Starting phenix.real_space_refine
on Tue Mar 11 15:31:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7p5m_13201/03_2025/7p5m_13201.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7p5m_13201/03_2025/7p5m_13201.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7p5m_13201/03_2025/7p5m_13201.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7p5m_13201/03_2025/7p5m_13201.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7p5m_13201/03_2025/7p5m_13201.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7p5m_13201/03_2025/7p5m_13201.cif"
  }
  resolution = 3.92
  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=  -0.000 sd=   0.005
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: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    4006      2.51       5
     N     976      2.21       5
     O    1176      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6204
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 3018
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 394, 3018
          Classifications: {'peptide': 394}
          Link IDs: {'PTRANS': 9, 'TRANS': 384}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3018
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 394, 3018
          Classifications: {'peptide': 394}
          Link IDs: {'PTRANS': 9, 'TRANS': 384}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 3.90, per 1000 atoms: 0.63
  Number of scatterers: 6204
  At special positions: 0
  Unit cell: (92.442, 70.308, 128.898, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      46     16.00
     O    1176      8.00
     N     976      7.00
     C    4006      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 274 " - pdb=" SG  CYS A 382 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 300 " - pdb=" SG  CYS A 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 274 " - pdb=" SG  CYS B 382 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 300 " - pdb=" SG  CYS B 367 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A 601 " - " ASN A 283 "
      " NAG A 602 " - " ASN A  31 "
      " NAG B 601 " - " ASN B 283 "
      " NAG B 602 " - " ASN B  31 "
      " NAG C   1 " - " ASN A 352 "
      " NAG D   1 " - " ASN A 129 "
      " NAG E   1 " - " ASN B 352 "
      " NAG F   1 " - " ASN B 129 "
  Time building additional restraints: 1.57
  Conformation dependent library (CDL) restraints added in 846.8 milliseconds
  

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1468

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 0 sheets defined
      89.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 18
    Processing helix  chain 'A' and resid 38 through 70
      removed outlier: 3.660A  pdb=" N   ALA A  70 " --> pdb=" O   TYR A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 159
      removed outlier: 4.199A  pdb=" N   LEU A 150 " --> pdb=" O   MET A 146 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   GLU A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 164
      removed outlier: 4.333A  pdb=" N   ALA A 163 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 187
    Processing helix  chain 'A' and resid 191 through 237
      removed outlier: 3.502A  pdb=" N   LEU A 234 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 276
      removed outlier: 3.654A  pdb=" N   LEU A 242 " --> pdb=" O   SER A 238 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ALA A 243 " --> pdb=" O   LYS A 239 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   SER A 244 " --> pdb=" O   CYS A 240 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ALA A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 285
    Processing helix  chain 'A' and resid 290 through 300
    Processing helix  chain 'A' and resid 308 through 337
      removed outlier: 3.971A  pdb=" N   VAL A 334 " --> pdb=" O   LEU A 330 " (cutoff:3.500A)
      Proline residue:  A 335  - end of helix
    Processing helix  chain 'A' and resid 341 through 365
    Processing helix  chain 'A' and resid 366 through 382
      removed outlier: 4.426A  pdb=" N   LEU A 370 " --> pdb=" O   ASP A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 414
      removed outlier: 3.682A  pdb=" N   GLN A 387 " --> pdb=" O   TYR A 383 " (cutoff:3.500A)
      Proline residue:  A 411  - end of helix
    Processing helix  chain 'B' and resid 11 through 19
    Processing helix  chain 'B' and resid 38 through 70
      removed outlier: 3.646A  pdb=" N   ALA B  70 " --> pdb=" O   TYR B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 159
      removed outlier: 4.245A  pdb=" N   LEU B 150 " --> pdb=" O   MET B 146 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   GLU B 159 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 164
      removed outlier: 4.284A  pdb=" N   ALA B 163 " --> pdb=" O   ILE B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 187
    Processing helix  chain 'B' and resid 191 through 237
      removed outlier: 3.611A  pdb=" N   LEU B 234 " --> pdb=" O   ALA B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 276
      removed outlier: 3.739A  pdb=" N   LEU B 242 " --> pdb=" O   SER B 238 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA B 243 " --> pdb=" O   LYS B 239 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   SER B 244 " --> pdb=" O   CYS B 240 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ALA B 276 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 285
    Processing helix  chain 'B' and resid 290 through 300
    Processing helix  chain 'B' and resid 308 through 337
      removed outlier: 4.127A  pdb=" N   VAL B 334 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
      Proline residue:  B 335  - end of helix
    Processing helix  chain 'B' and resid 341 through 365
    Processing helix  chain 'B' and resid 366 through 383
      removed outlier: 4.418A  pdb=" N   LEU B 370 " --> pdb=" O   ASP B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 409
      removed outlier: 3.543A  pdb=" N   GLN B 387 " --> pdb=" O   TYR B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 414

    562 hydrogen bonds defined for protein.
