Starting phenix.real_space_refine
on Tue Mar 11 15:43:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y6l_38990/03_2025/8y6l_38990_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y6l_38990/03_2025/8y6l_38990.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y6l_38990/03_2025/8y6l_38990.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y6l_38990/03_2025/8y6l_38990.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y6l_38990/03_2025/8y6l_38990_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y6l_38990/03_2025/8y6l_38990_neut.cif"
  }
  resolution = 3.4
  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=   0.001 sd=   0.032
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      50      5.16       5
     C    4112      2.51       5
     N    1028      2.21       5
     O    1066      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6256
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 409, 3128
          Classifications: {'peptide': 409}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 393}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 3128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 409, 3128
          Classifications: {'peptide': 409}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 393}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
  Time building chain proxies: 4.11, per 1000 atoms: 0.66
  Number of scatterers: 6256
  At special positions: 0
  Unit cell: (71.76, 105.04, 78, 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      50     16.00
     O    1066      8.00
     N    1028      7.00
     C    4112      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 502 " - pdb=" SG  CYS A 512 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 502 " - pdb=" SG  CYS B 512 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.60
  Conformation dependent library (CDL) restraints added in 873.0 milliseconds
  

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1496

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 2 sheets defined
      66.7% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 49
    Processing helix  chain 'A' and resid 60 through 73
    Processing helix  chain 'A' and resid 81 through 85
      removed outlier: 3.711A  pdb=" N   PHE A  85 " --> pdb=" O   MET A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 98
      removed outlier: 3.943A  pdb=" N   LEU A  91 " --> pdb=" O   ASN A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 114
      removed outlier: 3.524A  pdb=" N   PHE A 112 " --> pdb=" O   LEU A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 234
      removed outlier: 4.448A  pdb=" N   VAL A 228 " --> pdb=" O   TYR A 224 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   VAL A 229 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   VAL A 234 " --> pdb=" O   TYR A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 245
    Processing helix  chain 'A' and resid 247 through 260
    Processing helix  chain 'A' and resid 279 through 284
    Processing helix  chain 'A' and resid 285 through 293
      removed outlier: 3.513A  pdb=" N   VAL A 289 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ASN A 293 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 308
      removed outlier: 3.770A  pdb=" N   PHE A 299 " --> pdb=" O   LEU A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 331
      removed outlier: 3.845A  pdb=" N   GLY A 330 " --> pdb=" O   GLY A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 362
    Processing helix  chain 'A' and resid 365 through 369
      removed outlier: 3.783A  pdb=" N   ARG A 369 " --> pdb=" O   ASP A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 387
      removed outlier: 4.181A  pdb=" N   GLY A 379 " --> pdb=" O   GLN A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 414
      removed outlier: 3.630A  pdb=" N   LEU A 407 " --> pdb=" O   ALA A 403 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   LEU A 414 " --> pdb=" O   VAL A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 467
    Processing helix  chain 'A' and resid 479 through 493
    Processing helix  chain 'A' and resid 501 through 505
    Processing helix  chain 'A' and resid 524 through 540
      removed outlier: 3.572A  pdb=" N   LEU A 540 " --> pdb=" O   PHE A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 544
    Processing helix  chain 'B' and resid 26 through 49
    Processing helix  chain 'B' and resid 60 through 73
    Processing helix  chain 'B' and resid 81 through 85
      removed outlier: 3.712A  pdb=" N   PHE B  85 " --> pdb=" O   MET B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 98
      removed outlier: 3.945A  pdb=" N   LEU B  91 " --> pdb=" O   ASN B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 114
      removed outlier: 3.524A  pdb=" N   PHE B 112 " --> pdb=" O   LEU B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 234
      removed outlier: 4.449A  pdb=" N   VAL B 228 " --> pdb=" O   TYR B 224 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   VAL B 229 " --> pdb=" O   THR B 225 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   VAL B 234 " --> pdb=" O   TYR B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 245
    Processing helix  chain 'B' and resid 247 through 260
    Processing helix  chain 'B' and resid 279 through 284
    Processing helix  chain 'B' and resid 285 through 293
      removed outlier: 3.512A  pdb=" N   VAL B 289 " --> pdb=" O   VAL B 285 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ASN B 293 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 308
      removed outlier: 3.771A  pdb=" N   PHE B 299 " --> pdb=" O   LEU B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 331
      removed outlier: 3.845A  pdb=" N   GLY B 330 " --> pdb=" O   GLY B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 336 through 362
    Processing helix  chain 'B' and resid 365 through 369
      removed outlier: 3.783A  pdb=" N   ARG B 369 " --> pdb=" O   ASP B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 387
      removed outlier: 4.181A  pdb=" N   GLY B 379 " --> pdb=" O   GLN B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 401 through 414
      removed outlier: 3.630A  pdb=" N   LEU B 407 " --> pdb=" O   ALA B 403 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   LEU B 414 " --> pdb=" O   VAL B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 467
    Processing helix  chain 'B' and resid 479 through 493
    Processing helix  chain 'B' and resid 501 through 505
    Processing helix  chain 'B' and resid 524 through 540
      removed outlier: 3.571A  pdb=" N   LEU B 540 " --> pdb=" O   PHE B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 541 through 544
    Processing sheet with id=AA1, first strand: chain 'A' and resid 419 through 420
    Processing sheet with id=AA2, first strand: chain 'A' and resid 551 through 552

    362 hydrogen bonds defined for protein.
