Starting phenix.real_space_refine
on Fri Aug 22 20:11:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8okd_16926/08_2025/8okd_16926.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8okd_16926/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8okd_16926/08_2025/8okd_16926.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8okd_16926/08_2025/8okd_16926.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8okd_16926/08_2025/8okd_16926.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8okd_16926/08_2025/8okd_16926.map"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.86, per 1000 atoms: 0.24
  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: 0.52
  Conformation dependent library (CDL) restraints added in 355.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 1.08
  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: 1.16

  Time building geometry restraints manager: 0.69 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:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.920
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.330
-------------------------------------------------------------------------------
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= 0.134
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG B 193 
 TYR   0.007   0.001   TYR A 160 
 PHE   0.034   0.002   PHE A 267 
 TRP   0.007   0.001   TRP A 352 
 HIS   0.002   0.001   HIS A 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8206)
  covalent geometry    : angle       0.50932 (11766)
  hydrogen bonds       : bond        0.15875 (  300)
  hydrogen bonds       : angle       5.60649 (  719)

*********************** 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  : 0.224 
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: 0.5942 (t0)
REVERT: B  247 GLN cc_start: 0.6086 (pt0) cc_final: 0.5368 (pm20)
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: 0.0992
  time to fit residues: 12.9160
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  : 0.177 
-------------------------------------------------------------------------------
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 49 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.0060
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.9602

-------------------------------------------------------------------------------
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 = 0.4365 r_free = 0.4365 target = 0.193340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.158816 restraints weight = 8805.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3991 rms_B_bonded: 1.33
r_work: 0.3773 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3626 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.1975

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= 0.186
  Angle     :  0.615   8.698  11766  Z= 0.318
  Chirality :  0.039   0.235   1406
  Planarity :  0.005   0.042    996
  Dihedral  : 21.174 162.594   2821
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 31.05 %
    Favored  : 64.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.85 (0.34), residues: 570
  helix:  1.48 (0.41), residues: 146
  sheet: -0.61 (0.50), residues: 90
  loop : -1.56 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 133 
 TYR   0.013   0.002   TYR A  76 
 PHE   0.025   0.002   PHE A 320 
 TRP   0.006   0.001   TRP B 352 
 HIS   0.003   0.001   HIS B 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 8206)
  covalent geometry    : angle       0.61460 (11766)
  hydrogen bonds       : bond        0.06083 (  300)
  hydrogen bonds       : angle       4.47853 (  719)

*********************** 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
  83 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 59
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A  119 LYS cc_start: 0.8442 (pttt) cc_final: 0.8172 (ptmm)
REVERT: A  304 ASN cc_start: 0.6939 (m-40) cc_final: 0.6136 (t0)
REVERT: A  316 MET cc_start: 0.6326 (ptp) cc_final: 0.5970 (ptt)
REVERT: B   72 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7595 (ptp)
REVERT: B   82 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7173 (mt0)
REVERT: B  156 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6703 (pt0)
REVERT: B  303 LEU cc_start: 0.7520 (pp) cc_final: 0.6840 (mt)
  outliers start: 24
  outliers final: 14
  residues processed: 77
  average time/residue: 0.0614
  time to fit residues: 6.8674
Evaluate side-chains
  68 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 51
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
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 A residue  289 ILE
Chi-restraints excluded: chain A residue  302 LEU
Chi-restraints excluded: chain A residue  361 MET
Chi-restraints excluded: chain B residue   72 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  194 THR
Chi-restraints excluded: chain B residue  279 VAL
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 23 optimal weight:    0.0980
   chunk 2 optimal weight:    4.9990
   chunk 36 optimal weight:    7.9990
   chunk 12 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.7782

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.197521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.163691 restraints weight = 8784.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.4037 rms_B_bonded: 1.37
r_work: 0.3820 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3672 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8206  Z= 0.107
  Angle     :  0.498   7.545  11766  Z= 0.260
  Chirality :  0.034   0.188   1406
  Planarity :  0.003   0.032    996
  Dihedral  : 20.880 157.282   2821
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 30.66 %
    Favored  : 66.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.62 (0.35), residues: 570
  helix:  1.59 (0.42), residues: 146
  sheet: -0.53 (0.50), residues: 90
  loop : -1.35 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 280 
 TYR   0.006   0.001   TYR A 160 
 PHE   0.021   0.001   PHE A 320 
 TRP   0.006   0.001   TRP A 352 
 HIS   0.002   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 8206)
  covalent geometry    : angle       0.49752 (11766)
  hydrogen bonds       : bond        0.04756 (  300)
  hydrogen bonds       : angle       4.05000 (  719)