    1680 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.62

  Time building geometry restraints manager: 1.82 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1918
        1.34 -     1.46: 1290
        1.46 -     1.58: 3062
        1.58 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 6332
  Sorted by residual:
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.67e+00
  bond pdb=" C1  NAG B 601 "
       pdb=" O5  NAG B 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.34e+00
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 2.01e+00
  bond pdb=" C1  NAG A 601 "
       pdb=" O5  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.97e+00
  bond pdb=" C1  NAG A 602 "
       pdb=" O5  NAG A 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.78e+00
  ... (remaining 6327 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 8391
        1.59 -     3.19: 201
        3.19 -     4.78: 25
        4.78 -     6.37: 8
        6.37 -     7.97: 5
  Bond angle restraints: 8630
  Sorted by residual:
  angle pdb=" C   LEU B 282 "
        pdb=" N   ASN B 283 "
        pdb=" CA  ASN B 283 "
      ideal   model   delta    sigma   weight residual
     122.65  116.56    6.09 1.60e+00 3.91e-01 1.45e+01
  angle pdb=" C   ASP B 166 "
        pdb=" N   TYR B 167 "
        pdb=" CA  TYR B 167 "
      ideal   model   delta    sigma   weight residual
     121.54  128.33   -6.79 1.91e+00 2.74e-01 1.26e+01
  angle pdb=" C   ASP A 166 "
        pdb=" N   TYR A 167 "
        pdb=" CA  TYR A 167 "
      ideal   model   delta    sigma   weight residual
     121.54  127.82   -6.28 1.91e+00 2.74e-01 1.08e+01
  angle pdb=" C   LEU A 282 "
        pdb=" N   ASN A 283 "
        pdb=" CA  ASN A 283 "
      ideal   model   delta    sigma   weight residual
     122.38  116.47    5.91 1.81e+00 3.05e-01 1.07e+01
  angle pdb=" N   VAL B  23 "
        pdb=" CA  VAL B  23 "
        pdb=" C   VAL B  23 "
      ideal   model   delta    sigma   weight residual
     113.71  110.95    2.76 9.50e-01 1.11e+00 8.42e+00
  ... (remaining 8625 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.30: 3538
       21.30 -    42.59: 249
       42.59 -    63.89: 39
       63.89 -    85.18: 6
       85.18 -   106.48: 16
  Dihedral angle restraints: 3848
    sinusoidal: 1562
      harmonic: 2286
  Sorted by residual:
  dihedral pdb=" CB  CYS A 300 "
           pdb=" SG  CYS A 300 "
           pdb=" SG  CYS A 367 "
           pdb=" CB  CYS A 367 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   61.58   31.42     1      1.00e+01 1.00e-02 1.41e+01
  dihedral pdb=" C2  NAG C   2 "
           pdb=" C3  NAG C   2 "
           pdb=" C4  NAG C   2 "
           pdb=" O4  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   68.63  106.48     1      3.00e+01 1.11e-03 1.37e+01
  dihedral pdb=" C2  NAG C   2 "
           pdb=" C3  NAG C   2 "
           pdb=" C4  NAG C   2 "
           pdb=" C5  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      53.78  -52.46  106.24     1      3.00e+01 1.11e-03 1.37e+01
  ... (remaining 3845 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 901
       0.051 -    0.102: 148
       0.102 -    0.152: 11
       0.152 -    0.203: 4
       0.203 -    0.254: 2
  Chirality restraints: 1066
  Sorted by residual:
  chirality pdb=" CA  ASN A 283 "
            pdb=" N   ASN A 283 "
            pdb=" C   ASN A 283 "
            pdb=" CB  ASN A 283 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" C1  NAG D   1 "
            pdb=" ND2 ASN A 129 "
            pdb=" C2  NAG D   1 "
            pdb=" O5  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.19   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" C1  NAG A 601 "
            pdb=" ND2 ASN A 283 "
            pdb=" C2  NAG A 601 "
            pdb=" O5  NAG A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 1063 not shown)

  Planarity restraints: 1058
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 283 "    0.001 2.00e-02 2.50e+03   3.05e-02 1.16e+01