    1044 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.52

  Time building geometry restraints manager: 1.89 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 930
        1.30 -     1.42: 1696
        1.42 -     1.55: 3680
        1.55 -     1.68: 0
        1.68 -     1.81: 88
  Bond restraints: 6394
  Sorted by residual:
  bond pdb=" C   CYS A 263 "
       pdb=" O   CYS A 263 "
    ideal  model  delta    sigma   weight residual
    1.235  1.168  0.067 1.10e-02 8.26e+03 3.69e+01
  bond pdb=" C   CYS B 263 "
       pdb=" O   CYS B 263 "
    ideal  model  delta    sigma   weight residual
    1.235  1.168  0.067 1.10e-02 8.26e+03 3.69e+01
  bond pdb=" C   SER A  75 "
       pdb=" O   SER A  75 "
    ideal  model  delta    sigma   weight residual
    1.235  1.168  0.067 1.26e-02 6.30e+03 2.87e+01
  bond pdb=" C   SER B  75 "
       pdb=" O   SER B  75 "
    ideal  model  delta    sigma   weight residual
    1.235  1.168  0.067 1.26e-02 6.30e+03 2.87e+01
  bond pdb=" C   SER B  76 "
       pdb=" O   SER B  76 "
    ideal  model  delta    sigma   weight residual
    1.235  1.189  0.047 1.26e-02 6.30e+03 1.38e+01
  ... (remaining 6389 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.55: 8356
        2.55 -     5.09: 278
        5.09 -     7.64: 32
        7.64 -    10.19: 12
       10.19 -    12.74: 2
  Bond angle restraints: 8680
  Sorted by residual:
  angle pdb=" CA  PRO A 422 "
        pdb=" N   PRO A 422 "
        pdb=" CD  PRO A 422 "
      ideal   model   delta    sigma   weight residual
     112.00   99.26   12.74 1.40e+00 5.10e-01 8.27e+01
  angle pdb=" CA  PRO B 422 "
        pdb=" N   PRO B 422 "
        pdb=" CD  PRO B 422 "
      ideal   model   delta    sigma   weight residual
     112.00   99.26   12.74 1.40e+00 5.10e-01 8.27e+01
  angle pdb=" C   CYS B 263 "
        pdb=" N   GLY B 264 "
        pdb=" CA  GLY B 264 "
      ideal   model   delta    sigma   weight residual
     123.08  114.20    8.88 1.35e+00 5.49e-01 4.33e+01
  angle pdb=" C   CYS A 263 "
        pdb=" N   GLY A 264 "
        pdb=" CA  GLY A 264 "
      ideal   model   delta    sigma   weight residual
     123.08  114.22    8.86 1.35e+00 5.49e-01 4.30e+01
  angle pdb=" C   THR B 259 "
        pdb=" CA  THR B 259 "
        pdb=" CB  THR B 259 "
      ideal   model   delta    sigma   weight residual
     110.74  101.57    9.17 1.66e+00 3.63e-01 3.05e+01
  ... (remaining 8675 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.99: 3146
       15.99 -    31.97: 388
       31.97 -    47.96: 154
       47.96 -    63.94: 38
       63.94 -    79.93: 8
  Dihedral angle restraints: 3734
    sinusoidal: 1402
      harmonic: 2332
  Sorted by residual:
  dihedral pdb=" C   PHE B 420 "
           pdb=" N   PHE B 420 "
           pdb=" CA  PHE B 420 "
           pdb=" CB  PHE B 420 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.00  -12.60     0      2.50e+00 1.60e-01 2.54e+01
  dihedral pdb=" C   PHE A 420 "
           pdb=" N   PHE A 420 "
           pdb=" CA  PHE A 420 "
           pdb=" CB  PHE A 420 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.02  -12.58     0      2.50e+00 1.60e-01 2.53e+01
  dihedral pdb=" C   THR A 105 "
           pdb=" N   THR A 105 "
           pdb=" CA  THR A 105 "
