Starting phenix.real_space_refine
on Fri Jul 25 10:35:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ofy_16863/07_2025/8ofy_16863.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ofy_16863/07_2025/8ofy_16863.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ofy_16863/07_2025/8ofy_16863.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ofy_16863/07_2025/8ofy_16863.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ofy_16863/07_2025/8ofy_16863.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ofy_16863/07_2025/8ofy_16863.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.023 sd=   0.424
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    5004      2.51       5
     N    1140      2.21       5
     O    1244      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7420
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 244, 1830
          Classifications: {'peptide': 244}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 13, 'TRANS': 230}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    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: 3.61, per 1000 atoms: 0.49
  Number of scatterers: 7420
  At special positions: 0
  Unit cell: (82.318, 82.318, 66.688, 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    1244      8.00
     N    1140      7.00
     C    5004      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: 1.64
  Conformation dependent library (CDL) restraints added in 957.5 milliseconds
  

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1696

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 0 sheets defined
      78.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 71 through 98
    Processing helix  chain 'A' and resid 102 through 126
      removed outlier: 5.685A  pdb=" N   GLY A 123 " --> pdb=" O   TYR A 119 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   ILE A 124 " --> pdb=" O   VAL A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 140
    Processing helix  chain 'A' and resid 144 through 146
      No H-bonds generated for 'chain 'A' and resid 144 through 146'
    Processing helix  chain 'A' and resid 147 through 178
      removed outlier: 5.612A  pdb=" N   ASP A 172 " --> pdb=" O   GLY A 168 " (cutoff:3.500A)
      removed outlier: 6.120A  pdb=" N   LEU A 173 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 195
      removed outlier: 4.084A  pdb=" N   PHE A 194 " --> pdb=" O   ILE A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 227
    Processing helix  chain 'A' and resid 236 through 252
    Processing helix  chain 'A' and resid 261 through 277
      removed outlier: 3.602A  pdb=" N   ASP A 265 " --> pdb=" O   ASN A 261 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLY A 267 " --> pdb=" O   SER A 263 " (cutoff:3.500A)
      Proline residue:  A 268  - end of helix
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 288 through 310
      Proline residue:  A 295  - end of helix
    Processing helix  chain 'B' and resid 71 through 98
    Processing helix  chain 'B' and resid 102 through 126
      removed outlier: 5.685A  pdb=" N   GLY B 123 " --> pdb=" O   TYR B 119 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   ILE B 124 " --> pdb=" O   VAL B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 140
    Processing helix  chain 'B' and resid 144 through 146
      No H-bonds generated for 'chain 'B' and resid 144 through 146'
    Processing helix  chain 'B' and resid 147 through 178
      removed outlier: 5.612A  pdb=" N   ASP B 172 " --> pdb=" O   GLY B 168 " (cutoff:3.500A)
      removed outlier: 6.120A  pdb=" N   LEU B 173 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 195
      removed outlier: 4.084A  pdb=" N   PHE B 194 " --> pdb=" O   ILE B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 227
    Processing helix  chain 'B' and resid 236 through 252
    Processing helix  chain 'B' and resid 261 through 277
      removed outlier: 3.602A  pdb=" N   ASP B 265 " --> pdb=" O   ASN B 261 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLY B 267 " --> pdb=" O   SER B 263 " (cutoff:3.500A)
      Proline residue:  B 268  - end of helix
    Processing helix  chain 'B' and resid 278 through 283
    Processing helix  chain 'B' and resid 288 through 310
      Proline residue:  B 295  - end of helix
    Processing helix  chain 'C' and resid 71 through 98
    Processing helix  chain 'C' and resid 102 through 126
      removed outlier: 5.685A  pdb=" N   GLY C 123 " --> pdb=" O   TYR C 119 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   ILE C 124 " --> pdb=" O   VAL C 120 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 140
    Processing helix  chain 'C' and resid 144 through 146
      No H-bonds generated for 'chain 'C' and resid 144 through 146'
    Processing helix  chain 'C' and resid 147 through 178
      removed outlier: 5.612A  pdb=" N   ASP C 172 " --> pdb=" O   GLY C 168 " (cutoff:3.500A)
      removed outlier: 6.120A  pdb=" N   LEU C 173 " --> pdb=" O   VAL C 169 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 195
      removed outlier: 4.084A  pdb=" N   PHE C 194 " --> pdb=" O   ILE C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 204 through 227
    Processing helix  chain 'C' and resid 236 through 252
    Processing helix  chain 'C' and resid 261 through 277
      removed outlier: 3.602A  pdb=" N   ASP C 265 " --> pdb=" O   ASN C 261 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLY C 267 " --> pdb=" O   SER C 263 " (cutoff:3.500A)
      Proline residue:  C 268  - end of helix
    Processing helix  chain 'C' and resid 278 through 283
    Processing helix  chain 'C' and resid 288 through 310
      Proline residue:  C 295  - end of helix
    Processing helix  chain 'D' and resid 71 through 98
    Processing helix  chain 'D' and resid 102 through 126
      removed outlier: 5.685A  pdb=" N   GLY D 123 " --> pdb=" O   TYR D 119 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   ILE D 124 " --> pdb=" O   VAL D 120 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 130 through 140
    Processing helix  chain 'D' and resid 144 through 146
      No H-bonds generated for 'chain 'D' and resid 144 through 146'
    Processing helix  chain 'D' and resid 147 through 178
      removed outlier: 5.612A  pdb=" N   ASP D 172 " --> pdb=" O   GLY D 168 " (cutoff:3.500A)
      removed outlier: 6.120A  pdb=" N   LEU D 173 " --> pdb=" O   VAL D 169 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 195
      removed outlier: 4.084A  pdb=" N   PHE D 194 " --> pdb=" O   ILE D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 204 through 227
    Processing helix  chain 'D' and resid 236 through 252
    Processing helix  chain 'D' and resid 261 through 277
      removed outlier: 3.602A  pdb=" N   ASP D 265 " --> pdb=" O   ASN D 261 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLY D 267 " --> pdb=" O   SER D 263 " (cutoff:3.500A)
      Proline residue:  D 268  - end of helix
    Processing helix  chain 'D' and resid 278 through 283
    Processing helix  chain 'D' and resid 288 through 310
      Proline residue:  D 295  - end of helix