        pdb=" CG  ASN A 283 "    0.032 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 283 "   -0.036 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 283 "    0.035 2.00e-02 2.50e+03
        pdb=" C1  NAG A 601 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 167 "    0.017 2.00e-02 2.50e+03   3.35e-02 1.12e+01
        pdb=" C   TYR B 167 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   TYR B 167 "    0.022 2.00e-02 2.50e+03
        pdb=" N   LEU B 168 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 167 "   -0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" C   TYR A 167 "    0.055 2.00e-02 2.50e+03
        pdb=" O   TYR A 167 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU A 168 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1055 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 823
        2.75 -     3.29: 6592
        3.29 -     3.82: 10801
        3.82 -     4.36: 11266
        4.36 -     4.90: 20145
  Nonbonded interactions: 49627
  Sorted by model distance:
  nonbonded pdb=" O   TYR A  41 "
            pdb=" OG  SER A  44 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   LEU A 154 "
            pdb=" OG  SER A 158 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OE2 GLU A 151 "
            pdb=" NE2 GLN A 175 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" OD1 ASN B  31 "
            pdb=" OG1 THR B  33 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OD2 ASP A  38 "
            pdb=" OG  SER A  40 "
     model   vdw
     2.259 3.040
  ... (remaining 49622 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     16.980
  Find NCS groups from input model:        0.370
  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:2.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
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   0.033   6332  Z= 0.225
  Angle     :  0.597   7.966   8630  Z= 0.297
  Chirality :  0.039   0.254   1066
  Planarity :  0.004   0.052   1050
  Dihedral  : 16.498 106.479   2368
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.52 (0.30), residues: 780
  helix:  2.66 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop :  0.33 (0.60), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 414 
 HIS   0.003   0.001   HIS B  18 
 PHE   0.020   0.001   PHE B 395 
 TYR   0.015   0.001   TYR B 216 
 ARG   0.004   0.000   ARG B  26 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7340 (t0) cc_final: 0.7015 (t0)
REVERT: A  406 MET cc_start: 0.8207 (tmm) cc_final: 0.7957 (tmm)
REVERT: B  127 ASP cc_start: 0.7753 (t0) cc_final: 0.7064 (t0)
REVERT: B  166 ASP cc_start: 0.7517 (p0) cc_final: 0.7070 (m-30)
REVERT: B  210 TYR cc_start: 0.6851 (t80) cc_final: 0.6566 (t80)
REVERT: B  341 GLU cc_start: 0.8057 (pp20) cc_final: 0.7557 (pp20)
REVERT: B  406 MET cc_start: 0.8378 (tmm) cc_final: 0.8087 (tmm)
REVERT: B  412 ARG cc_start: 0.8042 (mtt180) cc_final: 0.7477 (ttm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.1575
  time to fit residues: 44.2342
Evaluate side-chains
  188 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0970
   chunk 70 optimal weight:    6.9990
   overall best weight:    0.7178

-------------------------------------------------------------------------------
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 = 0.3944 r_free = 0.3944 target = 0.176370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.151333 restraints weight = 8571.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.155139 restraints weight = 5052.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.157589 restraints weight = 3506.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.1089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6332  Z= 0.189
  Angle     :  0.589   7.742   8630  Z= 0.293
  Chirality :  0.039   0.193   1066
  Planarity :  0.004   0.053   1050
  Dihedral  : 11.478  76.709   1090
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 11.93 %
    Favored  : 86.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.60 (0.29), residues: 780
