Starting phenix.real_space_refine
on Wed Mar 12 05:55:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jy8_36723/03_2025/8jy8_36723.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jy8_36723/03_2025/8jy8_36723.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jy8_36723/03_2025/8jy8_36723.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jy8_36723/03_2025/8jy8_36723.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jy8_36723/03_2025/8jy8_36723.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jy8_36723/03_2025/8jy8_36723.cif"
  }
  resolution = 2.45
  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=   0.260
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      32      5.16       5
     C    4988      2.51       5
     N    1132      2.21       5
     O    1240      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: 7392
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1823
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 13, 'TRANS': 228}
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'PNT': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 3.96, per 1000 atoms: 0.54
  Number of scatterers: 7392
  At special positions: 0
  Unit cell: (92.568, 92.568, 63.84, 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      32     16.00
     O    1240      8.00
     N    1132      7.00
     C    4988      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: 1.79
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1680

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 0 sheets defined
      74.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 71 through 98
    Processing helix  chain 'A' and resid 103 through 122
      removed outlier: 3.678A  pdb=" N   VAL A 120 " --> pdb=" O   MET A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 140
      removed outlier: 3.508A  pdb=" N   THR A 134 " --> pdb=" O   ASN A 130 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ALA A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL A 139 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   PHE A 140 " --> pdb=" O   GLY A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 170
    Processing helix  chain 'A' and resid 172 through 177
    Processing helix  chain 'A' and resid 190 through 195
      removed outlier: 4.104A  pdb=" N   PHE A 194 " --> pdb=" O   ILE A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 226
      removed outlier: 3.659A  pdb=" N   ILE A 208 " --> pdb=" O   ILE A 204 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   THR A 215 " --> pdb=" O   GLU A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 253
    Processing helix  chain 'A' and resid 261 through 276
      Proline residue:  A 268  - end of helix
    Processing helix  chain 'A' and resid 282 through 287
      removed outlier: 3.610A  pdb=" N   TYR A 286 " --> pdb=" O   SER A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 310
      removed outlier: 3.523A  pdb=" N   LEU A 292 " --> pdb=" O   PHE A 288 " (cutoff:3.500A)
      Proline residue:  A 295  - end of helix
    Processing helix  chain 'B' and resid 72 through 98
    Processing helix  chain 'B' and resid 103 through 122
      removed outlier: 3.678A  pdb=" N   VAL B 120 " --> pdb=" O   MET B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 140
      removed outlier: 3.508A  pdb=" N   THR B 134 " --> pdb=" O   ASN B 130 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ALA B 138 " --> pdb=" O   THR B 134 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL B 139 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   PHE B 140 " --> pdb=" O   GLY B 136 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 170
    Processing helix  chain 'B' and resid 172 through 177
    Processing helix  chain 'B' and resid 190 through 195
      removed outlier: 4.104A  pdb=" N   PHE B 194 " --> pdb=" O   ILE B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 226
      removed outlier: 3.659A  pdb=" N   ILE B 208 " --> pdb=" O   ILE B 204 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   THR B 215 " --> pdb=" O   GLU B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 253
    Processing helix  chain 'B' and resid 261 through 276
      Proline residue:  B 268  - end of helix
    Processing helix  chain 'B' and resid 282 through 287
      removed outlier: 3.610A  pdb=" N   TYR B 286 " --> pdb=" O   SER B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 310
      removed outlier: 3.523A  pdb=" N   LEU B 292 " --> pdb=" O   PHE B 288 " (cutoff:3.500A)
      Proline residue:  B 295  - end of helix
    Processing helix  chain 'C' and resid 72 through 98
    Processing helix  chain 'C' and resid 103 through 122
      removed outlier: 3.678A  pdb=" N   VAL C 120 " --> pdb=" O   MET C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 140
