Starting phenix.real_space_refine
on Wed Mar 12 01:47:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cgx_45588/03_2025/9cgx_45588.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cgx_45588/03_2025/9cgx_45588.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cgx_45588/03_2025/9cgx_45588.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cgx_45588/03_2025/9cgx_45588.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cgx_45588/03_2025/9cgx_45588.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cgx_45588/03_2025/9cgx_45588.cif"
  }
  resolution = 2.97
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S       6      5.16       5
     C    2142      2.51       5
     N     630      2.21       5
     O     642      1.98       5
     H    3540      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6960
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1160
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
    Chain: "B"
      Number of atoms: 1160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1160
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
    Chain: "C"
      Number of atoms: 1160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1160
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
    Chain: "D"
      Number of atoms: 1160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1160
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
    Chain: "E"
      Number of atoms: 1160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1160
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
    Chain: "F"
      Number of atoms: 1160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 1160
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 3, 'TRANS': 70}
  Time building chain proxies: 4.38, per 1000 atoms: 0.63
  Number of scatterers: 6960
  At special positions: 0
  Unit cell: (149.46, 76.32, 33.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       6     16.00
     O     642      8.00
     N     630      7.00
     C    2142      6.00
     H    3540      1.00
    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: 1.81
  Conformation dependent library (CDL) restraints added in 599.9 milliseconds
  

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  780

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 20 sheets defined
      0.0% alpha, 44.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 310
      removed outlier: 6.762A  pdb=" N   ILE A 308 " --> pdb=" O   VAL C 309 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
    Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322
    Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330
    Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340
      removed outlier: 6.649A  pdb=" N   VAL A 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 7.974A  pdb=" N   LYS C 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   VAL A 339 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   VAL C 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 8.059A  pdb=" N   LYS E 340 " --> pdb=" O   VAL C 337 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   VAL C 339 " --> pdb=" O   LYS E 340 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 344
    Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 356
      removed outlier: 6.844A  pdb=" N   SER A 356 " --> pdb=" O   GLY C 355 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   SER C 356 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362
    Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 371
      removed outlier: 6.444A  pdb=" N   LYS A 370 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 378
    Processing sheet with id=AB2, first strand: chain 'B' and resid 308 through 310
      removed outlier: 6.680A  pdb=" N   ILE B 308 " --> pdb=" O   VAL D 309 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ILE D 308 " --> pdb=" O   VAL F 309 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 313 through 314
    Processing sheet with id=AB4, first strand: chain 'B' and resid 317 through 322
    Processing sheet with id=AB5, first strand: chain 'B' and resid 329 through 330
    Processing sheet with id=AB6, first strand: chain 'B' and resid 336 through 340
      removed outlier: 6.545A  pdb=" N   VAL B 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 8.041A  pdb=" N   LYS D 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   VAL B 339 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   VAL D 337 " --> pdb=" O   GLU F 338 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   LYS F 340 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   VAL D 339 " --> pdb=" O   LYS F 340 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'B' and resid 343 through 347
      removed outlier: 6.325A  pdb=" N   LEU B 344 " --> pdb=" O   ASP D 345 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   LYS D 347 " --> pdb=" O   LEU B 344 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   PHE B 346 " --> pdb=" O   LYS D 347 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LEU D 344 " --> pdb=" O   ASP F 345 " (cutoff:3.500A)
      removed outlier: 7.921A  pdb=" N   LYS F 347 " --> pdb=" O   LEU D 344 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   PHE D 346 " --> pdb=" O   LYS F 347 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'B' and resid 351 through 356
      removed outlier: 6.819A  pdb=" N   SER B 356 " --> pdb=" O   GLY D 355 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   SER D 356 " --> pdb=" O   GLY F 355 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 359 through 362
    Processing sheet with id=AC1, first strand: chain 'B' and resid 369 through 371
    Processing sheet with id=AC2, first strand: chain 'B' and resid 369 through 371

    90 hydrogen bonds defined for protein.