    544 hydrogen bonds defined for protein.
    1632 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: 2.15

  Time building geometry restraints manager: 1.99 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1420
        1.34 -     1.46: 2312
        1.46 -     1.58: 3868
        1.58 -     1.70: 0
        1.70 -     1.81: 52
  Bond restraints: 7652
  Sorted by residual:
  bond pdb=" C9  PNT C 401 "
       pdb=" N2  PNT C 401 "
    ideal  model  delta    sigma   weight residual
    1.368  1.284  0.084 2.00e-02 2.50e+03 1.76e+01
  bond pdb=" C9  PNT D 401 "
       pdb=" N2  PNT D 401 "
    ideal  model  delta    sigma   weight residual
    1.368  1.284  0.084 2.00e-02 2.50e+03 1.76e+01
  bond pdb=" C9  PNT A 401 "
       pdb=" N2  PNT A 401 "
    ideal  model  delta    sigma   weight residual
    1.368  1.284  0.084 2.00e-02 2.50e+03 1.76e+01
  bond pdb=" C9  PNT B 401 "
       pdb=" N2  PNT B 401 "
    ideal  model  delta    sigma   weight residual
    1.368  1.284  0.084 2.00e-02 2.50e+03 1.76e+01
  bond pdb=" C9  PNT A 401 "
       pdb=" N1  PNT A 401 "
    ideal  model  delta    sigma   weight residual
    1.279  1.343 -0.064 2.00e-02 2.50e+03 1.01e+01
  ... (remaining 7647 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.11: 9080
        2.11 -     4.22: 1168
        4.22 -     6.33: 156
        6.33 -     8.44: 24
        8.44 -    10.55: 12
  Bond angle restraints: 10440
  Sorted by residual:
  angle pdb=" CA  ASN C 202 "
        pdb=" CB  ASN C 202 "
        pdb=" CG  ASN C 202 "
      ideal   model   delta    sigma   weight residual
     112.60  117.71   -5.11 1.00e+00 1.00e+00 2.61e+01
  angle pdb=" CA  ASN D 202 "
        pdb=" CB  ASN D 202 "
        pdb=" CG  ASN D 202 "
      ideal   model   delta    sigma   weight residual
     112.60  117.71   -5.11 1.00e+00 1.00e+00 2.61e+01
  angle pdb=" CA  ASN A 202 "
        pdb=" CB  ASN A 202 "
        pdb=" CG  ASN A 202 "
      ideal   model   delta    sigma   weight residual
     112.60  117.71   -5.11 1.00e+00 1.00e+00 2.61e+01
  angle pdb=" CA  ASN B 202 "
        pdb=" CB  ASN B 202 "
        pdb=" CG  ASN B 202 "
      ideal   model   delta    sigma   weight residual
     112.60  117.71   -5.11 1.00e+00 1.00e+00 2.61e+01
  angle pdb=" C   ASN C 230 "
        pdb=" CA  ASN C 230 "
        pdb=" CB  ASN C 230 "
      ideal   model   delta    sigma   weight residual
     110.42  119.89   -9.47 1.99e+00 2.53e-01 2.26e+01
  ... (remaining 10435 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.03 -    19.05: 3932
       19.05 -    38.06: 220
       38.06 -    57.07: 48
       57.07 -    76.08: 16
       76.08 -    95.10: 16
  Dihedral angle restraints: 4232
    sinusoidal: 1512
      harmonic: 2720
  Sorted by residual:
  dihedral pdb=" CA  SER A 282 "
           pdb=" C   SER A 282 "
           pdb=" N   HIS A 283 "
           pdb=" CA  HIS A 283 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.02  -19.98     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  SER B 282 "
           pdb=" C   SER B 282 "
           pdb=" N   HIS B 283 "
           pdb=" CA  HIS B 283 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.02  -19.98     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  SER D 282 "
           pdb=" C   SER D 282 "
           pdb=" N   HIS D 283 "
           pdb=" CA  HIS D 283 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.02  -19.98     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 4229 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 756
       0.061 -    0.121: 304
       0.121 -    0.181: 84
       0.181 -    0.241: 8
       0.241 -    0.302: 4
  Chirality restraints: 1156
  Sorted by residual:
  chirality pdb=" CA  ASN B 202 "
            pdb=" N   ASN B 202 "
            pdb=" C   ASN B 202 "
            pdb=" CB  ASN B 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.27e+00
  chirality pdb=" CA  ASN A 202 "
            pdb=" N   ASN A 202 "
            pdb=" C   ASN A 202 "
            pdb=" CB  ASN A 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.27e+00
  chirality pdb=" CA  ASN C 202 "
            pdb=" N   ASN C 202 "
            pdb=" C   ASN C 202 "
            pdb=" CB  ASN C 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.27e+00
  ... (remaining 1153 not shown)