  helix:  2.71 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop :  0.36 (0.59), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 414 
 HIS   0.001   0.000   HIS B 359 
 PHE   0.014   0.001   PHE A  47 
 TYR   0.011   0.001   TYR B 167 
 ARG   0.003   0.000   ARG B 192 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 212
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7365 (t0) cc_final: 0.6881 (t0)
REVERT: B  127 ASP cc_start: 0.7754 (t0) cc_final: 0.7119 (t0)
REVERT: B  166 ASP cc_start: 0.7584 (p0) cc_final: 0.6838 (m-30)
REVERT: B  172 LYS cc_start: 0.8760 (tppt) cc_final: 0.8559 (tppt)
REVERT: B  210 TYR cc_start: 0.6755 (t80) cc_final: 0.6344 (t80)
REVERT: B  325 GLN cc_start: 0.7376 (mp10) cc_final: 0.7148 (mp10)
REVERT: B  341 GLU cc_start: 0.7894 (pp20) cc_final: 0.7416 (pp20)
REVERT: B  406 MET cc_start: 0.8459 (tmm) cc_final: 0.8211 (tmm)
REVERT: B  412 ARG cc_start: 0.7965 (mtt180) cc_final: 0.7285 (ttm170)
  outliers start: 13
  outliers final: 10
  residues processed: 214
  average time/residue: 0.1412
  time to fit residues: 41.7067
Evaluate side-chains
  209 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 199
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0970
   chunk 16 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.7378

-------------------------------------------------------------------------------
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 = 0.3927 r_free = 0.3927 target = 0.174898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.149950 restraints weight = 8794.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.153559 restraints weight = 5241.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.155942 restraints weight = 3678.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.1402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6332  Z= 0.195
  Angle     :  0.596   8.422   8630  Z= 0.288
  Chirality :  0.039   0.194   1066
  Planarity :  0.004   0.056   1050
  Dihedral  :  8.710  55.997   1090
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.97 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.63 (0.29), residues: 780
  helix:  2.75 (0.19), residues: 664
  sheet:  None (None), residues: 0
  loop :  0.25 (0.60), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 414 
 HIS   0.001   0.000   HIS B  18 
 PHE   0.020   0.001   PHE A  47 
 TYR   0.008   0.001   TYR B 374 
 ARG   0.003   0.000   ARG B 295 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 221
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7442 (t0) cc_final: 0.6790 (t0)
REVERT: A  412 ARG cc_start: 0.7764 (mtt180) cc_final: 0.7205 (ttm170)
REVERT: B  127 ASP cc_start: 0.7802 (t0) cc_final: 0.7134 (t0)
REVERT: B  166 ASP cc_start: 0.7911 (p0) cc_final: 0.7508 (p0)
REVERT: B  210 TYR cc_start: 0.6816 (t80) cc_final: 0.6542 (t80)
REVERT: B  325 GLN cc_start: 0.7576 (mp10) cc_final: 0.7323 (mp10)
REVERT: B  341 GLU cc_start: 0.8035 (pp20) cc_final: 0.7481 (pp20)
REVERT: B  406 MET cc_start: 0.8580 (tmm) cc_final: 0.8272 (tmm)
REVERT: B  412 ARG cc_start: 0.7995 (mtt180) cc_final: 0.7256 (ttm170)
  outliers start: 13
  outliers final: 10
  residues processed: 223
  average time/residue: 0.1451
  time to fit residues: 44.5249
Evaluate side-chains
  216 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 206
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 7 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0770
   chunk 74 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 52 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.5138

-------------------------------------------------------------------------------
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 = 0.3954 r_free = 0.3954 target = 0.177485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.152858 restraints weight = 8808.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.156484 restraints weight = 5248.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.158621 restraints weight = 3697.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6332  Z= 0.173