      removed outlier: 3.509A  pdb=" N   THR C 134 " --> pdb=" O   ASN C 130 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ALA C 138 " --> pdb=" O   THR C 134 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL C 139 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   PHE C 140 " --> pdb=" O   GLY C 136 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 170
    Processing helix  chain 'C' and resid 172 through 177
    Processing helix  chain 'C' and resid 190 through 195
      removed outlier: 4.104A  pdb=" N   PHE C 194 " --> pdb=" O   ILE C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 226
      removed outlier: 3.659A  pdb=" N   ILE C 208 " --> pdb=" O   ILE C 204 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   THR C 215 " --> pdb=" O   GLU C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 236 through 253
    Processing helix  chain 'C' and resid 261 through 276
      Proline residue:  C 268  - end of helix
    Processing helix  chain 'C' and resid 282 through 287
      removed outlier: 3.610A  pdb=" N   TYR C 286 " --> pdb=" O   SER C 282 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 288 through 310
      removed outlier: 3.522A  pdb=" N   LEU C 292 " --> pdb=" O   PHE C 288 " (cutoff:3.500A)
      Proline residue:  C 295  - end of helix
    Processing helix  chain 'D' and resid 72 through 98
    Processing helix  chain 'D' and resid 103 through 122
      removed outlier: 3.678A  pdb=" N   VAL D 120 " --> pdb=" O   MET D 116 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 130 through 140
      removed outlier: 3.508A  pdb=" N   THR D 134 " --> pdb=" O   ASN D 130 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ALA D 138 " --> pdb=" O   THR D 134 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   VAL D 139 " --> pdb=" O   VAL D 135 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   PHE D 140 " --> pdb=" O   GLY D 136 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 147 through 170
    Processing helix  chain 'D' and resid 172 through 177
    Processing helix  chain 'D' and resid 190 through 195
      removed outlier: 4.104A  pdb=" N   PHE D 194 " --> pdb=" O   ILE D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 204 through 226
      removed outlier: 3.659A  pdb=" N   ILE D 208 " --> pdb=" O   ILE D 204 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   THR D 215 " --> pdb=" O   GLU D 211 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 236 through 253
    Processing helix  chain 'D' and resid 261 through 276
      Proline residue:  D 268  - end of helix
    Processing helix  chain 'D' and resid 282 through 287
      removed outlier: 3.610A  pdb=" N   TYR D 286 " --> pdb=" O   SER D 282 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 288 through 310
      removed outlier: 3.522A  pdb=" N   LEU D 292 " --> pdb=" O   PHE D 288 " (cutoff:3.500A)
      Proline residue:  D 295  - end of helix

    481 hydrogen bonds defined for protein.
    1443 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: 1.93

  Time building geometry restraints manager: 2.09 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: 2196
        1.34 -     1.46: 1735
        1.46 -     1.57: 3641
        1.57 -     1.69: 0
        1.69 -     1.81: 52
  Bond restraints: 7624
  Sorted by residual:
  bond pdb=" C9  PNT A 401 "
       pdb=" N1  PNT A 401 "
    ideal  model  delta    sigma   weight residual
    1.279  1.389 -0.110 2.00e-02 2.50e+03 3.03e+01
  bond pdb=" C9  PNT B 401 "
       pdb=" N1  PNT B 401 "
    ideal  model  delta    sigma   weight residual
    1.279  1.389 -0.110 2.00e-02 2.50e+03 3.03e+01
  bond pdb=" C9  PNT C 401 "
       pdb=" N1  PNT C 401 "
    ideal  model  delta    sigma   weight residual
    1.279  1.389 -0.110 2.00e-02 2.50e+03 3.03e+01
  bond pdb=" C9  PNT D 401 "
       pdb=" N1  PNT D 401 "
    ideal  model  delta    sigma   weight residual
    1.279  1.389 -0.110 2.00e-02 2.50e+03 3.01e+01
  bond pdb=" C9  PNT A 401 "
       pdb=" N2  PNT A 401 "
    ideal  model  delta    sigma   weight residual
    1.368  1.311  0.057 2.00e-02 2.50e+03 8.23e+00
  ... (remaining 7619 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 10272
        2.36 -     4.73: 100
        4.73 -     7.09: 16
        7.09 -     9.46: 0
        9.46 -    11.82: 8
  Bond angle restraints: 10396
  Sorted by residual:
  angle pdb=" C4  PNT C 401 "
        pdb=" C9  PNT C 401 "
        pdb=" N2  PNT C 401 "
      ideal   model   delta    sigma   weight residual
     115.38  127.20  -11.82 3.00e+00 1.11e-01 1.55e+01
  angle pdb=" C4  PNT B 401 "
        pdb=" C9  PNT B 401 "
        pdb=" N2  PNT B 401 "
      ideal   model   delta    sigma   weight residual
     115.38  127.20  -11.82 3.00e+00 1.11e-01 1.55e+01
  angle pdb=" C4  PNT A 401 "
        pdb=" C9  PNT A 401 "
        pdb=" N2  PNT A 401 "
      ideal   model   delta    sigma   weight residual
     115.38  127.20  -11.82 3.00e+00 1.11e-01 1.55e+01
  angle pdb=" C4  PNT D 401 "
        pdb=" C9  PNT D 401 "
        pdb=" N2  PNT D 401 "
      ideal   model   delta    sigma   weight residual
     115.38  127.17  -11.79 3.00e+00 1.11e-01 1.55e+01
  angle pdb=" N1  PNT D 401 "