  Planarity restraints: 1316
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 246 "    0.033 2.00e-02 2.50e+03   2.62e-02 1.20e+01
        pdb=" CG  PHE A 246 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 246 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 246 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 246 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 246 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 246 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 246 "    0.033 2.00e-02 2.50e+03   2.62e-02 1.20e+01
        pdb=" CG  PHE D 246 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 246 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 246 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 246 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 246 "    0.018 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 246 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 246 "   -0.033 2.00e-02 2.50e+03   2.62e-02 1.20e+01
        pdb=" CG  PHE B 246 "    0.057 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 246 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 246 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 246 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 246 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 246 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1313 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 56
        2.71 -     3.26: 7664
        3.26 -     3.80: 13252
        3.80 -     4.35: 17652
        4.35 -     4.90: 28350
  Nonbonded interactions: 66974
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A  94 "
            pdb=" O   ASN B 251 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" OG1 THR B  94 "
            pdb=" O   ASN C 251 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" O   ASN A 251 "
            pdb=" OG1 THR D  94 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" OG1 THR C  94 "
            pdb=" O   ASN D 251 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" O   GLY A 235 "
            pdb=" OH  TYR B 236 "
     model   vdw
     2.491 3.040
  ... (remaining 66969 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: 0.06
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 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:             0.190
  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:             0.020
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     18.930
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5943
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      :  0.009   0.084   7652  Z= 0.581
  Angle     :  1.507  10.552  10440  Z= 1.002
  Chirality :  0.069   0.302   1156
  Planarity :  0.009   0.069   1316
  Dihedral  : 15.132  95.097   2536
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.41 %
    Allowed  :  3.72 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  :  4.97 %
    Favored  : 92.82 %
  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: -0.53 (0.25), residues: 968
  helix:  0.17 (0.17), residues: 632
  sheet:  None (None), residues: 0
  loop : -1.19 (0.37), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.005   TRP D 289 
 HIS   0.012   0.004   HIS D 177 
 PHE   0.057   0.008   PHE D 246 
 TYR   0.040   0.007   TYR A 151 
 ARG   0.018   0.006   ARG D 269 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16195 (  544)
  hydrogen bonds       : angle       6.97414 ( 1632)
  covalent geometry    : bond        0.00888 ( 7652)
  covalent geometry    : angle       1.50664 (10440)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.684 
Fit side-chains
REVERT: A  248 MET cc_start: 0.6966 (mmt) cc_final: 0.6379 (mmt)
REVERT: B  248 MET cc_start: 0.6967 (mmt) cc_final: 0.6377 (mmt)
REVERT: C  248 MET cc_start: 0.6968 (mmt) cc_final: 0.6380 (mmt)
REVERT: D  248 MET cc_start: 0.6967 (mmt) cc_final: 0.6378 (mmt)
  outliers start: 16
  outliers final: 4
  residues processed: 144
  average time/residue: 0.2047
  time to fit residues: 39.1088
Evaluate side-chains
  120 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 116
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain B residue  174 LEU
Chi-restraints excluded: chain C residue  174 LEU
Chi-restraints excluded: chain D residue  174 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 72 optimal weight:   10.0000
   chunk 40 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 56 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  81 ASN
A 137 ASN
B  81 ASN
B 137 ASN
C  81 ASN
C 137 ASN
D  81 ASN
D 137 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.145273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.129007 restraints weight = 8554.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.132295 restraints weight = 5341.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.134625 restraints weight = 3718.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7652  Z= 0.168
  Angle     :  0.642   6.189  10440  Z= 0.329
  Chirality :  0.042   0.153   1156
  Planarity :  0.005   0.037   1316
  Dihedral  : 11.704  87.374   1096
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  7.73 %
    Favored  : 91.16 %
  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:  1.09 (0.26), residues: 968
  helix:  1.54 (0.18), residues: 656
  sheet:  None (None), residues: 0
  loop : -1.02 (0.39), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 289 
 HIS   0.001   0.001   HIS B 312 
 PHE   0.009   0.002   PHE D 304 
 TYR   0.026   0.002   TYR B 206 
 ARG   0.001   0.000   ARG B  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04733 (  544)
  hydrogen bonds       : angle       5.25063 ( 1632)
  covalent geometry    : bond        0.00376 ( 7652)
  covalent geometry    : angle       0.64204 (10440)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 148
  time to evaluate  : 0.725 
Fit side-chains
REVERT: A  140 PHE cc_start: 0.7776 (m-10) cc_final: 0.7487 (m-80)
REVERT: A  196 MET cc_start: 0.6790 (mmt) cc_final: 0.6551 (mmt)
REVERT: A  219 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7182 (mp)
REVERT: B  140 PHE cc_start: 0.7776 (m-10) cc_final: 0.7487 (m-80)
REVERT: B  196 MET cc_start: 0.6788 (mmt) cc_final: 0.6553 (mmt)
REVERT: B  219 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7190 (mp)
REVERT: C  140 PHE cc_start: 0.7774 (m-10) cc_final: 0.7487 (m-80)
REVERT: C  196 MET cc_start: 0.6788 (mmt) cc_final: 0.6550 (mmt)
REVERT: C  219 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7185 (mp)
REVERT: D  140 PHE cc_start: 0.7771 (m-10) cc_final: 0.7486 (m-80)
REVERT: D  196 MET cc_start: 0.6782 (mmt) cc_final: 0.6543 (mmt)
REVERT: D  219 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7181 (mp)
  outliers start: 8
  outliers final: 4
  residues processed: 156
  average time/residue: 0.2026
  time to fit residues: 42.1915
Evaluate side-chains
  140 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 132
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  247 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 83 optimal weight:    8.9990
   chunk 20 optimal weight:    4.9990
   chunk 56 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 89 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    1.0586

