    0.0060
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 64 optimal weight:   20.0000
   chunk 51 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 65 optimal weight:   10.0000
   overall best weight:    0.5196

-------------------------------------------------------------------------------
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 = 0.4415 r_free = 0.4415 target = 0.198301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.163971 restraints weight = 8818.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.4050 rms_B_bonded: 1.41
r_work: 0.3842 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3692 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.2797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8206  Z= 0.133
  Angle     :  0.484   7.347  11766  Z= 0.254
  Chirality :  0.034   0.180   1406
  Planarity :  0.003   0.030    996
  Dihedral  : 20.778 154.063   2818
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 29.49 %
    Favored  : 67.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.35), residues: 570
  helix:  1.49 (0.42), residues: 146
  sheet: -0.38 (0.50), residues: 90
  loop : -1.42 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 352 
 HIS   0.006   0.001   HIS B  64 
 PHE   0.020   0.001   PHE A 320 
 TYR   0.006   0.001   TYR A 160 
 ARG   0.006   0.000   ARG B 280 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 53
  time to evaluate  : 0.643 
Fit side-chains
REVERT: A  282 MET cc_start: 0.6527 (mpp) cc_final: 0.6193 (mtm)
REVERT: A  304 ASN cc_start: 0.6320 (m-40) cc_final: 0.5575 (t0)
REVERT: A  316 MET cc_start: 0.6453 (ptp) cc_final: 0.6223 (ptt)
REVERT: B   82 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.7320 (mp10)
REVERT: B  156 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6541 (pt0)
REVERT: B  303 LEU cc_start: 0.7479 (pp) cc_final: 0.6642 (mt)
REVERT: B  350 GLN cc_start: 0.6676 (OUTLIER) cc_final: 0.6297 (mt0)
  outliers start: 16
  outliers final: 7
  residues processed: 68
  average time/residue: 0.1678
  time to fit residues: 16.5214
Evaluate side-chains
  57 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  350 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 46 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   chunk 43 optimal weight:    0.7980
   chunk 67 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9990
   chunk 29 optimal weight:    6.9990
   chunk 69 optimal weight:    7.9990
   chunk 55 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
B  64 HIS
B 347 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.192682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.157053 restraints weight = 8783.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3991 rms_B_bonded: 1.42
r_work: 0.3776 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3625 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8206  Z= 0.209
  Angle     :  0.540   7.825  11766  Z= 0.280
  Chirality :  0.036   0.216   1406
  Planarity :  0.004   0.046    996
  Dihedral  : 20.853 154.549   2818
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 27.73 %
    Favored  : 67.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.35), residues: 570
  helix:  1.48 (0.43), residues: 146
  sheet: -0.37 (0.51), residues: 90
  loop : -1.46 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 352 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.025   0.002   PHE A 320 
 TYR   0.011   0.001   TYR A 195 
 ARG   0.005   0.000   ARG B 280 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 48
  time to evaluate  : 0.634 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.6424 (mp10)
REVERT: A  304 ASN cc_start: 0.6366 (m-40) cc_final: 0.5615 (t0)
REVERT: A  316 MET cc_start: 0.6804 (ptp) cc_final: 0.6493 (ptt)
REVERT: B   64 HIS cc_start: 0.6725 (OUTLIER) cc_final: 0.6177 (t-90)
REVERT: B   82 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.7361 (mp10)
REVERT: B  156 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6544 (pt0)
REVERT: B  282 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.5985 (mtt)
REVERT: B  303 LEU cc_start: 0.7270 (pp) cc_final: 0.6591 (mt)
REVERT: B  350 GLN cc_start: 0.6709 (OUTLIER) cc_final: 0.6276 (mt0)
  outliers start: 25
  outliers final: 16
  residues processed: 68
  average time/residue: 0.2061
  time to fit residues: 19.1383
Evaluate side-chains
  68 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 46
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 GLN
Chi-restraints excluded: chain A residue   84 ASN
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  268 GLU
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  350 GLN
Chi-restraints excluded: chain B residue  362 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   chunk 15 optimal weight:    0.7980
   chunk 70 optimal weight:    7.9990
   chunk 32 optimal weight:    2.9990
   chunk 59 optimal weight:    7.9990
   chunk 18 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
B  64 HIS
B 347 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.192770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.158019 restraints weight = 8870.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.3980 rms_B_bonded: 1.41
r_work: 0.3765 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3614 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8206  Z= 0.245
  Angle     :  0.566   8.100  11766  Z= 0.293
  Chirality :  0.038   0.236   1406
  Planarity :  0.004   0.035    996
  Dihedral  : 20.898 154.826   2818
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 25.59 %
    Favored  : 68.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.34), residues: 570
  helix:  1.32 (0.42), residues: 146
  sheet: -0.47 (0.50), residues: 90
  loop : -1.50 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 177 
 HIS   0.005   0.001   HIS B  64 
 PHE   0.027   0.002   PHE A 320 
 TYR   0.012   0.001   TYR A 195 
 ARG   0.006   0.001   ARG B  62 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 51
  time to evaluate  : 0.667 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.6458 (mp10)
REVERT: A  304 ASN cc_start: 0.6399 (m-40) cc_final: 0.5651 (t0)
REVERT: A  316 MET cc_start: 0.6791 (ptp) cc_final: 0.6537 (ptt)
REVERT: B   64 HIS cc_start: 0.6827 (OUTLIER) cc_final: 0.6514 (t-90)