*********************** 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
  75 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
REVERT: A  282 MET cc_start: 0.6491 (mpp) cc_final: 0.6249 (mtm)
REVERT: A  304 ASN cc_start: 0.6523 (m-40) cc_final: 0.5889 (t0)
REVERT: A  316 MET cc_start: 0.6153 (ptp) cc_final: 0.5882 (ptt)
REVERT: B   72 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7404 (ptp)
REVERT: B  156 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6583 (pt0)
REVERT: B  303 LEU cc_start: 0.7456 (pp) cc_final: 0.6807 (mt)
  outliers start: 15
  outliers final: 8
  residues processed: 72
  average time/residue: 0.0631
  time to fit residues: 6.7372
Evaluate side-chains
  60 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
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  302 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue   72 MET
Chi-restraints excluded: chain B residue  156 GLU
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  249 VAL
Chi-restraints excluded: chain B residue  279 VAL
Chi-restraints excluded: chain B residue  318 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0040
   chunk 41 optimal weight:    2.9990
   chunk 33 optimal weight:    0.2980
   chunk 56 optimal weight:    3.9990
   chunk 45 optimal weight:    0.3980
   chunk 14 optimal weight:    0.0020
   chunk 43 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.3000

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

Flipped N/Q/H residues before XYZ refinement:
A 126 GLN
A 135 GLN
B 347 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.203456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.169098 restraints weight = 9052.890|
|-----------------------------------------------------------------------------|
r_work (start): 0.4098 rms_B_bonded: 1.50
r_work: 0.3886 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3735 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.2607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8206  Z= 0.090
  Angle     :  0.457   7.315  11766  Z= 0.238
  Chirality :  0.033   0.162   1406
  Planarity :  0.003   0.046    996
  Dihedral  : 20.723 153.425   2818
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 31.45 %
    Favored  : 66.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.35), residues: 570
  helix:  1.90 (0.42), residues: 146
  sheet: -0.19 (0.51), residues: 90
  loop : -1.33 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 280 
 TYR   0.005   0.001   TYR A 216 
 PHE   0.019   0.001   PHE A 320 
 TRP   0.005   0.001   TRP A 352 
 HIS   0.002   0.000   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00182 ( 8206)
  covalent geometry    : angle       0.45707 (11766)
  hydrogen bonds       : bond        0.03928 (  300)
  hydrogen bonds       : angle       3.78512 (  719)

*********************** 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
  72 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A  266 GLN cc_start: 0.8026 (pt0) cc_final: 0.7824 (pt0)
REVERT: A  304 ASN cc_start: 0.6270 (m-40) cc_final: 0.5447 (t0)
REVERT: A  316 MET cc_start: 0.5850 (ptp) cc_final: 0.5614 (ptt)
REVERT: B  303 LEU cc_start: 0.7520 (pp) cc_final: 0.6794 (mt)
REVERT: B  350 GLN cc_start: 0.6657 (OUTLIER) cc_final: 0.6269 (mt0)
  outliers start: 8
  outliers final: 5
  residues processed: 70
  average time/residue: 0.0643
  time to fit residues: 6.7732
Evaluate side-chains
  60 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
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  318 VAL
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  350 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0870
   chunk 43 optimal weight:    6.9990
   chunk 10 optimal weight:    3.9990
   chunk 70 optimal weight:    8.9990
   chunk 17 optimal weight:    7.9990
   chunk 35 optimal weight:    6.9990
   chunk 58 optimal weight:   10.0000
   chunk 47 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    1.0360

-------------------------------------------------------------------------------
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 = 0.4399 r_free = 0.4399 target = 0.196533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.161787 restraints weight = 8843.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.4042 rms_B_bonded: 1.39
r_work: 0.3831 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3685 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
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   0.025   8206  Z= 0.118
  Angle     :  0.492   7.265  11766  Z= 0.254
  Chirality :  0.034   0.176   1406
  Planarity :  0.004   0.049    996
  Dihedral  : 20.725 154.876   2818
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 28.12 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.35), residues: 570
  helix:  1.66 (0.42), residues: 158
  sheet: -0.19 (0.51), residues: 90
  loop : -1.33 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 280 
 TYR   0.009   0.001   TYR B 276 
 PHE   0.024   0.001   PHE A 320 
 TRP   0.005   0.001   TRP A 352 
 HIS   0.002   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8206)
  covalent geometry    : angle       0.49184 (11766)
  hydrogen bonds       : bond        0.04490 (  300)
  hydrogen bonds       : angle       3.84092 (  719)