    267 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: 2.22

  Time building geometry restraints manager: 2.23 seconds

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

  Histogram of bond lengths:
        0.95 -     1.12: 3534
        1.12 -     1.29: 576
        1.29 -     1.47: 1061
        1.47 -     1.64: 1837
        1.64 -     1.81: 6
  Bond restraints: 7014
  Sorted by residual:
  bond pdb=" N   VAL B 363 "
       pdb=" H   VAL B 363 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" N   GLY A 366 "
       pdb=" H   GLY A 366 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" N   VAL B 339 "
       pdb=" H   VAL B 339 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" N   LYS D 347 "
       pdb=" H   LYS D 347 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  bond pdb=" N   SER E 324 "
       pdb=" H   SER E 324 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
  ... (remaining 7009 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.54: 10618
        2.54 -     5.07: 1645
        5.07 -     7.61: 487
        7.61 -    10.14: 24
       10.14 -    12.68: 6
  Bond angle restraints: 12780
  Sorted by residual:
  angle pdb=" CA  PHE E 346 "
        pdb=" CB  PHE E 346 "
        pdb=" CG  PHE E 346 "
      ideal   model   delta    sigma   weight residual
     113.80  121.32   -7.52 1.00e+00 1.00e+00 5.66e+01
  angle pdb=" CA  ASP A 358 "
        pdb=" CB  ASP A 358 "
        pdb=" CG  ASP A 358 "
      ideal   model   delta    sigma   weight residual
     112.60  118.57   -5.97 1.00e+00 1.00e+00 3.57e+01
  angle pdb=" CA  ASP B 358 "
        pdb=" CB  ASP B 358 "
        pdb=" CG  ASP B 358 "
      ideal   model   delta    sigma   weight residual
     112.60  118.55   -5.95 1.00e+00 1.00e+00 3.54e+01
  angle pdb=" CA  ASP B 345 "
        pdb=" CB  ASP B 345 "
        pdb=" CG  ASP B 345 "
      ideal   model   delta    sigma   weight residual
     112.60  118.51   -5.91 1.00e+00 1.00e+00 3.49e+01
  angle pdb=" CA  ASP C 345 "
        pdb=" CB  ASP C 345 "
        pdb=" CG  ASP C 345 "
      ideal   model   delta    sigma   weight residual
     112.60  118.35   -5.75 1.00e+00 1.00e+00 3.30e+01
  ... (remaining 12775 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 2851
       17.63 -    35.25: 204
       35.25 -    52.88: 85
       52.88 -    70.50: 84
       70.50 -    88.13: 4
  Dihedral angle restraints: 3228
    sinusoidal: 1848
      harmonic: 1380
  Sorted by residual:
  dihedral pdb=" CA  LEU B 325 "
           pdb=" C   LEU B 325 "
           pdb=" N   GLY B 326 "
           pdb=" CA  GLY B 326 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.78  -29.22     0      5.00e+00 4.00e-02 3.41e+01
  dihedral pdb=" CA  LEU E 325 "
           pdb=" C   LEU E 325 "
           pdb=" N   GLY E 326 "
           pdb=" CA  GLY E 326 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.80  -29.20     0      5.00e+00 4.00e-02 3.41e+01
  dihedral pdb=" CA  LEU D 325 "
           pdb=" C   LEU D 325 "
           pdb=" N   GLY D 326 "
           pdb=" CA  GLY D 326 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.89  -29.11     0      5.00e+00 4.00e-02 3.39e+01
  ... (remaining 3225 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 230
       0.056 -    0.113: 169
       0.113 -    0.169: 73
       0.169 -    0.225: 34
       0.225 -    0.282: 10
  Chirality restraints: 516
  Sorted by residual:
  chirality pdb=" CA  ARG C 379 "
            pdb=" N   ARG C 379 "
            pdb=" C   ARG C 379 "
            pdb=" CB  ARG C 379 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" CA  ARG F 349 "
            pdb=" N   ARG F 349 "
            pdb=" C   ARG F 349 "
            pdb=" CB  ARG F 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CA  ARG D 379 "
            pdb=" N   ARG D 379 "
            pdb=" C   ARG D 379 "
            pdb=" CB  ARG D 379 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.64e+00
  ... (remaining 513 not shown)

  Planarity restraints: 1014
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E 346 "   -0.168 2.00e-02 2.50e+03   1.18e-01 4.15e+02
        pdb=" CG  PHE E 346 "    0.167 2.00e-02 2.50e+03
        pdb=" CD1 PHE E 346 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 PHE E 346 "    0.147 2.00e-02 2.50e+03
        pdb=" CE1 PHE E 346 "    0.064 2.00e-02 2.50e+03
        pdb=" CE2 PHE E 346 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE E 346 "    0.030 2.00e-02 2.50e+03
        pdb=" HD1 PHE E 346 "   -0.134 2.00e-02 2.50e+03
        pdb=" HD2 PHE E 346 "    0.107 2.00e-02 2.50e+03
        pdb=" HE1 PHE E 346 "    0.083 2.00e-02 2.50e+03
        pdb=" HE2 PHE E 346 "   -0.208 2.00e-02 2.50e+03
        pdb=" HZ  PHE E 346 "   -0.054 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 346 "   -0.101 2.00e-02 2.50e+03   5.35e-02 8.57e+01
        pdb=" CG  PHE B 346 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 346 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 346 "    0.021 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 346 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 346 "    0.028 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 346 "   -0.027 2.00e-02 2.50e+03
        pdb=" HD1 PHE B 346 "    0.107 2.00e-02 2.50e+03