        pdb=" C9  PNT D 401 "
        pdb=" N2  PNT D 401 "
      ideal   model   delta    sigma   weight residual
     125.71  114.42   11.29 3.00e+00 1.11e-01 1.42e+01
  ... (remaining 10391 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.36: 4048
       32.36 -    64.73: 152
       64.73 -    97.09: 12
       97.09 -   129.45: 0
      129.45 -   161.81: 4
  Dihedral angle restraints: 4216
    sinusoidal: 1520
      harmonic: 2696
  Sorted by residual:
  dihedral pdb=" C10 PNT D 401 "
           pdb=" C7  PNT D 401 "
           pdb=" C8  PNT D 401 "
           pdb=" O1  PNT D 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.84   19.03  161.81     1      3.00e+01 1.11e-03 2.08e+01
  dihedral pdb=" C10 PNT B 401 "
           pdb=" C7  PNT B 401 "
           pdb=" C8  PNT B 401 "
           pdb=" O1  PNT B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.84   19.04  161.80     1      3.00e+01 1.11e-03 2.08e+01
  dihedral pdb=" C10 PNT C 401 "
           pdb=" C7  PNT C 401 "
           pdb=" C8  PNT C 401 "
           pdb=" O1  PNT C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.84   19.06  161.78     1      3.00e+01 1.11e-03 2.08e+01
  ... (remaining 4213 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 719
       0.032 -    0.065: 329
       0.065 -    0.097: 74
       0.097 -    0.129: 22
       0.129 -    0.162: 4
  Chirality restraints: 1148
  Sorted by residual:
  chirality pdb=" CA  ASN C 137 "
            pdb=" N   ASN C 137 "
            pdb=" C   ASN C 137 "
            pdb=" CB  ASN C 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.54e-01
  chirality pdb=" CA  ASN D 137 "
            pdb=" N   ASN D 137 "
            pdb=" C   ASN D 137 "
            pdb=" CB  ASN D 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.54e-01
  chirality pdb=" CA  ASN B 137 "
            pdb=" N   ASN B 137 "
            pdb=" C   ASN B 137 "
            pdb=" CB  ASN B 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.49e-01
  ... (remaining 1145 not shown)

  Planarity restraints: 1308
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN D 137 "   -0.013 2.00e-02 2.50e+03   2.57e-02 6.61e+00
        pdb=" C   ASN D 137 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ASN D 137 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ALA D 138 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C 137 "    0.013 2.00e-02 2.50e+03   2.57e-02 6.61e+00
        pdb=" C   ASN C 137 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   ASN C 137 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ALA C 138 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 137 "   -0.013 2.00e-02 2.50e+03   2.57e-02 6.59e+00
        pdb=" C   ASN A 137 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ASN A 137 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ALA A 138 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1305 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 2717
        2.85 -     3.37: 7150
        3.37 -     3.88: 13091
        3.88 -     4.39: 14895
        4.39 -     4.90: 25485
  Nonbonded interactions: 63338
  Sorted by model distance:
  nonbonded pdb=" O   MET B 156 "
            pdb=" OG1 THR B 159 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" O   MET C 156 "
            pdb=" OG1 THR C 159 "
     model   vdw
     2.344 3.040
  nonbonded pdb=" O   MET D 156 "
            pdb=" OG1 THR D 159 "
     model   vdw
     2.344 3.040
  nonbonded pdb=" O   MET A 156 "
            pdb=" OG1 THR A 159 "
     model   vdw
     2.344 3.040
  nonbonded pdb=" N   ASP A  73 "
            pdb=" OD1 ASP A  73 "
     model   vdw
     2.367 3.120
  ... (remaining 63333 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.090
  Process input model:                     18.850
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
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      :  0.005   0.110   7624  Z= 0.322
  Angle     :  0.690  11.821  10396  Z= 0.340
  Chirality :  0.038   0.162   1148
  Planarity :  0.006   0.030   1308
  Dihedral  : 17.048 161.815   2536
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 21.43 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.27), residues: 960
  helix:  0.82 (0.21), residues: 628
  sheet:  None (None), residues: 0
  loop : -1.55 (0.30), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 289 
 HIS   0.001   0.000   HIS C 283 
 PHE   0.010   0.001   PHE A 246 
 TYR   0.007   0.001   TYR D 206 
 ARG   0.002   0.001   ARG D 146 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.767 
Fit side-chains
REVERT: A  172 ASP cc_start: 0.6769 (t0) cc_final: 0.6429 (t0)
REVERT: A  196 MET cc_start: 0.7386 (mmt) cc_final: 0.7173 (mmt)
REVERT: A  308 TYR cc_start: 0.6031 (t80) cc_final: 0.5784 (t80)
REVERT: B  172 ASP cc_start: 0.6718 (t0) cc_final: 0.6394 (t0)
REVERT: B  196 MET cc_start: 0.7376 (mmt) cc_final: 0.7165 (mmt)
REVERT: B  308 TYR cc_start: 0.6007 (t80) cc_final: 0.5779 (t80)