  Angle     :  0.592   8.583   8630  Z= 0.288
  Chirality :  0.039   0.258   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  6.624  53.541   1090
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 20.64 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.69 (0.29), residues: 780
  helix:  2.82 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.03 (0.58), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B  18 
 PHE   0.020   0.002   PHE A  47 
 TYR   0.008   0.001   TYR A 374 
 ARG   0.002   0.000   ARG B  26 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 217
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7479 (t0) cc_final: 0.6666 (t0)
REVERT: A  412 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7217 (ttm170)
REVERT: B  127 ASP cc_start: 0.7816 (t0) cc_final: 0.7110 (t0)
REVERT: B  166 ASP cc_start: 0.8306 (p0) cc_final: 0.7331 (p0)
REVERT: B  210 TYR cc_start: 0.6934 (t80) cc_final: 0.6561 (t80)
REVERT: B  325 GLN cc_start: 0.7570 (mp10) cc_final: 0.7318 (mp10)
REVERT: B  341 GLU cc_start: 0.8104 (pp20) cc_final: 0.7548 (pp20)
REVERT: B  406 MET cc_start: 0.8686 (tmm) cc_final: 0.8302 (tmm)
REVERT: B  412 ARG cc_start: 0.8030 (mtt180) cc_final: 0.7137 (ttm170)
  outliers start: 12
  outliers final: 10
  residues processed: 219
  average time/residue: 0.1520
  time to fit residues: 45.2469
Evaluate side-chains
  218 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 208
  time to evaluate  : 0.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 21 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0070
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.6800

-------------------------------------------------------------------------------
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 = 0.3928 r_free = 0.3928 target = 0.175123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.150738 restraints weight = 8799.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.154431 restraints weight = 5257.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.156543 restraints weight = 3678.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6332  Z= 0.187
  Angle     :  0.584   7.552   8630  Z= 0.283
  Chirality :  0.038   0.248   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  5.952  46.844   1090
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 23.09 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.77 (0.29), residues: 780
  helix:  2.88 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.08 (0.58), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B 359 
 PHE   0.022   0.002   PHE B 173 
 TYR   0.008   0.001   TYR A 374 
 ARG   0.002   0.000   ARG A 192 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 212
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7491 (t0) cc_final: 0.6869 (t70)
REVERT: A  166 ASP cc_start: 0.8077 (p0) cc_final: 0.7589 (p0)
REVERT: A  378 LEU cc_start: 0.8166 (mt) cc_final: 0.7917 (mp)
REVERT: A  412 ARG cc_start: 0.7776 (mtt180) cc_final: 0.7239 (ttm170)
REVERT: B  166 ASP cc_start: 0.8061 (p0) cc_final: 0.7685 (p0)
REVERT: B  210 TYR cc_start: 0.6839 (t80) cc_final: 0.6511 (t80)
REVERT: B  337 PHE cc_start: 0.6765 (m-10) cc_final: 0.6434 (m-10)
REVERT: B  341 GLU cc_start: 0.7948 (pp20) cc_final: 0.7550 (pp20)
REVERT: B  366 ASP cc_start: 0.8883 (t0) cc_final: 0.8675 (t70)
REVERT: B  406 MET cc_start: 0.8673 (tmm) cc_final: 0.8333 (tmm)
  outliers start: 12
  outliers final: 11
  residues processed: 214
  average time/residue: 0.1408
  time to fit residues: 41.5036
Evaluate side-chains
  220 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 209
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 12 optimal weight:    0.2980
   chunk 25 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3928 r_free = 0.3928 target = 0.175164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.149824 restraints weight = 8669.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.153663 restraints weight = 5087.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.156219 restraints weight = 3530.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6332  Z= 0.222