        pdb=" HD2 PHE B 346 "    0.033 2.00e-02 2.50e+03
        pdb=" HE1 PHE B 346 "   -0.007 2.00e-02 2.50e+03
        pdb=" HE2 PHE B 346 "    0.046 2.00e-02 2.50e+03
        pdb=" HZ  PHE B 346 "   -0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS D 330 "   -0.106 2.00e-02 2.50e+03   5.93e-02 7.91e+01
        pdb=" CG  HIS D 330 "    0.069 2.00e-02 2.50e+03
        pdb=" ND1 HIS D 330 "    0.039 2.00e-02 2.50e+03
        pdb=" CD2 HIS D 330 "    0.066 2.00e-02 2.50e+03
        pdb=" CE1 HIS D 330 "    0.021 2.00e-02 2.50e+03
        pdb=" NE2 HIS D 330 "    0.037 2.00e-02 2.50e+03
        pdb=" HD2 HIS D 330 "   -0.003 2.00e-02 2.50e+03
        pdb=" HE1 HIS D 330 "   -0.047 2.00e-02 2.50e+03
        pdb=" HE2 HIS D 330 "   -0.077 2.00e-02 2.50e+03
  ... (remaining 1011 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 517
        2.17 -     2.77: 11836
        2.77 -     3.38: 18315
        3.38 -     3.99: 24527
        3.99 -     4.60: 34690
  Nonbonded interactions: 89885
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 314 "
            pdb=" HG  SER C 316 "
     model   vdw
     1.556 2.450
  nonbonded pdb=" OD1 ASP F 314 "
            pdb=" HG  SER F 316 "
     model   vdw
     1.568 2.450
  nonbonded pdb=" OD1 ASP B 314 "
            pdb=" HG  SER B 316 "
     model   vdw
     1.585 2.450
  nonbonded pdb=" OD1 ASP D 314 "
            pdb=" HG  SER D 316 "
     model   vdw
     1.593 2.450
  nonbonded pdb=" OD1 ASP E 314 "
            pdb=" HG  SER E 316 "
     model   vdw
     1.605 2.450
  ... (remaining 89880 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             4.190
  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:             0.130
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     20.200
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6155
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      :  0.011   0.037   3474  Z= 0.722
  Angle     :  2.027  12.677   4644  Z= 1.311
  Chirality :  0.094   0.282    516
  Planarity :  0.012   0.098    594
  Dihedral  : 13.192  88.128   1344
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  2.78 %
    Allowed  :  4.86 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  :  3.08 %
    Favored  : 94.10 %
  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: -2.56 (0.32), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.24), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.016   0.004   HIS E 362 
 PHE   0.164   0.019   PHE E 346 
 TYR   0.060   0.020   TYR E 310 
 ARG   0.010   0.002   ARG F 349 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8129 (tttt) cc_final: 0.7598 (ttmm)
REVERT: A  331 LYS cc_start: 0.8052 (mttt) cc_final: 0.7781 (mttp)
REVERT: A  338 GLU cc_start: 0.7369 (tt0) cc_final: 0.6876 (mm-30)
REVERT: A  342 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6872 (mp0)
REVERT: A  369 LYS cc_start: 0.7903 (mttt) cc_final: 0.7614 (mmtp)
REVERT: B  321 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7873 (mtpt)
REVERT: B  338 GLU cc_start: 0.7849 (tt0) cc_final: 0.7341 (mp0)
REVERT: B  342 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6638 (mp0)
REVERT: B  348 ASP cc_start: 0.7879 (t0) cc_final: 0.7648 (t0)
REVERT: B  351 GLN cc_start: 0.7893 (mt0) cc_final: 0.7691 (mt0)
REVERT: B  373 THR cc_start: 0.7127 (m) cc_final: 0.6817 (p)
REVERT: B  379 ARG cc_start: 0.6423 (ttt180) cc_final: 0.5833 (ttp-110)
REVERT: C  315 LEU cc_start: 0.8292 (mt) cc_final: 0.8069 (mm)
REVERT: C  321 LYS cc_start: 0.7320 (mtmt) cc_final: 0.7071 (mtpt)
REVERT: C  338 GLU cc_start: 0.7060 (tt0) cc_final: 0.6805 (tt0)
REVERT: C  340 LYS cc_start: 0.7668 (mtmt) cc_final: 0.7024 (tptp)
REVERT: C  345 ASP cc_start: 0.7836 (m-30) cc_final: 0.7597 (m-30)
REVERT: C  349 ARG cc_start: 0.6841 (mtm180) cc_final: 0.6505 (mtp85)
REVERT: C  369 LYS cc_start: 0.7169 (mttt) cc_final: 0.6521 (mtpt)
REVERT: D  315 LEU cc_start: 0.8368 (mt) cc_final: 0.7936 (mm)
REVERT: D  317 LYS cc_start: 0.6758 (mttp) cc_final: 0.6283 (ttmt)
REVERT: D  321 LYS cc_start: 0.7159 (ttmt) cc_final: 0.6203 (tmtt)
REVERT: D  338 GLU cc_start: 0.7010 (tt0) cc_final: 0.6116 (mt-10)
REVERT: D  340 LYS cc_start: 0.6788 (mttt) cc_final: 0.6460 (mtpt)
REVERT: E  311 LYS cc_start: 0.7346 (tttt) cc_final: 0.6449 (tppt)
REVERT: E  317 LYS cc_start: 0.6759 (mttt) cc_final: 0.6460 (ttpt)
REVERT: E  321 LYS cc_start: 0.7212 (mtmt) cc_final: 0.6021 (mmtm)
REVERT: E  327 ASN cc_start: 0.7408 (t0) cc_final: 0.7195 (t0)
REVERT: E  343 LYS cc_start: 0.7732 (mttt) cc_final: 0.6382 (mmpt)
REVERT: E  353 LYS cc_start: 0.7912 (tttt) cc_final: 0.7571 (tttm)
REVERT: E  370 LYS cc_start: 0.7962 (tttt) cc_final: 0.5911 (mttt)
REVERT: F  311 LYS cc_start: 0.7423 (tttt) cc_final: 0.6566 (tppt)
REVERT: F  327 ASN cc_start: 0.7434 (m-40) cc_final: 0.7180 (m-40)
REVERT: F  331 LYS cc_start: 0.7292 (mttt) cc_final: 0.5391 (tmtt)
REVERT: F  338 GLU cc_start: 0.7201 (tt0) cc_final: 0.6440 (mp0)
REVERT: F  343 LYS cc_start: 0.7277 (mptt) cc_final: 0.6524 (mmtm)
REVERT: F  358 ASP cc_start: 0.7483 (m-30) cc_final: 0.7216 (m-30)
  outliers start: 11
  outliers final: 3
  residues processed: 138
  average time/residue: 2.8895
  time to fit residues: 407.8934
Evaluate side-chains