           pdb=" CB  THR A 105 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -132.81   10.81     0      2.50e+00 1.60e-01 1.87e+01
  ... (remaining 3731 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 954
       0.084 -    0.168: 64
       0.168 -    0.252: 18
       0.252 -    0.336: 6
       0.336 -    0.420: 4
  Chirality restraints: 1046
  Sorted by residual:
  chirality pdb=" CA  PHE B 420 "
            pdb=" N   PHE B 420 "
            pdb=" C   PHE B 420 "
            pdb=" CB  PHE B 420 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.93   -0.42 2.00e-01 2.50e+01 4.41e+00
  chirality pdb=" CA  PHE A 420 "
            pdb=" N   PHE A 420 "
            pdb=" C   PHE A 420 "
            pdb=" CB  PHE A 420 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.93   -0.42 2.00e-01 2.50e+01 4.38e+00
  chirality pdb=" CA  ASN B 262 "
            pdb=" N   ASN B 262 "
            pdb=" C   ASN B 262 "
            pdb=" CB  ASN B 262 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.00e+00
  ... (remaining 1043 not shown)

  Planarity restraints: 1056
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 416 "    0.025 2.00e-02 2.50e+03   4.84e-02 2.34e+01
        pdb=" C   PRO B 416 "   -0.084 2.00e-02 2.50e+03
        pdb=" O   PRO B 416 "    0.030 2.00e-02 2.50e+03
        pdb=" N   TYR B 417 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 416 "   -0.025 2.00e-02 2.50e+03   4.82e-02 2.33e+01
        pdb=" C   PRO A 416 "    0.083 2.00e-02 2.50e+03
        pdb=" O   PRO A 416 "   -0.030 2.00e-02 2.50e+03
        pdb=" N   TYR A 417 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  56 "   -0.072 5.00e-02 4.00e+02   1.08e-01 1.88e+01
        pdb=" N   PRO B  57 "    0.187 5.00e-02 4.00e+02
        pdb=" CA  PRO B  57 "   -0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO B  57 "   -0.058 5.00e-02 4.00e+02
  ... (remaining 1053 not shown)

  Histogram of nonbonded interaction distances:
        1.40 -     2.10: 2
        2.10 -     2.80: 1831
        2.80 -     3.50: 9202
        3.50 -     4.20: 14318
        4.20 -     4.90: 26322
  Nonbonded interactions: 51675
  Sorted by model distance:
  nonbonded pdb=" CE2 PHE A 342 "
            pdb=" CD  PRO A 422 "
     model   vdw
     1.397 3.740
  nonbonded pdb=" CE2 PHE B 342 "
            pdb=" CD  PRO B 422 "
     model   vdw
     1.398 3.740
  nonbonded pdb=" N   GLN B 375 "
            pdb=" OE1 GLN B 375 "
     model   vdw
     2.119 3.120
  nonbonded pdb=" N   GLN A 375 "
            pdb=" OE1 GLN A 375 "
     model   vdw
     2.119 3.120
  nonbonded pdb=" OG  SER B 247 "
            pdb=" OG1 THR B 250 "
     model   vdw
     2.157 3.040
  ... (remaining 51670 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     17.860
  Find NCS groups from input model:        0.110
  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:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
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      :  0.006   0.067   6394  Z= 0.387
  Angle     :  1.015  12.735   8680  Z= 0.653
  Chirality :  0.059   0.420   1046
  Planarity :  0.007   0.108   1056
  Dihedral  : 17.310  79.927   2232
  Min Nonbonded Distance : 1.397

Molprobity Statistics.