  Angle     :  0.605   8.804   8630  Z= 0.295
  Chirality :  0.039   0.251   1066
  Planarity :  0.004   0.056   1050
  Dihedral  :  5.649  41.439   1090
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 24.01 %
    Favored  : 73.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.81 (0.29), residues: 780
  helix:  2.89 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.02 (0.60), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  12 
 HIS   0.002   0.001   HIS B 359 
 PHE   0.022   0.002   PHE B 173 
 TYR   0.009   0.001   TYR B 374 
 ARG   0.003   0.001   ARG A 192 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 216
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7480 (t0) cc_final: 0.6819 (t70)
REVERT: A  166 ASP cc_start: 0.8025 (p0) cc_final: 0.7574 (p0)
REVERT: A  412 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7216 (ttm170)
REVERT: B  166 ASP cc_start: 0.7692 (p0) cc_final: 0.7402 (p0)
REVERT: B  209 GLU cc_start: 0.7741 (tp30) cc_final: 0.7512 (tp30)
REVERT: B  210 TYR cc_start: 0.6860 (t80) cc_final: 0.6499 (t80)
REVERT: B  325 GLN cc_start: 0.7699 (mp10) cc_final: 0.7065 (mp10)
REVERT: B  337 PHE cc_start: 0.6834 (m-10) cc_final: 0.6588 (m-10)
REVERT: B  341 GLU cc_start: 0.7866 (pp20) cc_final: 0.7462 (pp20)
REVERT: B  366 ASP cc_start: 0.8973 (t0) cc_final: 0.8772 (t70)
REVERT: B  406 MET cc_start: 0.8631 (tmm) cc_final: 0.8263 (tmm)
  outliers start: 18
  outliers final: 17
  residues processed: 220
  average time/residue: 0.1391
  time to fit residues: 42.3380
Evaluate side-chains
  227 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 210
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  395 PHE
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 69 optimal weight:    0.6980
   chunk 38 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 76 optimal weight:    0.6980
   chunk 3 optimal weight:    0.3980
   chunk 59 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3939 r_free = 0.3939 target = 0.176413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.151344 restraints weight = 8686.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.155229 restraints weight = 5081.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.157733 restraints weight = 3506.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6332  Z= 0.181
  Angle     :  0.595   7.875   8630  Z= 0.288
  Chirality :  0.038   0.240   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  5.419  39.261   1090
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 25.23 %
    Favored  : 72.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.87 (0.29), residues: 780
  helix:  2.93 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.05 (0.59), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B  22 
 PHE   0.023   0.002   PHE B 173 
 TYR   0.009   0.001   TYR B 374 
 ARG   0.002   0.000   ARG B 295 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 222
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7498 (t0) cc_final: 0.6842 (t70)
REVERT: A  166 ASP cc_start: 0.7958 (p0) cc_final: 0.7481 (p0)
REVERT: A  209 GLU cc_start: 0.7628 (tp30) cc_final: 0.7404 (tp30)
REVERT: A  412 ARG cc_start: 0.7583 (mtt180) cc_final: 0.7120 (ttm170)
REVERT: B  166 ASP cc_start: 0.7749 (p0) cc_final: 0.7444 (p0)
REVERT: B  210 TYR cc_start: 0.6868 (t80) cc_final: 0.6513 (t80)
REVERT: B  325 GLN cc_start: 0.7773 (mp10) cc_final: 0.7174 (mp10)
REVERT: B  337 PHE cc_start: 0.6760 (m-10) cc_final: 0.6510 (m-10)
REVERT: B  341 GLU cc_start: 0.7880 (pp20) cc_final: 0.7475 (pp20)
REVERT: B  406 MET cc_start: 0.8577 (tmm) cc_final: 0.8234 (tmm)
  outliers start: 15
  outliers final: 15
  residues processed: 226
  average time/residue: 0.1414
  time to fit residues: 44.2794
Evaluate side-chains
  236 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 221
  time to evaluate  : 0.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   61 ILE