  104 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.598 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  361 THR
Chi-restraints excluded: chain D residue  361 THR
Chi-restraints excluded: chain F residue  361 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.154504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.128791 restraints weight = 11048.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.4031 rms_B_bonded: 2.03
r_work: 0.3940 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3836 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.3626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   3474  Z= 0.237
  Angle     :  0.759   6.927   4644  Z= 0.386
  Chirality :  0.053   0.138    516
  Planarity :  0.003   0.023    594
  Dihedral  :  7.979  24.444    459
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.18 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 11.28 %
    Favored  : 87.18 %
  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: -2.35 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.78 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 362 
 PHE   0.017   0.002   PHE E 346 
 TYR   0.012   0.002   TYR C 310 
 ARG   0.003   0.001   ARG E 349 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 GLU cc_start: 0.8115 (tt0) cc_final: 0.7594 (mp0)
REVERT: A  342 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7353 (mp0)
REVERT: A  351 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7912 (mt0)
REVERT: A  379 ARG cc_start: 0.6003 (ttt180) cc_final: 0.4851 (ttp80)
REVERT: B  338 GLU cc_start: 0.8394 (tt0) cc_final: 0.7863 (mp0)
REVERT: B  342 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6923 (mp0)
REVERT: B  343 LYS cc_start: 0.7912 (mptt) cc_final: 0.7471 (mppt)
REVERT: B  348 ASP cc_start: 0.8005 (t0) cc_final: 0.7623 (t0)
REVERT: B  351 GLN cc_start: 0.8287 (mt0) cc_final: 0.8045 (mt0)
REVERT: B  379 ARG cc_start: 0.6542 (ttt180) cc_final: 0.5593 (ttp-110)
REVERT: C  338 GLU cc_start: 0.8137 (tt0) cc_final: 0.7622 (tm-30)
REVERT: C  340 LYS cc_start: 0.8548 (mtmt) cc_final: 0.7846 (tptp)
REVERT: C  349 ARG cc_start: 0.7538 (mtm180) cc_final: 0.6912 (mtp85)
REVERT: D  317 LYS cc_start: 0.7540 (mttp) cc_final: 0.7073 (ptmt)
REVERT: D  321 LYS cc_start: 0.7864 (ttmt) cc_final: 0.6975 (tmmt)
REVERT: D  340 LYS cc_start: 0.7993 (mttt) cc_final: 0.7723 (mtpt)
REVERT: D  343 LYS cc_start: 0.7999 (mptp) cc_final: 0.7714 (mmtt)
REVERT: D  348 ASP cc_start: 0.8136 (t70) cc_final: 0.7897 (t70)
REVERT: E  311 LYS cc_start: 0.7417 (tttt) cc_final: 0.6528 (tppt)
REVERT: E  317 LYS cc_start: 0.7176 (mttt) cc_final: 0.6970 (ptmt)
REVERT: F  311 LYS cc_start: 0.7691 (tttt) cc_final: 0.6698 (tppt)
REVERT: F  331 LYS cc_start: 0.8697 (mttt) cc_final: 0.7002 (tmtt)
REVERT: F  343 LYS cc_start: 0.7602 (mptt) cc_final: 0.7303 (mmtm)
REVERT: F  348 ASP cc_start: 0.7892 (t0) cc_final: 0.7523 (t0)
  outliers start: 6
  outliers final: 2
  residues processed: 104
  average time/residue: 2.9526
  time to fit residues: 314.2634
Evaluate side-chains
  90 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 SER
Chi-restraints excluded: chain A residue  351 GLN
Chi-restraints excluded: chain B residue  341 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 37 optimal weight:    0.4980
   chunk 28 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0970
   chunk 0 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.5178

-------------------------------------------------------------------------------
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 = 0.4350 r_free = 0.4350 target = 0.157392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.132033 restraints weight = 10807.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.4051 rms_B_bonded: 1.89
r_work: 0.3962 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3860 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.4865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   3474  Z= 0.171
  Angle     :  0.603   4.280   4644  Z= 0.309
  Chirality :  0.052   0.134    516
  Planarity :  0.003   0.025    594
  Dihedral  :  7.015  20.181    456
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 2.30
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  6.71 %
    Favored  : 93.06 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 17.18 %
    Favored  : 81.03 %
  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: -2.32 (0.34), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.76 (0.26), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 362 
 PHE   0.012   0.002   PHE E 346 
 TYR   0.010   0.002   TYR C 310 
 ARG   0.006   0.001   ARG B 349 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7261 (mp0)
REVERT: A  351 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7967 (mt0)
REVERT: A  369 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7549 (mttm)
REVERT: A  379 ARG cc_start: 0.5929 (ttt180) cc_final: 0.3535 (mmp-170)
REVERT: B  342 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7010 (mp0)
REVERT: B  343 LYS cc_start: 0.7992 (mptt) cc_final: 0.7585 (mppt)
REVERT: B  351 GLN cc_start: 0.8176 (mt0) cc_final: 0.7966 (mt0)
REVERT: B  379 ARG cc_start: 0.6314 (ttt180) cc_final: 0.5483 (ttp-110)
REVERT: C  349 ARG cc_start: 0.7642 (mtm180) cc_final: 0.7066 (mtp85)