  All-atom Clashscore : 18.84
  Ramachandran Plot:
    Outliers :  1.50 %
    Allowed  :  9.98 %
    Favored  : 88.53 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 20.88 %
    Favored  : 75.59 %
  Cbeta Deviations :  1.07 %
  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: -1.61 (0.29), residues: 802
  helix: -0.42 (0.23), residues: 492
  sheet:  None (None), residues: 0
  loop : -2.06 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 551 
 HIS   0.007   0.001   HIS B 546 
 PHE   0.015   0.002   PHE B 543 
 TYR   0.010   0.001   TYR B 224 
 ARG   0.002   0.000   ARG B 369 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 168
  time to evaluate  : 0.733 
Fit side-chains
REVERT: A   77 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7682 (mmp)
REVERT: A  341 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.6482 (mmm160)
REVERT: A  549 GLN cc_start: 0.7379 (mm110) cc_final: 0.6925 (mp10)
REVERT: B   77 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7652 (mmp)
REVERT: B  341 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.6408 (mmm160)
REVERT: B  549 GLN cc_start: 0.7346 (mm110) cc_final: 0.7032 (mp10)
  outliers start: 24
  outliers final: 14
  residues processed: 184
  average time/residue: 0.1826
  time to fit residues: 43.9091
Evaluate side-chains
  163 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  338 SER
Chi-restraints excluded: chain A residue  341 ARG
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  546 HIS
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  338 SER
Chi-restraints excluded: chain B residue  341 ARG
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  546 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    0.4980
   chunk 60 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 24 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 72 optimal weight:    0.1980
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
A  26 HIS
B  26 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.212033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.190635 restraints weight = 7883.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.4220 rms_B_bonded: 1.90
r_work: 0.4103 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3969 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   6394  Z= 0.238
  Angle     :  0.723   9.284   8680  Z= 0.361
  Chirality :  0.042   0.136   1046
  Planarity :  0.006   0.075   1056
  Dihedral  :  8.684  59.993    904
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  9.60 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 21.62 %
    Favored  : 72.50 %
  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: -0.97 (0.29), residues: 802
  helix:  0.06 (0.22), residues: 506
  sheet:  None (None), residues: 0
  loop : -1.81 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 551 
 HIS   0.003   0.001   HIS B 389 
 PHE   0.014   0.002   PHE A 265 
 TYR   0.020   0.002   TYR A 224 
 ARG   0.005   0.001   ARG B 504 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 166
  time to evaluate  : 0.671 
Fit side-chains
REVERT: A  337 SER cc_start: 0.8061 (OUTLIER) cc_final: 0.7696 (m)
REVERT: A  341 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.6103 (mmm160)
REVERT: A  453 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8153 (mt)
REVERT: A  535 MET cc_start: 0.5429 (ttt) cc_final: 0.5186 (mtp)
REVERT: B   77 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7931 (mmt)
REVERT: B  341 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.6077 (mmm160)
REVERT: B  453 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8166 (mt)
REVERT: B  535 MET cc_start: 0.5452 (ttt) cc_final: 0.5192 (mtp)
  outliers start: 40
  outliers final: 21
  residues processed: 190
  average time/residue: 0.1716
  time to fit residues: 43.1564
Evaluate side-chains
  172 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  341 ARG
Chi-restraints excluded: chain A residue  366 ASP
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  546 HIS
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  224 TYR
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  341 ARG
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  540 LEU
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  546 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 54 optimal weight:    0.3980
   chunk 23 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.211136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.189519 restraints weight = 7930.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.4208 rms_B_bonded: 1.90
r_work: 0.4093 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3961 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6394  Z= 0.232
  Angle     :  0.681   9.122   8680  Z= 0.334
  Chirality :  0.041   0.177   1046
  Planarity :  0.005   0.066   1056
  Dihedral  :  8.128  58.438    898
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.98 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  7.50 %
    Allowed  : 20.44 %
    Favored  : 72.06 %
  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: -0.76 (0.29), residues: 802
  helix:  0.22 (0.22), residues: 504
  sheet:  None (None), residues: 0
  loop : -1.71 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 516 
 HIS   0.003   0.001   HIS B 216 
 PHE   0.014   0.002   PHE A 275 
 TYR   0.019   0.002   TYR A 224 
 ARG   0.002   0.000   ARG A 504 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 158
  time to evaluate  : 0.607 
Fit side-chains
REVERT: A   49 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8059 (mp)
REVERT: A   91 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6499 (mp)
REVERT: A  341 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6243 (mmm160)