REVERT: C  172 ASP cc_start: 0.6776 (t0) cc_final: 0.6437 (t0)
REVERT: C  196 MET cc_start: 0.7430 (mmt) cc_final: 0.7203 (mmt)
REVERT: C  308 TYR cc_start: 0.5999 (t80) cc_final: 0.5767 (t80)
REVERT: D  172 ASP cc_start: 0.6768 (t0) cc_final: 0.6429 (t0)
REVERT: D  196 MET cc_start: 0.7435 (mmt) cc_final: 0.7209 (mmt)
REVERT: D  308 TYR cc_start: 0.6035 (t80) cc_final: 0.5781 (t80)
  outliers start: 12
  outliers final: 4
  residues processed: 142
  average time/residue: 0.9021
  time to fit residues: 137.6369
Evaluate side-chains
  102 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue  222 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 40 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 75 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN
B 250 ASN
C 250 ASN
D 250 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.188357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.166285 restraints weight = 7081.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3786 rms_B_bonded: 1.15
r_work: 0.3683 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3586 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7624  Z= 0.219
  Angle     :  0.586   7.434  10396  Z= 0.302
  Chirality :  0.038   0.127   1148
  Planarity :  0.005   0.037   1308
  Dihedral  : 12.686 145.582   1080
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 17.99 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.27), residues: 960
  helix:  1.84 (0.21), residues: 628
  sheet:  None (None), residues: 0
  loop : -1.43 (0.30), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 192 
 HIS   0.002   0.001   HIS D 128 
 PHE   0.017   0.002   PHE D 246 
 TYR   0.009   0.001   TYR C  71 
 ARG   0.001   0.000   ARG B 269 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.779 
Fit side-chains
REVERT: A  145 TRP cc_start: 0.7852 (m100) cc_final: 0.7413 (m100)
REVERT: A  237 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7708 (mt-10)
REVERT: A  258 LEU cc_start: 0.7626 (tp) cc_final: 0.7377 (tp)
REVERT: A  309 PHE cc_start: 0.6307 (m-10) cc_final: 0.6079 (m-10)
REVERT: B  145 TRP cc_start: 0.7851 (m100) cc_final: 0.7412 (m100)
REVERT: B  237 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7689 (mt-10)
REVERT: B  258 LEU cc_start: 0.7644 (tp) cc_final: 0.7374 (tp)
REVERT: C  145 TRP cc_start: 0.7834 (m100) cc_final: 0.7403 (m100)
REVERT: C  237 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7665 (mt-10)
REVERT: C  258 LEU cc_start: 0.7712 (tp) cc_final: 0.7434 (tp)
REVERT: D  145 TRP cc_start: 0.7868 (m100) cc_final: 0.7442 (m100)
REVERT: D  237 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7744 (mt-10)
REVERT: D  258 LEU cc_start: 0.7637 (tp) cc_final: 0.7387 (tp)
REVERT: D  309 PHE cc_start: 0.6295 (m-10) cc_final: 0.6063 (m-10)
  outliers start: 21
  outliers final: 6
  residues processed: 136
  average time/residue: 0.8437
  time to fit residues: 123.7787
Evaluate side-chains
  123 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  237 GLU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  237 GLU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain C residue  237 GLU
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  237 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 20 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0470
   chunk 75 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 10 optimal weight:    0.7980
   chunk 70 optimal weight:    0.3980
   chunk 30 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.8280

-------------------------------------------------------------------------------
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 = 0.3999 r_free = 0.3999 target = 0.186430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.163663 restraints weight = 7128.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 1.18
r_work: 0.3645 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3548 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7624  Z= 0.233
  Angle     :  0.592   8.562  10396  Z= 0.303
  Chirality :  0.038   0.118   1148
  Planarity :  0.005   0.038   1308
  Dihedral  : 13.508 167.706   1080
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 14.15 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.27), residues: 960
  helix:  1.80 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -1.30 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 289 
 HIS   0.003   0.001   HIS D 128 
 PHE   0.017   0.002   PHE A 246 
 TYR   0.005   0.001   TYR B 236 
 ARG   0.001   0.000   ARG A 269 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 112
  time to evaluate  : 0.718 
Fit side-chains
  outliers start: 32
  outliers final: 14
  residues processed: 133
  average time/residue: 0.8968
  time to fit residues: 128.3822
Evaluate side-chains
  115 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 SER
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  146 ARG
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain D residue   95 SER
Chi-restraints excluded: chain D residue  146 ARG