*********************** 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
  74 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 52
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A  275 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7698 (tt)
REVERT: A  304 ASN cc_start: 0.6322 (m-40) cc_final: 0.5534 (t0)
REVERT: A  316 MET cc_start: 0.6438 (ptp) cc_final: 0.6181 (ptt)
REVERT: B   64 HIS cc_start: 0.6844 (OUTLIER) cc_final: 0.6382 (t-90)
REVERT: B   82 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7352 (mp10)
REVERT: B  156 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6546 (pt0)
REVERT: B  303 LEU cc_start: 0.7523 (pp) cc_final: 0.6804 (mt)
  outliers start: 22
  outliers final: 13
  residues processed: 67
  average time/residue: 0.0660
  time to fit residues: 6.5320
Evaluate side-chains
  68 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 51
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  275 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 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  318 VAL
Chi-restraints excluded: chain B residue  362 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 69 optimal weight:    9.9990
   chunk 59 optimal weight:    7.9990
   chunk 36 optimal weight:    0.6980
   chunk 66 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   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 347 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.193593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.158022 restraints weight = 8831.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.4001 rms_B_bonded: 1.42
r_work: 0.3803 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3656 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.2848

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= 0.147
  Angle     :  0.535   7.806  11766  Z= 0.277
  Chirality :  0.036   0.219   1406
  Planarity :  0.004   0.046    996
  Dihedral  : 20.793 154.707   2818
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 28.32 %
    Favored  : 66.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.35), residues: 570
  helix:  1.67 (0.43), residues: 146
  sheet: -0.39 (0.51), residues: 90
  loop : -1.39 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 280 
 TYR   0.010   0.001   TYR A 195 
 PHE   0.026   0.002   PHE A 320 
 TRP   0.006   0.001   TRP A 352 
 HIS   0.003   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 8206)
  covalent geometry    : angle       0.53467 (11766)
  hydrogen bonds       : bond        0.05270 (  300)
  hydrogen bonds       : angle       3.92875 (  719)

*********************** 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
  77 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 53
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A  247 GLN cc_start: 0.6000 (mt0) cc_final: 0.5665 (tm-30)
REVERT: A  304 ASN cc_start: 0.6417 (m-40) cc_final: 0.5650 (t0)
REVERT: A  316 MET cc_start: 0.6649 (ptp) cc_final: 0.6413 (ptt)
REVERT: B   82 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7335 (mp10)
REVERT: B  156 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6539 (pt0)
REVERT: B  303 LEU cc_start: 0.7311 (pp) cc_final: 0.6675 (mt)
REVERT: B  304 ASN cc_start: 0.6994 (m-40) cc_final: 0.6747 (m-40)
REVERT: B  350 GLN cc_start: 0.6681 (OUTLIER) cc_final: 0.6264 (mt0)
  outliers start: 24
  outliers final: 16
  residues processed: 69
  average time/residue: 0.0715
  time to fit residues: 7.2197
Evaluate side-chains
  69 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 50
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 B residue   72 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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   chunk 69 optimal weight:    8.9990
   chunk 35 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 19 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 58 optimal weight:    7.9990
   overall best weight:    2.0984

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

Flipped N/Q/H residues before XYZ refinement:
A  84 ASN
B  64 HIS
B 347 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.191822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.155311 restraints weight = 8847.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3957 rms_B_bonded: 1.41
r_work: 0.3754 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3608 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.3144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8206  Z= 0.188
  Angle     :  0.595   8.406  11766  Z= 0.307
  Chirality :  0.039   0.255   1406
  Planarity :  0.004   0.034    996
  Dihedral  : 20.956 154.901   2818
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 27.15 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.02 (0.34), residues: 570
  helix:  0.91 (0.41), residues: 158
  sheet: -0.43 (0.50), residues: 90
  loop : -1.63 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 280 
 TYR   0.013   0.002   TYR A 195 
 PHE   0.028   0.002   PHE A 320 
 TRP   0.007   0.001   TRP A 177 
 HIS   0.005   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 8206)
  covalent geometry    : angle       0.59453 (11766)
  hydrogen bonds       : bond        0.06175 (  300)
  hydrogen bonds       : angle       4.17546 (  719)