REVERT: A  453 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8183 (mt)
REVERT: B   49 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8048 (mp)
REVERT: B   77 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.6556 (mpt)
REVERT: B   91 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6569 (mp)
REVERT: B  341 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6211 (mmm160)
REVERT: B  453 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8183 (mt)
  outliers start: 51
  outliers final: 31
  residues processed: 189
  average time/residue: 0.1652
  time to fit residues: 41.4105
Evaluate side-chains
  181 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 141
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   49 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  265 PHE
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  341 ARG
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  450 MET
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  516 TRP
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  546 HIS
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  224 TYR
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  265 PHE
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  341 ARG
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  509 ASP
Chi-restraints excluded: chain B residue  516 TRP
Chi-restraints excluded: chain B residue  540 LEU
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  546 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 64 optimal weight:    7.9990
   chunk 65 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 2 optimal weight:    4.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4411 r_free = 0.4411 target = 0.211411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.189899 restraints weight = 7986.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.4243 rms_B_bonded: 1.91
r_work: 0.4111 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
moved from start:          0.2334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6394  Z= 0.221
  Angle     :  0.660   8.831   8680  Z= 0.323
  Chirality :  0.040   0.132   1046
  Planarity :  0.005   0.057   1056
  Dihedral  :  7.720  58.281    897
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.35 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  6.18 %
    Allowed  : 22.50 %
    Favored  : 71.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.30), residues: 802
  helix:  0.38 (0.23), residues: 506
  sheet:  None (None), residues: 0
  loop : -1.45 (0.39), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 516 
 HIS   0.003   0.001   HIS A 216 
 PHE   0.014   0.001   PHE B 265 
 TYR   0.019   0.002   TYR B 224 
 ARG   0.002   0.000   ARG A 504 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 160
  time to evaluate  : 0.660 
Fit side-chains
REVERT: A   91 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6502 (mp)
REVERT: A  453 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8088 (mt)
REVERT: B   49 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7978 (mp)
REVERT: B   77 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7618 (mmt)
REVERT: B   91 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6493 (mp)
REVERT: B  453 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8084 (mt)
  outliers start: 42
  outliers final: 25
  residues processed: 185
  average time/residue: 0.1685
  time to fit residues: 41.5657
Evaluate side-chains
  175 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 144
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  265 PHE
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  516 TRP
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  546 HIS
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  224 TYR
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  265 PHE
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  509 ASP
Chi-restraints excluded: chain B residue  516 TRP
Chi-restraints excluded: chain B residue  540 LEU
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  546 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 69 optimal weight:    0.0570
   chunk 8 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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 = 0.4285 r_free = 0.4285 target = 0.204120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.181512 restraints weight = 7926.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.4059 rms_B_bonded: 2.12
r_work: 0.3954 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6394  Z= 0.221
  Angle     :  0.689   9.666   8680  Z= 0.338
  Chirality :  0.040   0.144   1046
  Planarity :  0.005   0.052   1056
  Dihedral  :  7.176  58.244    886
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.23 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  6.47 %
    Allowed  : 22.79 %
    Favored  : 70.74 %
  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: -0.41 (0.31), residues: 802
  helix:  0.42 (0.23), residues: 506
  sheet:  None (None), residues: 0
  loop : -1.41 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 516 
 HIS   0.002   0.001   HIS A 216 
 PHE   0.014   0.001   PHE B 342 
 TYR   0.018   0.002   TYR B 224 
 ARG   0.005   0.000   ARG A 324 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 155
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A   91 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6321 (mp)
REVERT: A  270 GLU cc_start: 0.8200 (mp0) cc_final: 0.7985 (mm-30)
REVERT: A  453 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7970 (mt)
REVERT: A  532 MET cc_start: 0.6551 (mtm) cc_final: 0.6154 (mtm)
REVERT: B   77 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7617 (mmt)
REVERT: B   91 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6447 (mp)