REVERT: B   82 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.7422 (mp10)
REVERT: B  156 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6560 (pt0)
REVERT: B  266 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8090 (pt0)
REVERT: B  303 LEU cc_start: 0.7285 (pp) cc_final: 0.6496 (mt)
REVERT: B  350 GLN cc_start: 0.6665 (OUTLIER) cc_final: 0.6256 (mt0)
  outliers start: 29
  outliers final: 16
  residues processed: 73
  average time/residue: 0.1834
  time to fit residues: 18.8827
Evaluate side-chains
  70 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 48
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 GLN
Chi-restraints excluded: chain A residue   84 ASN
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  350 GLN
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  362 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 18 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
B  64 HIS
B 347 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.193757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.157676 restraints weight = 8896.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3985 rms_B_bonded: 1.56
r_work: 0.3765 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3612 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8206  Z= 0.196
  Angle     :  0.536   7.824  11766  Z= 0.278
  Chirality :  0.036   0.221   1406
  Planarity :  0.004   0.035    996
  Dihedral  : 20.859 154.476   2818
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 25.98 %
    Favored  : 68.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.35), residues: 570
  helix:  1.11 (0.42), residues: 158
  sheet: -0.36 (0.51), residues: 90
  loop : -1.44 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 352 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.024   0.002   PHE A 320 
 TYR   0.010   0.001   TYR A 195 
 ARG   0.006   0.000   ARG B 280 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 50
  time to evaluate  : 0.718 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.6424 (mp10)
REVERT: A  131 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6781 (t0)
REVERT: A  316 MET cc_start: 0.6733 (ptp) cc_final: 0.6452 (ptt)
REVERT: B   64 HIS cc_start: 0.6577 (OUTLIER) cc_final: 0.6140 (t-90)
REVERT: B   82 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7400 (mp10)
REVERT: B   92 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7933 (mmtt)
REVERT: B  156 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6508 (pt0)
REVERT: B  282 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6673 (tpp)
REVERT: B  303 LEU cc_start: 0.7240 (pp) cc_final: 0.6475 (mt)
REVERT: B  350 GLN cc_start: 0.6688 (OUTLIER) cc_final: 0.6286 (mt0)
  outliers start: 29
  outliers final: 17
  residues processed: 72
  average time/residue: 0.1903
  time to fit residues: 19.0917
Evaluate side-chains
  73 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 48
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 GLN
Chi-restraints excluded: chain A residue   84 ASN
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue   92 LYS
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  350 GLN
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  362 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 7 optimal weight:    0.7980
   chunk 37 optimal weight:    5.9990
   chunk 69 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 45 optimal weight:    9.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
B  64 HIS
B 347 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.190999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.155814 restraints weight = 8904.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3977 rms_B_bonded: 1.37
r_work: 0.3767 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3619 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.3223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8206  Z= 0.251
  Angle     :  0.573   8.124  11766  Z= 0.298
  Chirality :  0.038   0.240   1406
  Planarity :  0.004   0.037    996
  Dihedral  : 20.922 155.212   2818
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 25.98 %
    Favored  : 68.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.35), residues: 570
  helix:  0.89 (0.42), residues: 158
  sheet: -0.39 (0.51), residues: 90
  loop : -1.47 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 177 
 HIS   0.005   0.001   HIS A 162 
 PHE   0.027   0.002   PHE A 320 
 TYR   0.012   0.002   TYR A 195 
 ARG   0.005   0.000   ARG B 280 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 48
  time to evaluate  : 0.600 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.6442 (mp10)
REVERT: A  131 ASP cc_start: 0.7150 (OUTLIER) cc_final: 0.6887 (t0)
REVERT: A  316 MET cc_start: 0.6830 (ptp) cc_final: 0.6496 (ptt)
REVERT: B   82 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.7403 (mp10)
REVERT: B   92 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7943 (mmtt)
REVERT: B  156 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6435 (pt0)
REVERT: B  266 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7926 (pt0)
REVERT: B  282 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6687 (tpp)
REVERT: B  303 LEU cc_start: 0.7283 (pp) cc_final: 0.6445 (mt)
REVERT: B  350 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.6277 (mt0)
  outliers start: 28
  outliers final: 16
  residues processed: 69
  average time/residue: 0.1549
  time to fit residues: 15.6554
Evaluate side-chains
  70 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 46
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 GLN
Chi-restraints excluded: chain A residue   84 ASN
Chi-restraints excluded: chain A residue   87 ASN
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue   92 LYS
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  265 CYS
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  350 GLN
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  362 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 48 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 60 optimal weight:    7.9990
   chunk 69 optimal weight:    8.9990
   chunk 5 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 18 optimal weight:    4.9990
   chunk 22 optimal weight:    0.4980
   chunk 1 optimal weight:    5.9990
   chunk 62 optimal weight:    7.9990
   overall best weight:    2.6386