REVERT: D  317 LYS cc_start: 0.7571 (mttp) cc_final: 0.7108 (ptmt)
REVERT: D  340 LYS cc_start: 0.8055 (mttt) cc_final: 0.7765 (mtpt)
REVERT: D  342 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7126 (mt-10)
REVERT: D  343 LYS cc_start: 0.8070 (mptp) cc_final: 0.7791 (mmtt)
REVERT: E  311 LYS cc_start: 0.7486 (tttt) cc_final: 0.6531 (tppt)
REVERT: F  311 LYS cc_start: 0.7767 (tttt) cc_final: 0.6916 (tppt)
REVERT: F  331 LYS cc_start: 0.8757 (mttt) cc_final: 0.7089 (tmtt)
REVERT: F  348 ASP cc_start: 0.8081 (t0) cc_final: 0.7872 (t0)
  outliers start: 7
  outliers final: 1
  residues processed: 84
  average time/residue: 2.9702
  time to fit residues: 255.4386
Evaluate side-chains
  76 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  351 GLN
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 40 optimal weight:    0.4980
   chunk 24 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
D 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.150783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.124622 restraints weight = 10983.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3949 rms_B_bonded: 1.87
r_work: 0.3858 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3757 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.5587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3474  Z= 0.276
  Angle     :  0.623   4.804   4644  Z= 0.315
  Chirality :  0.051   0.134    516
  Planarity :  0.003   0.027    594
  Dihedral  :  7.064  21.826    456
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.33 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 17.69 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.51 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.91 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 329 
 PHE   0.012   0.002   PHE D 346 
 TYR   0.013   0.003   TYR C 310 
 ARG   0.002   0.000   ARG A 379 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7259 (mp0)
REVERT: A  369 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7934 (mttm)
REVERT: A  379 ARG cc_start: 0.6028 (ttt180) cc_final: 0.3625 (mmp-170)
REVERT: B  311 LYS cc_start: 0.7942 (tttt) cc_final: 0.7197 (tmmt)
REVERT: B  331 LYS cc_start: 0.8926 (mttt) cc_final: 0.8685 (mtpt)
REVERT: B  340 LYS cc_start: 0.8551 (mttt) cc_final: 0.8326 (mttt)
REVERT: B  342 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7087 (mp0)
REVERT: B  343 LYS cc_start: 0.8135 (mptt) cc_final: 0.7702 (mppt)
REVERT: B  351 GLN cc_start: 0.8280 (mt0) cc_final: 0.8058 (mt0)
REVERT: B  379 ARG cc_start: 0.6563 (ttt180) cc_final: 0.5731 (ttp-110)
REVERT: D  317 LYS cc_start: 0.7512 (mttp) cc_final: 0.7022 (ptmt)
REVERT: D  340 LYS cc_start: 0.8047 (mttt) cc_final: 0.7635 (mtpt)
REVERT: D  342 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7265 (tt0)
REVERT: D  343 LYS cc_start: 0.8195 (mptp) cc_final: 0.7891 (mmtt)
REVERT: E  311 LYS cc_start: 0.7568 (tttt) cc_final: 0.6705 (tptt)
REVERT: E  314 ASP cc_start: 0.8142 (t0) cc_final: 0.7910 (t0)
REVERT: F  343 LYS cc_start: 0.7994 (mptt) cc_final: 0.7566 (mppt)
REVERT: F  353 LYS cc_start: 0.8606 (tttm) cc_final: 0.8399 (tttm)
REVERT: F  370 LYS cc_start: 0.8388 (tttt) cc_final: 0.6740 (mttt)
  outliers start: 8
  outliers final: 2
  residues processed: 90
  average time/residue: 3.0554
  time to fit residues: 281.4073
Evaluate side-chains
  76 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  356 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 1 optimal weight:    0.4980
   chunk 26 optimal weight:    0.3980
   chunk 4 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
D 307 GLN
E 351 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.152746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.126754 restraints weight = 10972.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 1.86
r_work: 0.3846 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3746 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.5960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3474  Z= 0.188
  Angle     :  0.562   4.497   4644  Z= 0.286
  Chirality :  0.051   0.139    516
  Planarity :  0.003   0.027    594
  Dihedral  :  6.752  19.669    456
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.64 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 17.69 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.54 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.92 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS A 362 
 PHE   0.007   0.001   PHE E 346 
 TYR   0.008   0.002   TYR C 310 
 ARG   0.001   0.000   ARG E 379 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8513 (mttm)
REVERT: A  342 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7180 (mp0)
REVERT: A  369 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7857 (mttm)
REVERT: A  379 ARG cc_start: 0.6193 (ttt180) cc_final: 0.3744 (mmp-170)
REVERT: B  331 LYS cc_start: 0.8918 (mttt) cc_final: 0.8668 (mtpt)
REVERT: B  340 LYS cc_start: 0.8512 (mttt) cc_final: 0.8264 (mttt)
REVERT: B  342 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7108 (mp0)
REVERT: B  343 LYS cc_start: 0.8109 (mptt) cc_final: 0.7674 (mppt)
REVERT: B  351 GLN cc_start: 0.8276 (mt0) cc_final: 0.8044 (mt0)
REVERT: B  379 ARG cc_start: 0.6572 (ttt180) cc_final: 0.5715 (ttp-110)