-------------------------------------------------------------------------------
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 = 0.3484 r_free = 0.3484 target = 0.145807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.129439 restraints weight = 8687.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.132719 restraints weight = 5426.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.135040 restraints weight = 3773.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.2785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7652  Z= 0.132
  Angle     :  0.604   7.050  10440  Z= 0.300
  Chirality :  0.041   0.132   1156
  Planarity :  0.005   0.043   1316
  Dihedral  : 11.055  87.060   1088
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  :  8.29 %
    Favored  : 90.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.27), residues: 968
  helix:  1.91 (0.19), residues: 656
  sheet:  None (None), residues: 0
  loop : -1.21 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 289 
 HIS   0.001   0.000   HIS D 128 
 PHE   0.022   0.002   PHE D 288 
 TYR   0.030   0.002   TYR B 206 
 ARG   0.006   0.001   ARG A 269 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04074 (  544)
  hydrogen bonds       : angle       4.88003 ( 1632)
  covalent geometry    : bond        0.00285 ( 7652)
  covalent geometry    : angle       0.60422 (10440)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 0.679 
Fit side-chains
REVERT: A  219 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7199 (mp)
REVERT: A  258 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8180 (pp)
REVERT: B  219 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7203 (mp)
REVERT: B  258 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8182 (pp)
REVERT: C  219 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7209 (mp)
REVERT: C  258 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8184 (pp)
REVERT: D  219 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7202 (mp)
REVERT: D  258 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8182 (pp)
  outliers start: 12
  outliers final: 4
  residues processed: 148
  average time/residue: 0.2177
  time to fit residues: 41.9520
Evaluate side-chains
  144 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 11 optimal weight:    0.0040
   chunk 45 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 37 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 90 optimal weight:    5.9990
   chunk 80 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    2.3598

-------------------------------------------------------------------------------
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 = 0.3463 r_free = 0.3463 target = 0.144880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.128333 restraints weight = 8710.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.131675 restraints weight = 5435.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.133817 restraints weight = 3769.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7652  Z= 0.180
  Angle     :  0.628   6.842  10440  Z= 0.311
  Chirality :  0.041   0.157   1156
  Planarity :  0.006   0.060   1316
  Dihedral  : 10.488  85.385   1088
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 11.60 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.26), residues: 968
  helix:  1.83 (0.19), residues: 656
  sheet:  None (None), residues: 0
  loop : -1.19 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 289 
 HIS   0.002   0.001   HIS B 128 
 PHE   0.012   0.002   PHE B 226 
 TYR   0.010   0.002   TYR D 306 
 ARG   0.006   0.001   ARG D 269 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04224 (  544)
  hydrogen bonds       : angle       4.81451 ( 1632)
  covalent geometry    : bond        0.00428 ( 7652)
  covalent geometry    : angle       0.62845 (10440)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A  219 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.6857 (mp)
REVERT: A  258 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8223 (pp)
REVERT: B  219 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.6873 (mp)
REVERT: B  258 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8219 (pp)
REVERT: C  219 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.6871 (mp)
REVERT: C  258 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8222 (pp)
REVERT: D  219 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.6865 (mp)
REVERT: D  258 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8221 (pp)
  outliers start: 20
  outliers final: 12
  residues processed: 144
  average time/residue: 0.2259
  time to fit residues: 42.2592
Evaluate side-chains
  152 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  307 LYS
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  307 LYS
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  258 LEU
Chi-restraints excluded: chain D residue  307 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 89 optimal weight:    0.8980
   chunk 69 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0050
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.5798

-------------------------------------------------------------------------------
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 = 0.3458 r_free = 0.3458 target = 0.143532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.125180 restraints weight = 8658.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.128829 restraints weight = 5332.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.131399 restraints weight = 3676.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.3436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7652  Z= 0.146
  Angle     :  0.588   7.268  10440  Z= 0.290
  Chirality :  0.040   0.122   1156
  Planarity :  0.005   0.044   1316
  Dihedral  : 10.572  86.989   1088
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 12.71 %
    Favored  : 83.98 %
  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:  1.54 (0.27), residues: 968
  helix:  2.01 (0.19), residues: 656
  sheet:  None (None), residues: 0
  loop : -1.17 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 289 
 HIS   0.001   0.000   HIS D 128 
 PHE   0.022   0.002   PHE D 185 
 TYR   0.009   0.001   TYR D 306 
 ARG   0.003   0.001   ARG B 269 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03825 (  544)
  hydrogen bonds       : angle       4.74905 ( 1632)
  covalent geometry    : bond        0.00343 ( 7652)
  covalent geometry    : angle       0.58757 (10440)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.749 
Fit side-chains
REVERT: A  219 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.6757 (mp)
REVERT: A  258 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8173 (pp)
REVERT: B  219 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.6772 (mp)
REVERT: B  258 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8176 (pp)
REVERT: C  219 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.6770 (mp)
REVERT: C  258 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8179 (pp)
REVERT: D  219 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.6772 (mp)
REVERT: D  258 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8178 (pp)
  outliers start: 24
  outliers final: 8
  residues processed: 152
  average time/residue: 0.2048
  time to fit residues: 42.1135
Evaluate side-chains
  140 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  307 LYS
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  307 LYS
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  258 LEU
Chi-restraints excluded: chain D residue  307 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0470
   chunk 28 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   overall best weight:    1.1684