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  395 PHE
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3931 r_free = 0.3931 target = 0.175614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.150529 restraints weight = 8687.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.154466 restraints weight = 5087.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.156879 restraints weight = 3511.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.2218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6332  Z= 0.214
  Angle     :  0.621   7.943   8630  Z= 0.300
  Chirality :  0.039   0.241   1066
  Planarity :  0.004   0.056   1050
  Dihedral  :  5.318  39.298   1090
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 25.08 %
    Favored  : 71.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.87 (0.29), residues: 780
  helix:  2.91 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.23 (0.60), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  12 
 HIS   0.002   0.001   HIS B 359 
 PHE   0.023   0.002   PHE B 173 
 TYR   0.008   0.001   TYR A 374 
 ARG   0.002   0.000   ARG B 164 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 224
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7472 (t0) cc_final: 0.6815 (t70)
REVERT: A  166 ASP cc_start: 0.7937 (p0) cc_final: 0.7414 (p0)
REVERT: A  412 ARG cc_start: 0.7518 (mtt180) cc_final: 0.7090 (ttm170)
REVERT: B  166 ASP cc_start: 0.7707 (p0) cc_final: 0.7368 (p0)
REVERT: B  210 TYR cc_start: 0.6861 (t80) cc_final: 0.6557 (t80)
REVERT: B  325 GLN cc_start: 0.7780 (mp10) cc_final: 0.7220 (mp10)
REVERT: B  337 PHE cc_start: 0.6732 (m-10) cc_final: 0.6447 (m-10)
REVERT: B  341 GLU cc_start: 0.7793 (pp20) cc_final: 0.7417 (pp20)
  outliers start: 20
  outliers final: 18
  residues processed: 232
  average time/residue: 0.1339
  time to fit residues: 43.2006
Evaluate side-chains
  236 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 218
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  294 THR
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  395 PHE
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3932 r_free = 0.3932 target = 0.175576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.151747 restraints weight = 8734.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.154929 restraints weight = 5091.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.158748 restraints weight = 3289.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6332  Z= 0.203
  Angle     :  0.629   8.017   8630  Z= 0.303
  Chirality :  0.039   0.243   1066
  Planarity :  0.004   0.056   1050
  Dihedral  :  5.220  39.292   1090
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 26.15 %
    Favored  : 71.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.83 (0.29), residues: 780
  helix:  2.88 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.19 (0.58), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B 359 
 PHE   0.023   0.002   PHE B 173 
 TYR   0.009   0.001   TYR B 374 
 ARG   0.002   0.000   ARG B 317 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 222
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7531 (t0) cc_final: 0.6855 (t70)
REVERT: A  166 ASP cc_start: 0.7979 (p0) cc_final: 0.7249 (p0)
REVERT: A  412 ARG cc_start: 0.7609 (mtt180) cc_final: 0.7178 (ttm170)
REVERT: B  166 ASP cc_start: 0.7763 (p0) cc_final: 0.7389 (p0)
REVERT: B  209 GLU cc_start: 0.7644 (tp30) cc_final: 0.7429 (tp30)
REVERT: B  210 TYR cc_start: 0.6837 (t80) cc_final: 0.6511 (t80)
REVERT: B  325 GLN cc_start: 0.7839 (mp10) cc_final: 0.7311 (mp10)
REVERT: B  337 PHE cc_start: 0.6740 (m-10) cc_final: 0.6502 (m-10)
REVERT: B  341 GLU cc_start: 0.7813 (pp20) cc_final: 0.7410 (pp20)
  outliers start: 17
  outliers final: 16
  residues processed: 228
  average time/residue: 0.1453
  time to fit residues: 45.3625
Evaluate side-chains
  234 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 218
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  245 MET