REVERT: C  342 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7423 (mt-10)
REVERT: D  317 LYS cc_start: 0.7536 (mttp) cc_final: 0.6992 (ttmt)
REVERT: D  340 LYS cc_start: 0.8088 (mttt) cc_final: 0.7635 (mtpt)
REVERT: D  342 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7248 (mt-10)
REVERT: D  343 LYS cc_start: 0.8120 (mptp) cc_final: 0.7798 (mmtt)
REVERT: E  314 ASP cc_start: 0.8204 (t0) cc_final: 0.7890 (t0)
REVERT: F  311 LYS cc_start: 0.8476 (tttp) cc_final: 0.7388 (tppt)
REVERT: F  343 LYS cc_start: 0.8023 (mptt) cc_final: 0.7631 (mppt)
  outliers start: 8
  outliers final: 2
  residues processed: 74
  average time/residue: 2.9266
  time to fit residues: 221.9988
Evaluate side-chains
  72 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 34 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
D 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.152371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.126019 restraints weight = 11026.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 1.87
r_work: 0.3832 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3731 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.6232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3474  Z= 0.212
  Angle     :  0.554   4.320   4644  Z= 0.283
  Chirality :  0.051   0.136    516
  Planarity :  0.003   0.026    594
  Dihedral  :  6.653  19.507    456
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.33 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 18.46 %
    Favored  : 79.74 %
  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: -2.61 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A 329 
 PHE   0.007   0.002   PHE F 378 
 TYR   0.009   0.002   TYR C 310 
 ARG   0.002   0.000   ARG E 379 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8098 (tttt) cc_final: 0.7770 (ttmm)
REVERT: A  331 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8536 (mttm)
REVERT: A  342 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7180 (mp0)
REVERT: A  369 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7966 (mttm)
REVERT: A  379 ARG cc_start: 0.6122 (ttt180) cc_final: 0.3786 (mmp-170)
REVERT: B  331 LYS cc_start: 0.8928 (mttt) cc_final: 0.8689 (mtpt)
REVERT: B  340 LYS cc_start: 0.8488 (mttt) cc_final: 0.8225 (mttt)
REVERT: B  342 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7092 (mp0)
REVERT: B  343 LYS cc_start: 0.8112 (mptt) cc_final: 0.7701 (mppt)
REVERT: B  351 GLN cc_start: 0.8338 (mt0) cc_final: 0.8083 (mt0)
REVERT: B  379 ARG cc_start: 0.6519 (ttt180) cc_final: 0.5642 (ttp-110)
REVERT: C  342 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7393 (mt-10)
REVERT: D  317 LYS cc_start: 0.7455 (mttp) cc_final: 0.6976 (ttmt)
REVERT: D  340 LYS cc_start: 0.8155 (mttt) cc_final: 0.7657 (mtpt)
REVERT: D  342 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7237 (mt-10)
REVERT: D  343 LYS cc_start: 0.8139 (mptp) cc_final: 0.7766 (mmtt)
REVERT: E  314 ASP cc_start: 0.8229 (t0) cc_final: 0.7960 (t0)
REVERT: F  311 LYS cc_start: 0.8402 (tttp) cc_final: 0.7379 (tppt)
REVERT: F  321 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7702 (mttp)
REVERT: F  343 LYS cc_start: 0.8071 (mptt) cc_final: 0.7641 (mppt)
REVERT: F  370 LYS cc_start: 0.8401 (tttt) cc_final: 0.6750 (mttt)
  outliers start: 7
  outliers final: 2
  residues processed: 84
  average time/residue: 2.7395
  time to fit residues: 235.9714
Evaluate side-chains
  82 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 77
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain F residue  321 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0270
   chunk 33 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 37 optimal weight:    0.4980
   overall best weight:    0.5038

-------------------------------------------------------------------------------
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 = 0.4289 r_free = 0.4289 target = 0.153234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.127524 restraints weight = 10834.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 1.85
r_work: 0.3862 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3763 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.6355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3474  Z= 0.159
  Angle     :  0.518   3.657   4644  Z= 0.266
  Chirality :  0.050   0.137    516
  Planarity :  0.003   0.026    594
  Dihedral  :  6.428  18.651    456
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.41 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 18.97 %
    Favored  : 79.74 %
  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: -2.61 (0.34), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.26), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS F 362 
 PHE   0.006   0.001   PHE E 346 
 TYR   0.007   0.001   TYR C 310 
 ARG   0.001   0.000   ARG D 349 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7145 (mp0)
REVERT: A  369 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7856 (mttm)
REVERT: B  331 LYS cc_start: 0.8899 (mttt) cc_final: 0.8669 (mtpt)
REVERT: B  340 LYS cc_start: 0.8470 (mttt) cc_final: 0.8171 (mttt)
REVERT: B  342 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7098 (mp0)
REVERT: B  343 LYS cc_start: 0.8091 (mptt) cc_final: 0.7689 (mppt)