-------------------------------------------------------------------------------
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 = 0.3471 r_free = 0.3471 target = 0.144501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.126298 restraints weight = 8689.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.129851 restraints weight = 5275.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.132354 restraints weight = 3619.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.3650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7652  Z= 0.132
  Angle     :  0.589   6.580  10440  Z= 0.287
  Chirality :  0.039   0.121   1156
  Planarity :  0.005   0.042   1316
  Dihedral  : 10.327  85.087   1088
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 14.36 %
    Favored  : 82.87 %
  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:  1.66 (0.27), residues: 968
  helix:  2.02 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop : -1.20 (0.38), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 289 
 HIS   0.001   0.000   HIS D 283 
 PHE   0.023   0.001   PHE D 185 
 TYR   0.008   0.001   TYR C 306 
 ARG   0.002   0.001   ARG A 269 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03592 (  544)
  hydrogen bonds       : angle       4.62983 ( 1632)
  covalent geometry    : bond        0.00308 ( 7652)
  covalent geometry    : angle       0.58927 (10440)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.661 
Fit side-chains
REVERT: A  219 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.6836 (mp)
REVERT: A  258 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8198 (pp)
REVERT: B  219 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.6846 (mp)
REVERT: B  258 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8202 (pp)
REVERT: C  219 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.6842 (mp)
REVERT: C  258 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8203 (pp)
REVERT: D  219 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.6841 (mp)
REVERT: D  258 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8201 (pp)
  outliers start: 20
  outliers final: 8
  residues processed: 144
  average time/residue: 0.2070
  time to fit residues: 39.4447
Evaluate side-chains
  136 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  307 LYS
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  258 LEU
Chi-restraints excluded: chain C residue  307 LYS
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  258 LEU
Chi-restraints excluded: chain D residue  307 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 35 optimal weight:    8.9990
   chunk 67 optimal weight:    8.9990
   chunk 15 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9990
   chunk 19 optimal weight:    8.9990
   chunk 43 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9990
   overall best weight:    2.7990