*********************** 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
  81 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 53
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.6508 (mp10)
REVERT: A  311 LYS cc_start: 0.5352 (mttp) cc_final: 0.5132 (mttp)
REVERT: A  316 MET cc_start: 0.6791 (ptp) cc_final: 0.6485 (ptt)
REVERT: B   64 HIS cc_start: 0.6789 (OUTLIER) cc_final: 0.6157 (t-90)
REVERT: B   82 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.7389 (mp10)
REVERT: B  156 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6484 (pt0)
REVERT: B  266 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8228 (pt0)
REVERT: B  304 ASN cc_start: 0.7034 (m-40) cc_final: 0.6594 (m-40)
REVERT: B  350 GLN cc_start: 0.6735 (OUTLIER) cc_final: 0.6272 (mt0)
  outliers start: 28
  outliers final: 15
  residues processed: 75
  average time/residue: 0.0669
  time to fit residues: 7.1151
Evaluate side-chains
  66 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 45
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
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  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   72 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  229 ASP
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 12 optimal weight:    3.9990
   chunk 65 optimal weight:   10.0000
   chunk 56 optimal weight:    3.9990
   chunk 62 optimal weight:    8.9990
   chunk 24 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0980
   chunk 22 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0870
   chunk 31 optimal weight:    1.9990
   chunk 71 optimal weight:   20.0000
   overall best weight:    1.0362

-------------------------------------------------------------------------------
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 = 0.4377 r_free = 0.4377 target = 0.194067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.157918 restraints weight = 8902.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.3996 rms_B_bonded: 1.41
r_work: 0.3801 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3649 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.3149

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= 0.123
  Angle     :  0.529  10.155  11766  Z= 0.273
  Chirality :  0.035   0.213   1406
  Planarity :  0.003   0.031    996
  Dihedral  : 20.815 154.175   2818
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 29.69 %
    Favored  : 66.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.75 (0.35), residues: 570
  helix:  1.10 (0.42), residues: 158
  sheet: -0.28 (0.52), residues: 90
  loop : -1.44 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 280 
 TYR   0.009   0.001   TYR A 314 
 PHE   0.034   0.002   PHE A  79 
 TRP   0.005   0.001   TRP A 352 
 HIS   0.009   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8206)
  covalent geometry    : angle       0.52923 (11766)
  hydrogen bonds       : bond        0.05105 (  300)
  hydrogen bonds       : angle       3.99877 (  719)

*********************** 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
  69 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
REVERT: A  131 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6766 (t0)
REVERT: A  316 MET cc_start: 0.6627 (ptp) cc_final: 0.6412 (ptt)
REVERT: B   82 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.7395 (mp10)
REVERT: B  303 LEU cc_start: 0.7357 (pp) cc_final: 0.6358 (mt)
REVERT: B  350 GLN cc_start: 0.6738 (OUTLIER) cc_final: 0.6330 (mt0)
  outliers start: 17
  outliers final: 13
  residues processed: 65
  average time/residue: 0.0844
  time to fit residues: 7.6205
Evaluate side-chains
  66 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 50
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  318 VAL
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain B residue   72 MET
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  171 ASP
Chi-restraints excluded: chain B residue  229 ASP
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  362 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 63 optimal weight:    8.9990
   chunk 41 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  84 ASN
B  64 HIS
B 347 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.188889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.152850 restraints weight = 8884.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3946 rms_B_bonded: 1.34
r_work: 0.3751 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3603 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.3371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8206  Z= 0.239
  Angle     :  0.672  11.076  11766  Z= 0.343
  Chirality :  0.042   0.272   1406
  Planarity :  0.005   0.035    996
  Dihedral  : 21.094 156.818   2818
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 27.93 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.34), residues: 570
  helix:  0.33 (0.40), residues: 172
  sheet: -0.41 (0.51), residues: 90
  loop : -1.77 (0.35), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 193 
 TYR   0.016   0.002   TYR A 314 
 PHE   0.029   0.002   PHE A 320 
 TRP   0.009   0.002   TRP A 177 
 HIS   0.006   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00550 ( 8206)
  covalent geometry    : angle       0.67228 (11766)
  hydrogen bonds       : bond        0.06921 (  300)
  hydrogen bonds       : angle       4.30721 (  719)