REVERT: B  351 GLN cc_start: 0.8330 (mt0) cc_final: 0.8067 (mt0)
REVERT: B  379 ARG cc_start: 0.6571 (ttt180) cc_final: 0.5385 (mpp80)
REVERT: C  342 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7406 (mt-10)
REVERT: D  317 LYS cc_start: 0.7472 (mttp) cc_final: 0.6979 (ttmt)
REVERT: D  340 LYS cc_start: 0.8182 (mttt) cc_final: 0.7679 (mtpt)
REVERT: D  342 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7247 (mt-10)
REVERT: D  343 LYS cc_start: 0.8078 (mptp) cc_final: 0.7805 (mmtt)
REVERT: E  314 ASP cc_start: 0.8222 (t0) cc_final: 0.7996 (t0)
REVERT: F  311 LYS cc_start: 0.8348 (tttp) cc_final: 0.7369 (tppt)
REVERT: F  343 LYS cc_start: 0.8040 (mptt) cc_final: 0.7654 (mppt)
  outliers start: 5
  outliers final: 2
  residues processed: 77
  average time/residue: 2.3960
  time to fit residues: 189.9253
Evaluate side-chains
  73 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 70
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 2 optimal weight:    0.4980
   chunk 12 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 20 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
D 307 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.153172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.127268 restraints weight = 10980.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3940 rms_B_bonded: 1.84
r_work: 0.3852 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3751 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.6459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3474  Z= 0.182
  Angle     :  0.524   3.766   4644  Z= 0.268
  Chirality :  0.050   0.136    516
  Planarity :  0.003   0.027    594
  Dihedral  :  6.399  18.607    456
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.10 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 20.00 %
    Favored  : 78.46 %
  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: -2.69 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.04 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 374 
 PHE   0.006   0.001   PHE E 346 
 TYR   0.007   0.002   TYR C 310 
 ARG   0.004   0.000   ARG F 349 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7168 (mp0)
REVERT: A  369 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7956 (mttm)
REVERT: A  379 ARG cc_start: 0.5935 (ttt180) cc_final: 0.3660 (mmp-170)
REVERT: B  331 LYS cc_start: 0.8907 (mttt) cc_final: 0.8679 (mtpt)
REVERT: B  342 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7079 (mp0)
REVERT: B  343 LYS cc_start: 0.8109 (mptt) cc_final: 0.7707 (mppt)
REVERT: B  351 GLN cc_start: 0.8329 (mt0) cc_final: 0.8085 (mt0)
REVERT: B  379 ARG cc_start: 0.6442 (ttt180) cc_final: 0.5330 (mpp80)
REVERT: C  342 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7406 (mt-10)
REVERT: D  317 LYS cc_start: 0.7466 (mttp) cc_final: 0.6988 (ttmt)
REVERT: D  340 LYS cc_start: 0.8172 (mttt) cc_final: 0.7646 (mtpt)
REVERT: D  342 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7255 (mt-10)
REVERT: D  343 LYS cc_start: 0.8086 (mptp) cc_final: 0.7792 (mmtt)
REVERT: E  314 ASP cc_start: 0.8206 (t0) cc_final: 0.7998 (t0)
REVERT: F  311 LYS cc_start: 0.8446 (tttp) cc_final: 0.7461 (tppt)
REVERT: F  343 LYS cc_start: 0.8070 (mptt) cc_final: 0.7686 (mppt)
REVERT: F  370 LYS cc_start: 0.8381 (tttt) cc_final: 0.6742 (mttt)
REVERT: F  379 ARG cc_start: 0.6203 (ttm170) cc_final: 0.5699 (ttp-110)
  outliers start: 6
  outliers final: 3
  residues processed: 76
  average time/residue: 2.6684
  time to fit residues: 209.2854
Evaluate side-chains
  77 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  356 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 30 optimal weight:    0.4980
   chunk 36 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0970
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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 = 0.4288 r_free = 0.4288 target = 0.153538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.127494 restraints weight = 10958.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3942 rms_B_bonded: 1.84
r_work: 0.3854 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3754 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.6557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3474  Z= 0.180
  Angle     :  0.519   3.726   4644  Z= 0.266
  Chirality :  0.050   0.137    516
  Planarity :  0.003   0.028    594
  Dihedral  :  6.354  18.778    456
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.87 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 20.51 %
    Favored  : 78.46 %
  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: -2.72 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.06 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 374 
 PHE   0.005   0.001   PHE E 378 
 TYR   0.007   0.002   TYR C 310 
 ARG   0.004   0.000   ARG F 349 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7159 (mp0)
REVERT: A  369 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8017 (mttm)
REVERT: B  311 LYS cc_start: 0.7762 (tttt) cc_final: 0.7078 (tmmt)
REVERT: B  331 LYS cc_start: 0.8908 (mttt) cc_final: 0.8682 (mtpt)
REVERT: B  342 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7116 (mp0)
REVERT: B  343 LYS cc_start: 0.8132 (mptt) cc_final: 0.7725 (mppt)