-------------------------------------------------------------------------------
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 = 0.3419 r_free = 0.3419 target = 0.140993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.124192 restraints weight = 8721.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.127305 restraints weight = 5429.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.129626 restraints weight = 3815.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.3742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   7652  Z= 0.198
  Angle     :  0.629   7.141  10440  Z= 0.311
  Chirality :  0.042   0.136   1156
  Planarity :  0.005   0.043   1316
  Dihedral  : 10.304  85.535   1088
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 13.26 %
    Favored  : 82.87 %
  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:  1.37 (0.26), residues: 968
  helix:  1.57 (0.18), residues: 704
  sheet:  None (None), residues: 0
  loop : -0.85 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 289 
 HIS   0.002   0.001   HIS B 128 
 PHE   0.018   0.002   PHE D 185 
 TYR   0.010   0.002   TYR C 306 
 ARG   0.003   0.001   ARG C 269 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04235 (  544)
  hydrogen bonds       : angle       4.75365 ( 1632)
  covalent geometry    : bond        0.00479 ( 7652)
  covalent geometry    : angle       0.62941 (10440)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 0.771 
Fit side-chains
REVERT: A  175 LYS cc_start: 0.7998 (mtpp) cc_final: 0.7515 (mttt)
REVERT: A  219 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.6955 (mp)
REVERT: B  175 LYS cc_start: 0.7995 (mtpp) cc_final: 0.7510 (mttt)
REVERT: B  219 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.6959 (mp)
REVERT: C  175 LYS cc_start: 0.7993 (mtpp) cc_final: 0.7507 (mttt)
REVERT: C  219 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.6963 (mp)
REVERT: D  175 LYS cc_start: 0.8001 (mtpp) cc_final: 0.7516 (mttt)
REVERT: D  219 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.6964 (mp)
  outliers start: 28
  outliers final: 12
  residues processed: 176
  average time/residue: 0.2225
  time to fit residues: 50.8222
Evaluate side-chains
  164 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain B residue  131 SER
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  307 LYS
Chi-restraints excluded: chain C residue  131 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  247 VAL
Chi-restraints excluded: chain C residue  307 LYS
Chi-restraints excluded: chain D residue  131 SER
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  247 VAL
Chi-restraints excluded: chain D residue  307 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 42 optimal weight:    0.5980
   chunk 69 optimal weight:    7.9990
   chunk 95 optimal weight:    0.9980
   chunk 48 optimal weight:    9.9990
   chunk 43 optimal weight:    0.0980
   chunk 65 optimal weight:    1.9990
   chunk 33 optimal weight:    8.9990
   chunk 73 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3500 r_free = 0.3500 target = 0.149703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.131953 restraints weight = 8830.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.135946 restraints weight = 4885.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.138759 restraints weight = 3162.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.4027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7652  Z= 0.127
  Angle     :  0.618   6.819  10440  Z= 0.301
  Chirality :  0.040   0.135   1156
  Planarity :  0.005   0.039   1316
  Dihedral  : 10.269  85.573   1088
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 16.57 %
    Favored  : 81.77 %