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  219 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0770
   chunk 53 optimal weight:    0.0170
   chunk 72 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 73 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 = 0.3974 r_free = 0.3974 target = 0.183750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.161151 restraints weight = 6822.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 1.17
r_work: 0.3620 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3515 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7624  Z= 0.190
  Angle     :  0.559   8.554  10396  Z= 0.281
  Chirality :  0.037   0.113   1148
  Planarity :  0.005   0.038   1308
  Dihedral  : 13.187 165.509   1076
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 14.56 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.27), residues: 960
  helix:  2.01 (0.20), residues: 636
  sheet:  None (None), residues: 0
  loop : -1.26 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 289 
 HIS   0.001   0.000   HIS D 128 
 PHE   0.014   0.002   PHE A 246 
 TYR   0.006   0.001   TYR C 206 
 ARG   0.001   0.000   ARG C 269 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 101
  time to evaluate  : 0.700 
Fit side-chains
REVERT: B  258 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7633 (mt)
REVERT: C  258 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7597 (mt)
  outliers start: 30
  outliers final: 14
  residues processed: 122
  average time/residue: 0.9536
  time to fit residues: 124.4053
Evaluate side-chains
  114 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 SER
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  146 ARG
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain D residue   95 SER
Chi-restraints excluded: chain D residue  146 ARG
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  219 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 95 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 60 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 94 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3958 r_free = 0.3958 target = 0.181997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.159052 restraints weight = 6801.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3711 rms_B_bonded: 1.16
r_work: 0.3597 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3493 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7624  Z= 0.215
  Angle     :  0.583   8.602  10396  Z= 0.294
  Chirality :  0.038   0.116   1148
  Planarity :  0.005   0.039   1308
  Dihedral  : 13.104 164.724   1076
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 14.15 %
    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:  1.41 (0.27), residues: 960
  helix:  1.95 (0.20), residues: 640
  sheet:  None (None), residues: 0
  loop : -1.23 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 289 
 HIS   0.003   0.001   HIS A 177 
 PHE   0.016   0.002   PHE D 246 
 TYR   0.006   0.001   TYR C 206 
 ARG   0.001   0.000   ARG A 269 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 106
  time to evaluate  : 0.801 
Fit side-chains
REVERT: A  258 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7740 (mt)
REVERT: B  258 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7740 (mt)
REVERT: C  258 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7715 (mt)
REVERT: D  258 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7694 (mt)
  outliers start: 35
  outliers final: 20
  residues processed: 127
  average time/residue: 0.9334
  time to fit residues: 127.0497
Evaluate side-chains
  130 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 106
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 SER
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  146 ARG
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain D residue   95 SER
Chi-restraints excluded: chain D residue  146 ARG
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  222 VAL
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 82 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3953 r_free = 0.3953 target = 0.181697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.158590 restraints weight = 6844.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 1.17
r_work: 0.3591 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3488 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7624  Z= 0.219
  Angle     :  0.589   8.570  10396  Z= 0.297
  Chirality :  0.038   0.115   1148
  Planarity :  0.005   0.039   1308
  Dihedral  : 13.097 166.010   1076
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 15.25 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.27), residues: 960
  helix:  2.04 (0.20), residues: 632
  sheet:  None (None), residues: 0
  loop : -1.34 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 289 
 HIS   0.002   0.001   HIS A 177 
 PHE   0.016   0.002   PHE D 246 
 TYR   0.007   0.001   TYR B 206 