REVERT: B  270 GLU cc_start: 0.8227 (mp0) cc_final: 0.8006 (mm-30)
REVERT: B  453 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7924 (mt)
REVERT: B  532 MET cc_start: 0.6556 (mtm) cc_final: 0.6147 (mtm)
  outliers start: 44
  outliers final: 29
  residues processed: 182
  average time/residue: 0.1866
  time to fit residues: 45.7423
Evaluate side-chains
  184 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 150
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  265 PHE
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  516 TRP
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  546 HIS
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  224 TYR
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  265 PHE
Chi-restraints excluded: chain B residue  359 CYS
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  421 VAL
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  509 ASP
Chi-restraints excluded: chain B residue  516 TRP
Chi-restraints excluded: chain B residue  540 LEU
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  546 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0570
   chunk 24 optimal weight:    0.5980
   chunk 20 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.6298

-------------------------------------------------------------------------------
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 = 0.4270 r_free = 0.4270 target = 0.201712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.177885 restraints weight = 7827.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.4032 rms_B_bonded: 2.21
r_work: 0.3928 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6394  Z= 0.217
  Angle     :  0.692   9.773   8680  Z= 0.340
  Chirality :  0.040   0.147   1046
  Planarity :  0.005   0.052   1056
  Dihedral  :  6.993  57.943    886
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.23 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 23.38 %
    Favored  : 71.03 %
  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: -0.24 (0.31), residues: 802
  helix:  0.53 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -1.29 (0.41), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 516 
 HIS   0.002   0.001   HIS B 389 
 PHE   0.020   0.001   PHE B  37 
 TYR   0.018   0.001   TYR A 224 
 ARG   0.002   0.000   ARG A 324 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 152
  time to evaluate  : 0.631 
Fit side-chains
REVERT: A   91 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6300 (mp)
REVERT: A  270 GLU cc_start: 0.8138 (mp0) cc_final: 0.7857 (mp0)
REVERT: A  411 MET cc_start: 0.6948 (tpp) cc_final: 0.6637 (mpp)
REVERT: A  453 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7888 (mt)
REVERT: B   77 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7551 (mmt)
REVERT: B   91 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6321 (mp)
REVERT: B  270 GLU cc_start: 0.8175 (mp0) cc_final: 0.7895 (mp0)
REVERT: B  453 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7880 (mt)
  outliers start: 38
  outliers final: 29
  residues processed: 176
  average time/residue: 0.1656
  time to fit residues: 39.1555
Evaluate side-chains
  172 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 138
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  265 PHE
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  465 ILE
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  516 TRP
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  546 HIS
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  224 TYR
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  265 PHE
Chi-restraints excluded: chain B residue  359 CYS
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  509 ASP
Chi-restraints excluded: chain B residue  516 TRP
Chi-restraints excluded: chain B residue  540 LEU
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  546 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.4274 r_free = 0.4274 target = 0.202297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.180731 restraints weight = 7876.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.4050 rms_B_bonded: 1.88
r_work: 0.3955 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3831 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.2860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6394  Z= 0.254
  Angle     :  0.712   9.639   8680  Z= 0.349
  Chirality :  0.041   0.153   1046
  Planarity :  0.005   0.047   1056
  Dihedral  :  7.003  58.491    885
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.10 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  6.47 %
    Allowed  : 23.38 %
    Favored  : 70.15 %
  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: -0.28 (0.30), residues: 802
  helix:  0.51 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -1.32 (0.40), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 516 
 HIS   0.004   0.001   HIS A 216 
 PHE   0.022   0.002   PHE A  37 
 TYR   0.017   0.002   TYR A 224 
 ARG   0.001   0.000   ARG B 504 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 146
  time to evaluate  : 0.617 
Fit side-chains
REVERT: A   91 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6482 (mp)
REVERT: A  453 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8110 (mt)
REVERT: B   77 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.6825 (mpt)
REVERT: B   91 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6470 (mp)
REVERT: B  324 ARG cc_start: 0.7913 (pmt-80) cc_final: 0.7592 (pmt-80)
REVERT: B  453 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8086 (mt)
REVERT: B  553 ILE cc_start: 0.8080 (mm) cc_final: 0.7850 (mm)
  outliers start: 44
  outliers final: 31
  residues processed: 172
  average time/residue: 0.1570
  time to fit residues: 36.4232
Evaluate side-chains