  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:  1.64 (0.27), residues: 968
  helix:  1.77 (0.19), residues: 704
  sheet:  None (None), residues: 0
  loop : -0.74 (0.41), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 289 
 HIS   0.001   0.000   HIS D 177 
 PHE   0.032   0.002   PHE D 209 
 TYR   0.014   0.001   TYR B 206 
 ARG   0.002   0.000   ARG D  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03490 (  544)
  hydrogen bonds       : angle       4.67801 ( 1632)
  covalent geometry    : bond        0.00288 ( 7652)
  covalent geometry    : angle       0.61833 (10440)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 140
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A  175 LYS cc_start: 0.7788 (mtpp) cc_final: 0.7316 (mttt)
REVERT: B  175 LYS cc_start: 0.7780 (mtpp) cc_final: 0.7308 (mttt)
REVERT: C  175 LYS cc_start: 0.7784 (mtpp) cc_final: 0.7312 (mttt)
REVERT: D  175 LYS cc_start: 0.7805 (mtpp) cc_final: 0.7330 (mttt)
  outliers start: 12
  outliers final: 8
  residues processed: 152
  average time/residue: 0.1977
  time to fit residues: 40.4493
Evaluate side-chains
  136 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 128
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain D residue   85 ILE
Chi-restraints excluded: chain D residue  152 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0570
   chunk 17 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    1.5902

-------------------------------------------------------------------------------
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 = 0.3487 r_free = 0.3487 target = 0.148376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.130275 restraints weight = 8911.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.134338 restraints weight = 4917.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.137144 restraints weight = 3196.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.4074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7652  Z= 0.148
  Angle     :  0.645   7.865  10440  Z= 0.309
  Chirality :  0.041   0.143   1156
  Planarity :  0.005   0.041   1316
  Dihedral  : 10.168  84.405   1088
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 18.23 %
    Favored  : 79.56 %
  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:  1.54 (0.27), residues: 968
  helix:  1.70 (0.19), residues: 704
  sheet:  None (None), residues: 0
  loop : -0.81 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 289 
 HIS   0.001   0.001   HIS B 128 
 PHE   0.025   0.002   PHE B 271 
 TYR   0.026   0.002   TYR A 206 
 ARG   0.001   0.000   ARG C  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03679 (  544)
  hydrogen bonds       : angle       4.62395 ( 1632)
  covalent geometry    : bond        0.00351 ( 7652)
  covalent geometry    : angle       0.64520 (10440)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 148
  time to evaluate  : 0.723 
Fit side-chains
REVERT: A  175 LYS cc_start: 0.7807 (mtpp) cc_final: 0.7357 (mttt)
REVERT: B  175 LYS cc_start: 0.7800 (mtpp) cc_final: 0.7349 (mttt)
REVERT: C  175 LYS cc_start: 0.7798 (mtpp) cc_final: 0.7344 (mttt)
REVERT: D  175 LYS cc_start: 0.7812 (mtpp) cc_final: 0.7355 (mttt)
  outliers start: 16
  outliers final: 8
  residues processed: 164
  average time/residue: 0.2169
  time to fit residues: 47.8896
Evaluate side-chains
  152 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 144
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  307 LYS
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  307 LYS
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  307 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 93 optimal weight:    7.9990
   chunk 64 optimal weight:    0.0870
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.8162