 ARG   0.001   0.000   ARG C 269 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 108
  time to evaluate  : 0.800 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7795 (tmm160)
REVERT: A  188 LYS cc_start: 0.6896 (ptpp) cc_final: 0.6668 (ptpt)
REVERT: A  258 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7712 (mt)
REVERT: B  258 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7738 (mt)
REVERT: C  258 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7684 (mt)
REVERT: D  188 LYS cc_start: 0.6889 (ptpp) cc_final: 0.6652 (ptpt)
  outliers start: 30
  outliers final: 19
  residues processed: 125
  average time/residue: 0.9423
  time to fit residues: 126.3562
Evaluate side-chains
  130 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 SER
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain B residue   95 SER
Chi-restraints excluded: chain B residue  146 ARG
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain C residue   95 SER
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain D residue   95 SER
Chi-restraints excluded: chain D residue  146 ARG
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  222 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3908 r_free = 0.3908 target = 0.177645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.153843 restraints weight = 6787.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 1.14
r_work: 0.3537 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3438 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.2919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   7624  Z= 0.333
  Angle     :  0.693   8.590  10396  Z= 0.354
  Chirality :  0.042   0.125   1148
  Planarity :  0.006   0.039   1308
  Dihedral  : 13.329 167.149   1076
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 14.97 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.26), residues: 960
  helix:  1.67 (0.20), residues: 632
  sheet:  None (None), residues: 0
  loop : -1.40 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 192 
 HIS   0.004   0.001   HIS A 177 
 PHE   0.019   0.003   PHE A 246 
 TYR   0.010   0.002   TYR D 119 
 ARG   0.001   0.000   ARG B 146 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 113
  time to evaluate  : 0.943 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7793 (tmm160)
REVERT: A  188 LYS cc_start: 0.6968 (ptpp) cc_final: 0.6744 (ptpt)
REVERT: D  188 LYS cc_start: 0.6899 (ptpp) cc_final: 0.6581 (ptpt)
  outliers start: 31
  outliers final: 18
  residues processed: 129
  average time/residue: 1.1467
  time to fit residues: 157.5576
Evaluate side-chains
  130 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  146 ARG
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain C residue  103 LEU
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue  103 LEU
Chi-restraints excluded: chain D residue  146 ARG
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  222 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0060
   overall best weight:    0.6396

-------------------------------------------------------------------------------
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 = 0.3947 r_free = 0.3947 target = 0.181225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.158291 restraints weight = 6802.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3696 rms_B_bonded: 1.13
r_work: 0.3586 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3486 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.2838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7624  Z= 0.206
  Angle     :  0.595   8.981  10396  Z= 0.296
  Chirality :  0.038   0.115   1148
  Planarity :  0.005   0.039   1308
  Dihedral  : 13.025 166.185   1076
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.90 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.27), residues: 960
  helix:  1.98 (0.20), residues: 632
  sheet:  None (None), residues: 0
  loop : -1.35 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 289 
 HIS   0.002   0.001   HIS A 177 
 PHE   0.015   0.002   PHE D 246 
 TYR   0.007   0.001   TYR D 236 
 ARG   0.001   0.000   ARG C 269 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.660 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7817 (tmm160)
REVERT: A  188 LYS cc_start: 0.6930 (ptpp) cc_final: 0.6722 (ptpt)
  outliers start: 20
  outliers final: 14
  residues processed: 118
  average time/residue: 1.2052
  time to fit residues: 152.4857
Evaluate side-chains
  122 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue  146 ARG
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue  146 ARG
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  222 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 90 optimal weight:    0.7980
   chunk 88 optimal weight:    0.0270
   chunk 80 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0970
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.7840

-------------------------------------------------------------------------------