  174 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 138
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  265 PHE
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  450 MET
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  516 TRP
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  546 HIS
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  224 TYR
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  265 PHE
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  450 MET
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  509 ASP
Chi-restraints excluded: chain B residue  516 TRP
Chi-restraints excluded: chain B residue  540 LEU
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  546 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 13 optimal weight:    0.3980
   chunk 59 optimal weight:    0.1980
   chunk 20 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 78 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4296 r_free = 0.4296 target = 0.205176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.184060 restraints weight = 7773.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.4086 rms_B_bonded: 1.87
r_work: 0.3994 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3867 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.3065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6394  Z= 0.214
  Angle     :  0.698  10.740   8680  Z= 0.341
  Chirality :  0.040   0.156   1046
  Planarity :  0.005   0.050   1056
  Dihedral  :  6.892  58.882    885
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  9.10 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 22.65 %
    Favored  : 71.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.31), residues: 802
  helix:  0.61 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -1.30 (0.40), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 516 
 HIS   0.002   0.001   HIS A 220 
 PHE   0.023   0.001   PHE B  37 
 TYR   0.017   0.001   TYR A 224 
 ARG   0.002   0.000   ARG B 504 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 151
  time to evaluate  : 0.628 
Fit side-chains
REVERT: A  270 GLU cc_start: 0.8210 (mp0) cc_final: 0.7957 (mm-30)
REVERT: A  324 ARG cc_start: 0.7924 (pmt-80) cc_final: 0.7633 (pmt-80)
REVERT: A  411 MET cc_start: 0.7082 (tpp) cc_final: 0.6841 (mpp)
REVERT: A  453 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8074 (mt)
REVERT: B   77 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.6746 (mpt)
REVERT: B   91 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6447 (mp)
REVERT: B  270 GLU cc_start: 0.8172 (mp0) cc_final: 0.7924 (mm-30)
REVERT: B  324 ARG cc_start: 0.7981 (pmt-80) cc_final: 0.7677 (pmt-80)
REVERT: B  411 MET cc_start: 0.7119 (tpp) cc_final: 0.6841 (mpp)
REVERT: B  453 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8052 (mt)
  outliers start: 41
  outliers final: 29
  residues processed: 177
  average time/residue: 0.1619
  time to fit residues: 38.7072
Evaluate side-chains
  177 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 144
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  265 PHE
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  516 TRP
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  546 HIS
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  224 TYR
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  265 PHE
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  509 ASP
Chi-restraints excluded: chain B residue  516 TRP
Chi-restraints excluded: chain B residue  540 LEU
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  546 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 27 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9990
   chunk 39 optimal weight:    0.1980
   chunk 24 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 79 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.205675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.184274 restraints weight = 7926.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.4084 rms_B_bonded: 1.90
r_work: 0.3989 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3862 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.3117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6394  Z= 0.213
  Angle     :  0.728  15.093   8680  Z= 0.352
  Chirality :  0.040   0.151   1046
  Planarity :  0.005   0.049   1056
  Dihedral  :  6.798  59.066    885
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.48 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 24.12 %
    Favored  : 70.74 %
  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: -0.20 (0.31), residues: 802
  helix:  0.59 (0.23), residues: 506
  sheet:  None (None), residues: 0
  loop : -1.35 (0.40), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 516 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.013   0.001   PHE B 342 
 TYR   0.017   0.001   TYR A 224 
 ARG   0.002   0.000   ARG B 504 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 154
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A   91 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6546 (mp)
REVERT: A  270 GLU cc_start: 0.8157 (mp0) cc_final: 0.7883 (mm-30)
REVERT: A  324 ARG cc_start: 0.7970 (pmt-80) cc_final: 0.7661 (pmt-80)
REVERT: A  411 MET cc_start: 0.7072 (tpp) cc_final: 0.6836 (mpp)
REVERT: A  453 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8072 (mt)
REVERT: B   77 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.6913 (mpt)
REVERT: B  270 GLU cc_start: 0.8182 (mp0) cc_final: 0.7860 (mm-30)
REVERT: B  324 ARG cc_start: 0.8049 (pmt-80) cc_final: 0.7683 (pmt-80)
REVERT: B  411 MET cc_start: 0.7127 (tpp) cc_final: 0.6849 (mpp)
REVERT: B  453 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8029 (mt)
  outliers start: 35
  outliers final: 28
  residues processed: 176