*********************** 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
  69 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 45
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7823 (OUTLIER) cc_final: 0.6512 (mp10)
REVERT: A  131 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6934 (t0)
REVERT: A  314 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.6799 (p90)
REVERT: A  316 MET cc_start: 0.6868 (ptp) cc_final: 0.6549 (ptt)
REVERT: B   82 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.7461 (mp10)
REVERT: B  156 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6555 (pt0)
REVERT: B  266 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8144 (pt0)
REVERT: B  304 ASN cc_start: 0.7031 (m-40) cc_final: 0.6706 (m-40)
REVERT: B  350 GLN cc_start: 0.6804 (OUTLIER) cc_final: 0.6338 (mt0)
  outliers start: 24
  outliers final: 16
  residues processed: 62
  average time/residue: 0.0541
  time to fit residues: 4.9875
Evaluate side-chains
  66 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 43
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
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  314 TYR
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   72 MET
Chi-restraints excluded: chain B residue   82 GLN
Chi-restraints excluded: chain B residue   84 ASN
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  315 SER
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 34 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 58 optimal weight:   10.0000
   chunk 63 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 66 optimal weight:    7.9990
   chunk 46 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.195175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.159485 restraints weight = 8824.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.4018 rms_B_bonded: 1.51
r_work: 0.3809 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3660 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.3301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8206  Z= 0.112
  Angle     :  0.521   9.353  11766  Z= 0.270
  Chirality :  0.035   0.201   1406
  Planarity :  0.003   0.030    996
  Dihedral  : 20.805 155.319   2818
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 30.27 %
    Favored  : 66.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.77 (0.35), residues: 570
  helix:  1.09 (0.42), residues: 158
  sheet: -0.20 (0.52), residues: 90
  loop : -1.49 (0.35), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 193 
 TYR   0.010   0.001   TYR A 314 
 PHE   0.029   0.002   PHE A  79 
 TRP   0.005   0.001   TRP A 352 
 HIS   0.003   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 8206)
  covalent geometry    : angle       0.52138 (11766)
  hydrogen bonds       : bond        0.04842 (  300)
  hydrogen bonds       : angle       3.99215 (  719)

********************** 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
  63 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: A  131 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6767 (t0)
REVERT: A  314 TYR cc_start: 0.7184 (OUTLIER) cc_final: 0.6675 (p90)
REVERT: A  316 MET cc_start: 0.6586 (ptp) cc_final: 0.6318 (ptt)
REVERT: B   82 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.7422 (mp10)
REVERT: B  266 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7939 (pt0)
REVERT: B  304 ASN cc_start: 0.7024 (m-40) cc_final: 0.6675 (m-40)
REVERT: B  350 GLN cc_start: 0.6708 (OUTLIER) cc_final: 0.6297 (mt0)
  outliers start: 15
  outliers final: 10
  residues processed: 59
  average time/residue: 0.0630
  time to fit residues: 5.5038
Evaluate side-chains
  62 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  314 TYR
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  320 PHE
Chi-restraints excluded: chain B residue   72 MET
Chi-restraints excluded: chain B residue   82 GLN
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  318 VAL
Chi-restraints excluded: chain B residue  350 GLN
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 58 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 71 optimal weight:   20.0000
   chunk 46 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.190496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.154559 restraints weight = 8901.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3960 rms_B_bonded: 1.37
r_work: 0.3762 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3611 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.3394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8206  Z= 0.195
  Angle     :  0.610   9.960  11766  Z= 0.313
  Chirality :  0.039   0.246   1406
  Planarity :  0.004   0.035    996
  Dihedral  : 20.964 157.007   2818
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 29.30 %
    Favored  : 66.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.98 (0.35), residues: 570
  helix:  0.80 (0.42), residues: 160
  sheet: -0.34 (0.52), residues: 90
  loop : -1.55 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 193 
 TYR   0.015   0.002   TYR A 314 
 PHE   0.028   0.002   PHE A 320 
 TRP   0.007   0.001   TRP A 177 
 HIS   0.009   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 8206)
  covalent geometry    : angle       0.60996 (11766)
  hydrogen bonds       : bond        0.06101 (  300)
  hydrogen bonds       : angle       4.17173 (  719)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2014.24 seconds
wall clock time: 35 minutes 5.59 seconds (2105.59 seconds total)