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 = 0.3943 r_free = 0.3943 target = 0.180703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.157283 restraints weight = 6909.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 1.16
r_work: 0.3577 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3477 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7624  Z= 0.221
  Angle     :  0.608   9.135  10396  Z= 0.304
  Chirality :  0.038   0.116   1148
  Planarity :  0.006   0.040   1308
  Dihedral  : 13.032 166.867   1076
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.62 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.26), residues: 960
  helix:  2.04 (0.19), residues: 632
  sheet:  None (None), residues: 0
  loop : -1.34 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 289 
 HIS   0.003   0.001   HIS A 177 
 PHE   0.016   0.002   PHE A 246 
 TYR   0.007   0.001   TYR B 206 
 ARG   0.002   0.000   ARG D  72 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.696 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7822 (tmm160)
REVERT: A  188 LYS cc_start: 0.6970 (ptpp) cc_final: 0.6761 (ptpt)
REVERT: B  258 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7747 (mt)
REVERT: C  258 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7709 (mt)
  outliers start: 20
  outliers final: 15
  residues processed: 118
  average time/residue: 1.1460
  time to fit residues: 143.2323
Evaluate side-chains
  124 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue  146 ARG
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain D residue  146 ARG
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  222 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 12 optimal weight:    0.0170
   chunk 68 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 73 optimal weight:    0.5980
   chunk 63 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.5218

-------------------------------------------------------------------------------
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 = 0.3962 r_free = 0.3962 target = 0.182645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.159857 restraints weight = 6984.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 1.15
r_work: 0.3606 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.3505 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7624  Z= 0.188
  Angle     :  0.577   8.944  10396  Z= 0.286
  Chirality :  0.037   0.113   1148
  Planarity :  0.005   0.039   1308
  Dihedral  : 12.836 166.982   1076
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.17 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.27), residues: 960
  helix:  2.27 (0.20), residues: 632
  sheet:  None (None), residues: 0
  loop : -1.34 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 289 
 HIS   0.002   0.001   HIS D 177 
 PHE   0.013   0.001   PHE D 246 
 TYR   0.008   0.001   TYR D 236 
 ARG   0.002   0.000   ARG D  72 

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

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

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1920 Ramachandran restraints generated.
    960 Oldfield, 0 Emsley, 960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.684 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7776 (tmm160)
  outliers start: 16
  outliers final: 14
  residues processed: 109
  average time/residue: 1.0039
  time to fit residues: 116.8740
Evaluate side-chains
  113 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 ARG
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain B residue  146 ARG
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  222 VAL
Chi-restraints excluded: chain D residue  146 ARG
Chi-restraints excluded: chain D residue  157 LEU
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  222 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 93 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 67 optimal weight:    0.6980
   chunk 56 optimal weight:    0.5980
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3951 r_free = 0.3951 target = 0.181546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.158438 restraints weight = 6884.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 1.16
r_work: 0.3589 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3489 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7624  Z= 0.209
  Angle     :  0.596   9.048  10396  Z= 0.296
  Chirality :  0.038   0.115   1148
  Planarity :  0.005   0.039   1308
  Dihedral  : 12.869 167.797   1076
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 17.03 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.26), residues: 960
  helix:  2.24 (0.19), residues: 632
  sheet:  None (None), residues: 0
  loop : -1.31 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 289 
 HIS   0.002   0.001   HIS D 177 
 PHE   0.017   0.002   PHE D 246 
 TYR   0.006   0.001   TYR B 236 
 ARG   0.002   0.000   ARG D  72 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5582.11 seconds
wall clock time: 95 minutes 57.31 seconds (5757.31 seconds total)