REVERT: B  351 GLN cc_start: 0.8334 (mt0) cc_final: 0.8070 (mt0)
REVERT: B  379 ARG cc_start: 0.6441 (ttt180) cc_final: 0.5331 (mpp80)
REVERT: C  342 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7407 (mt-10)
REVERT: D  317 LYS cc_start: 0.7348 (mttp) cc_final: 0.6852 (ttmt)
REVERT: D  340 LYS cc_start: 0.8183 (mttt) cc_final: 0.7653 (mtpt)
REVERT: D  342 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7261 (mt-10)
REVERT: D  343 LYS cc_start: 0.8090 (mptp) cc_final: 0.7788 (mmtt)
REVERT: E  314 ASP cc_start: 0.8209 (t0) cc_final: 0.8007 (t0)
REVERT: F  311 LYS cc_start: 0.8428 (tttp) cc_final: 0.7455 (tppt)
REVERT: F  343 LYS cc_start: 0.8057 (mptt) cc_final: 0.7665 (mppt)
REVERT: F  370 LYS cc_start: 0.8430 (tttt) cc_final: 0.6763 (mttt)
  outliers start: 4
  outliers final: 2
  residues processed: 73
  average time/residue: 2.5129
  time to fit residues: 188.7279
Evaluate side-chains
  74 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  325 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C 368 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.151917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.125591 restraints weight = 11171.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3933 rms_B_bonded: 1.87
r_work: 0.3838 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3737 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.6626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3474  Z= 0.221
  Angle     :  0.541   3.884   4644  Z= 0.276
  Chirality :  0.050   0.136    516
  Planarity :  0.003   0.028    594
  Dihedral  :  6.479  19.467    456
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  8.10 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 20.26 %
    Favored  : 78.21 %
  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: -2.80 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 374 
 PHE   0.006   0.001   PHE F 346 
 TYR   0.009   0.002   TYR C 310 
 ARG   0.005   0.001   ARG F 349 

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8079 (tttt) cc_final: 0.7763 (ttmm)
REVERT: A  331 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8537 (mttm)
REVERT: A  342 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7160 (mp0)
REVERT: A  369 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8054 (mttm)
REVERT: A  379 ARG cc_start: 0.5817 (ttt180) cc_final: 0.3675 (mmp-170)
REVERT: B  311 LYS cc_start: 0.7856 (tttt) cc_final: 0.7148 (tmmt)
REVERT: B  331 LYS cc_start: 0.8934 (mttt) cc_final: 0.8702 (mtpt)
REVERT: B  342 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7157 (mp0)
REVERT: B  343 LYS cc_start: 0.8210 (mptt) cc_final: 0.7793 (mppt)
REVERT: B  351 GLN cc_start: 0.8404 (mt0) cc_final: 0.8140 (mt0)
REVERT: B  379 ARG cc_start: 0.6547 (ttt180) cc_final: 0.5442 (mpp80)
REVERT: C  316 SER cc_start: 0.9049 (p) cc_final: 0.8773 (p)
REVERT: C  342 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7416 (mt-10)
REVERT: D  317 LYS cc_start: 0.7350 (mttp) cc_final: 0.6812 (ttmt)
REVERT: D  340 LYS cc_start: 0.8188 (mttt) cc_final: 0.7656 (mtpt)
REVERT: D  342 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7275 (mt-10)
REVERT: D  343 LYS cc_start: 0.8104 (mptp) cc_final: 0.7782 (mmtt)
REVERT: E  314 ASP cc_start: 0.8222 (t0) cc_final: 0.7987 (t0)
REVERT: F  311 LYS cc_start: 0.8452 (tttp) cc_final: 0.7481 (tppt)
REVERT: F  343 LYS cc_start: 0.8085 (mptt) cc_final: 0.7671 (mppt)
REVERT: F  370 LYS cc_start: 0.8439 (tttt) cc_final: 0.6768 (mttt)
  outliers start: 6
  outliers final: 3
  residues processed: 74
  average time/residue: 2.5192
  time to fit residues: 191.8164
Evaluate side-chains
  78 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  331 LYS
Chi-restraints excluded: chain A residue  356 SER
Chi-restraints excluded: chain A residue  369 LYS
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain B residue  356 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 28 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 12 optimal weight:    0.4980
   chunk 21 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4282 r_free = 0.4282 target = 0.153223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.127064 restraints weight = 10960.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.3945 rms_B_bonded: 1.85
r_work: 0.3853 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3753 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.6679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3474  Z= 0.177
  Angle     :  0.520   3.730   4644  Z= 0.266
  Chirality :  0.050   0.136    516
  Planarity :  0.003   0.027    594
  Dihedral  :  6.329  18.868    456
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.23 %
    Allowed  :  7.87 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 20.51 %
    Favored  : 78.21 %
  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: -2.78 (0.33), residues: 432
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.25), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS C 374 
 PHE   0.006   0.001   PHE E 346 
 TYR   0.006   0.001   TYR C 310 
 ARG   0.005   0.000   ARG F 349 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6944.48 seconds
wall clock time: 118 minutes 12.56 seconds (7092.56 seconds total)