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  395 PHE
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3920 r_free = 0.3920 target = 0.174407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.149330 restraints weight = 8850.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.153206 restraints weight = 5119.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.155776 restraints weight = 3519.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6332  Z= 0.230
  Angle     :  0.641   7.972   8630  Z= 0.311
  Chirality :  0.040   0.249   1066
  Planarity :  0.004   0.056   1050
  Dihedral  :  5.181  39.278   1090
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 26.45 %
    Favored  : 70.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.80 (0.29), residues: 780
  helix:  2.84 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.34 (0.59), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  12 
 HIS   0.002   0.001   HIS B 359 
 PHE   0.024   0.002   PHE B 173 
 TYR   0.009   0.001   TYR B 167 
 ARG   0.007   0.001   ARG A 295 

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

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

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1560 Ramachandran restraints generated.
    780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 217
  time to evaluate  : 0.648 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 ASP cc_start: 0.7524 (t0) cc_final: 0.6827 (t70)
REVERT: A  166 ASP cc_start: 0.7992 (p0) cc_final: 0.7426 (p0)
REVERT: A  412 ARG cc_start: 0.7570 (mtt180) cc_final: 0.7134 (ttm170)
REVERT: B  166 ASP cc_start: 0.7719 (p0) cc_final: 0.7389 (p0)
REVERT: B  209 GLU cc_start: 0.7767 (tp30) cc_final: 0.7480 (tp30)
REVERT: B  210 TYR cc_start: 0.6821 (t80) cc_final: 0.6483 (t80)
REVERT: B  325 GLN cc_start: 0.7805 (mp10) cc_final: 0.7282 (mp10)
REVERT: B  337 PHE cc_start: 0.6717 (m-10) cc_final: 0.6485 (m-10)
REVERT: B  341 GLU cc_start: 0.7840 (pp20) cc_final: 0.7413 (pp20)
  outliers start: 18
  outliers final: 16
  residues processed: 225
  average time/residue: 0.1367
  time to fit residues: 43.3867
Evaluate side-chains
  231 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 215
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  245 MET
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  395 PHE
Chi-restraints excluded: chain A residue  408 CYS
Chi-restraints excluded: chain B residue   42 GLN
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  351 LEU
Chi-restraints excluded: chain B residue  356 SER
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  395 PHE
Chi-restraints excluded: chain B residue  408 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0870
   chunk 59 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 55 optimal weight:    0.3980
   chunk 16 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.5558

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.176031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.151270 restraints weight = 8885.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.155225 restraints weight = 5110.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.157808 restraints weight = 3493.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6332  Z= 0.188
  Angle     :  0.644  11.542   8630  Z= 0.306
  Chirality :  0.039   0.236   1066
  Planarity :  0.004   0.057   1050
  Dihedral  :  5.105  38.854   1090
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 26.61 %
    Favored  : 70.95 %
  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:  3.90 (0.29), residues: 780
  helix:  2.92 (0.19), residues: 668
  sheet:  None (None), residues: 0
  loop :  0.33 (0.58), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  12 
 HIS   0.001   0.000   HIS B  22 
 PHE   0.024   0.002   PHE B 173 
 TYR   0.009   0.001   TYR B 374 
 ARG   0.007   0.001   ARG A 295 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1950.25 seconds
wall clock time: 34 minutes 40.61 seconds (2080.61 seconds total)