  average time/residue: 0.1611
  time to fit residues: 38.4498
Evaluate side-chains
  181 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 149
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  265 PHE
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  516 TRP
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  546 HIS
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  224 TYR
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  265 PHE
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  509 ASP
Chi-restraints excluded: chain B residue  516 TRP
Chi-restraints excluded: chain B residue  540 LEU
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  546 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 57 optimal weight:    0.6980
   chunk 56 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  87 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.205154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.182162 restraints weight = 7929.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.4060 rms_B_bonded: 2.12
r_work: 0.3953 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6394  Z= 0.232
  Angle     :  0.759  16.798   8680  Z= 0.364
  Chirality :  0.041   0.153   1046
  Planarity :  0.005   0.051   1056
  Dihedral  :  6.760  59.141    885
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 13.74
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.48 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 25.29 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.31), residues: 802
  helix:  0.62 (0.23), residues: 502
  sheet:  None (None), residues: 0
  loop : -1.42 (0.39), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 516 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.013   0.001   PHE B 265 
 TYR   0.017   0.001   TYR A 224 
 ARG   0.001   0.000   ARG B 504 

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

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

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1604 Ramachandran restraints generated.
    802 Oldfield, 0 Emsley, 802 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 151
  time to evaluate  : 0.628 
Fit side-chains
REVERT: A   91 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6601 (mp)
REVERT: A  270 GLU cc_start: 0.8097 (mp0) cc_final: 0.7810 (mm-30)
REVERT: A  324 ARG cc_start: 0.7922 (pmt-80) cc_final: 0.7657 (pmt-80)
REVERT: A  411 MET cc_start: 0.6890 (tpp) cc_final: 0.6642 (mpp)
REVERT: A  453 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8015 (mt)
REVERT: B   49 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7449 (mp)
REVERT: B   77 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.6820 (mpt)
REVERT: B  270 GLU cc_start: 0.8046 (mp0) cc_final: 0.7749 (mm-30)
REVERT: B  324 ARG cc_start: 0.7960 (pmt-80) cc_final: 0.7700 (pmt-80)
REVERT: B  453 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.7980 (mt)
  outliers start: 32
  outliers final: 27
  residues processed: 174
  average time/residue: 0.1519
  time to fit residues: 36.0906
Evaluate side-chains
  179 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 147
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  224 TYR
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  265 PHE
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  497 SER
Chi-restraints excluded: chain A residue  509 ASP
Chi-restraints excluded: chain A residue  516 TRP
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  546 HIS
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   77 MET
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  224 TYR
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  253 ILE
Chi-restraints excluded: chain B residue  265 PHE
Chi-restraints excluded: chain B residue  377 LEU
Chi-restraints excluded: chain B residue  453 LEU
Chi-restraints excluded: chain B residue  509 ASP
Chi-restraints excluded: chain B residue  516 TRP
Chi-restraints excluded: chain B residue  540 LEU
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  546 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0980
   chunk 78 optimal weight:    0.6980
   chunk 40 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   chunk 68 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 67 optimal weight:    0.3980
   chunk 47 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0870
   overall best weight:    0.3958

-------------------------------------------------------------------------------
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 = 0.4322 r_free = 0.4322 target = 0.207541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.184735 restraints weight = 7985.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.4116 rms_B_bonded: 2.12
r_work: 0.4013 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work (final): 0.4013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          0.3355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6394  Z= 0.191
  Angle     :  0.745  15.363   8680  Z= 0.358
  Chirality :  0.041   0.156   1046
  Planarity :  0.005   0.052   1056
  Dihedral  :  6.626  59.881    884
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.10 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 25.15 %
    Favored  : 69.85 %
  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: -0.19 (0.31), residues: 802
  helix:  0.61 (0.23), residues: 504
  sheet:  None (None), residues: 0
  loop : -1.36 (0.40), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 516 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.012   0.001   PHE A 265 
 TYR   0.016   0.001   TYR A 224 
 ARG   0.001   0.000   ARG B 504 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3009.74 seconds
wall clock time: 52 minutes 24.73 seconds (3144.73 seconds total)