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

Flipped N/Q/H residues before XYZ refinement:
A  84 ASN
B 347 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.188842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.153171 restraints weight = 8833.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 1.42
r_work: 0.3739 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3589 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.3448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8206  Z= 0.327
  Angle     :  0.653   8.609  11766  Z= 0.336
  Chirality :  0.042   0.270   1406
  Planarity :  0.005   0.037    996
  Dihedral  : 21.123 158.378   2818
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 25.78 %
    Favored  : 68.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.34), residues: 570
  helix:  0.26 (0.40), residues: 170
  sheet: -0.51 (0.50), residues: 90
  loop : -1.71 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 177 
 HIS   0.006   0.001   HIS A 162 
 PHE   0.029   0.002   PHE A 320 
 TYR   0.016   0.002   TYR A 195 
 ARG   0.005   0.001   ARG B 280 

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 48
  time to evaluate  : 0.608 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.6519 (mp10)
REVERT: A  131 ASP cc_start: 0.7176 (OUTLIER) cc_final: 0.6913 (t0)
REVERT: A  316 MET cc_start: 0.6780 (ptp) cc_final: 0.6505 (ptt)
REVERT: B   82 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7515 (mp10)
REVERT: B   92 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8021 (mmtt)
REVERT: B  156 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6533 (pt0)
REVERT: B  266 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8025 (pt0)
REVERT: B  282 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.6664 (tpp)
REVERT: B  350 GLN cc_start: 0.6802 (OUTLIER) cc_final: 0.6333 (mt0)
  outliers start: 28
  outliers final: 18
  residues processed: 67
  average time/residue: 0.1709
  time to fit residues: 16.7429
Evaluate side-chains
  71 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 45
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 GLN
Chi-restraints excluded: chain A residue   84 ASN
Chi-restraints excluded: chain A residue  131 ASP
Chi-restraints excluded: chain A residue  161 THR
Chi-restraints excluded: chain A residue  286 LEU
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue   84 ASN
Chi-restraints excluded: chain B residue   92 LYS
Chi-restraints excluded: chain B residue  105 SER
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  229 ASP
Chi-restraints excluded: chain B residue  265 CYS
Chi-restraints excluded: chain B residue  266 GLN
Chi-restraints excluded: chain B residue  282 MET
Chi-restraints excluded: chain B residue  285 ILE
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  320 PHE
Chi-restraints excluded: chain B residue  350 GLN
Chi-restraints excluded: chain B residue  361 MET
Chi-restraints excluded: chain B residue  362 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 64 optimal weight:   20.0000
   chunk 11 optimal weight:    0.0270
   chunk 8 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 66 optimal weight:    7.9990
   chunk 65 optimal weight:   10.0000
   chunk 23 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.7238

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

Flipped N/Q/H residues before XYZ refinement:
B 347 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.195420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.160325 restraints weight = 8858.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.4029 rms_B_bonded: 1.43
r_work: 0.3820 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3674 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.3369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8206  Z= 0.145
  Angle     :  0.517   9.117  11766  Z= 0.269
  Chirality :  0.035   0.197   1406
  Planarity :  0.003   0.033    996
  Dihedral  : 20.830 156.134   2818
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 27.73 %
    Favored  : 68.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.35), residues: 570
  helix:  0.86 (0.42), residues: 160
  sheet: -0.32 (0.51), residues: 90
  loop : -1.49 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 352 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.021   0.001   PHE A 320 
 TYR   0.008   0.001   TYR A 211 
 ARG   0.006   0.000   ARG B 280 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4266.42 seconds
wall clock time: 73 minutes 35.12 seconds (4415.12 seconds total)