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

Flipped N/Q/H residues before XYZ refinement:
A 285 ASN
B 285 ASN
C 285 ASN
D 285 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.152414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.133859 restraints weight = 8668.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.138001 restraints weight = 4800.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.140640 restraints weight = 3116.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.4235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7652  Z= 0.135
  Angle     :  0.649   7.730  10440  Z= 0.317
  Chirality :  0.040   0.134   1156
  Planarity :  0.005   0.041   1316
  Dihedral  : 10.070  84.347   1088
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 18.78 %
    Favored  : 78.45 %
  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:  1.56 (0.27), residues: 968
  helix:  1.79 (0.19), residues: 704
  sheet:  None (None), residues: 0
  loop : -1.05 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 289 
 HIS   0.002   0.001   HIS C 283 
 PHE   0.030   0.002   PHE A 209 
 TYR   0.028   0.001   TYR C 206 
 ARG   0.002   0.001   ARG A  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03394 (  544)
  hydrogen bonds       : angle       4.58034 ( 1632)
  covalent geometry    : bond        0.00305 ( 7652)
  covalent geometry    : angle       0.64879 (10440)

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

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

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1936 Ramachandran restraints generated.
    968 Oldfield, 0 Emsley, 968 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.749 
Fit side-chains
REVERT: A  175 LYS cc_start: 0.7736 (mtpp) cc_final: 0.7332 (mttt)
REVERT: A  219 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6606 (mp)
REVERT: B  175 LYS cc_start: 0.7724 (mtpp) cc_final: 0.7316 (mttt)
REVERT: B  219 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6599 (mp)
REVERT: C  175 LYS cc_start: 0.7731 (mtpp) cc_final: 0.7326 (mttt)
REVERT: C  219 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.6603 (mp)
REVERT: D  175 LYS cc_start: 0.7829 (mtpp) cc_final: 0.7394 (mttt)
REVERT: D  219 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6607 (mp)
  outliers start: 20
  outliers final: 12
  residues processed: 159
  average time/residue: 0.1980
  time to fit residues: 42.1841
Evaluate side-chains
  152 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 136
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  219 LEU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  152 ILE
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  307 LYS
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  152 ILE
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  307 LYS
Chi-restraints excluded: chain D residue   85 ILE
Chi-restraints excluded: chain D residue  152 ILE
Chi-restraints excluded: chain D residue  219 LEU
Chi-restraints excluded: chain D residue  307 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 96
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0670
   chunk 24 optimal weight:   10.0000
   chunk 34 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 89 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9990
   chunk 43 optimal weight:    8.9990
   overall best weight:    0.7722

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

Flipped N/Q/H residues before XYZ refinement:
A 285 ASN
B 285 ASN
C 285 ASN
D 285 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.152363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.134123 restraints weight = 8719.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.138138 restraints weight = 4838.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.140937 restraints weight = 3145.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.4352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7652  Z= 0.134
  Angle     :  0.657   9.908  10440  Z= 0.317
  Chirality :  0.041   0.145   1156
  Planarity :  0.005   0.043   1316
  Dihedral  :  9.957  83.707   1088
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 19.75 %
    Favored  : 76.93 %
  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:  1.53 (0.27), residues: 968
  helix:  1.84 (0.19), residues: 700
  sheet:  None (None), residues: 0
  loop : -1.23 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 289 
 HIS   0.002   0.001   HIS B 283 
 PHE   0.033   0.002   PHE B 209 
 TYR   0.013   0.001   TYR A 206 
 ARG   0.002   0.001   ARG B  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03320 (  544)
  hydrogen bonds       : angle       4.53065 ( 1632)
  covalent geometry    : bond        0.00303 ( 7652)
  covalent geometry    : angle       0.65662 (10440)

===============================================================================
Job complete
usr+sys time: 2232.63 seconds
wall clock time: 40 minutes 11.78 seconds (2411.78 seconds total)