Starting phenix.real_space_refine
on Mon Apr 28 18:17:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9euy_19989/04_2025/9euy_19989_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9euy_19989/04_2025/9euy_19989.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9euy_19989/04_2025/9euy_19989.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9euy_19989/04_2025/9euy_19989.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9euy_19989/04_2025/9euy_19989_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9euy_19989/04_2025/9euy_19989_neut.cif"
  }
  resolution = 2.95
  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=   0.022
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      38      5.16       5
     C    4942      2.51       5
     N    1400      2.21       5
     O    1466      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7846
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3880
          Classifications: {'peptide': 492}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 463}
    Chain: "B"
      Number of atoms: 3880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3880
          Classifications: {'peptide': 492}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 463}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'LBV': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'LBV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.35, per 1000 atoms: 0.81
  Number of scatterers: 7846
  At special positions: 0
  Unit cell: (85.284, 105.156, 119.232, 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      38     16.00
     O    1466      8.00
     N    1400      7.00
     C    4942      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.16
  Conformation dependent library (CDL) restraints added in 892.7 milliseconds
  

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1824

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 6 sheets defined
      42.4% alpha, 19.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 15
    Processing helix  chain 'A' and resid 44 through 50
    Processing helix  chain 'A' and resid 60 through 78
      Proline residue:  A  66  - end of helix
    Processing helix  chain 'A' and resid 116 through 134
      removed outlier: 3.830A  pdb=" N   ILE A 120 " --> pdb=" O   ASP A 116 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   SER A 122 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 137
      No H-bonds generated for 'chain 'A' and resid 135 through 137'
    Processing helix  chain 'A' and resid 139 through 156
    Processing helix  chain 'A' and resid 191 through 195
    Processing helix  chain 'A' and resid 196 through 206
    Processing helix  chain 'A' and resid 244 through 254
    Processing helix  chain 'A' and resid 285 through 332
    Processing helix  chain 'A' and resid 334 through 340
    Processing helix  chain 'A' and resid 345 through 350
      removed outlier: 3.627A  pdb=" N   LEU A 349 " --> pdb=" O   GLY A 345 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ILE A 350 " --> pdb=" O   ILE A 346 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 345 through 350'
    Processing helix  chain 'A' and resid 370 through 382
    Processing helix  chain 'A' and resid 430 through 437
      removed outlier: 3.934A  pdb=" N   TRP A 437 " --> pdb=" O   HIS A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 468
    Processing helix  chain 'A' and resid 475 through 492
    Processing helix  chain 'B' and resid 11 through 15
    Processing helix  chain 'B' and resid 44 through 50
    Processing helix  chain 'B' and resid 64 through 77
      removed outlier: 4.351A  pdb=" N   VAL B  68 " --> pdb=" O   VAL B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 134
    Processing helix  chain 'B' and resid 135 through 137
      No H-bonds generated for 'chain 'B' and resid 135 through 137'
    Processing helix  chain 'B' and resid 139 through 156
      removed outlier: 3.550A  pdb=" N   ASP B 149 " --> pdb=" O   SER B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 195
    Processing helix  chain 'B' and resid 196 through 206
    Processing helix  chain 'B' and resid 244 through 254
    Processing helix  chain 'B' and resid 285 through 332
      removed outlier: 4.018A  pdb=" N   ARG B 330 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 340
    Processing helix  chain 'B' and resid 345 through 349
    Processing helix  chain 'B' and resid 370 through 382
    Processing helix  chain 'B' and resid 418 through 421
      removed outlier: 4.045A  pdb=" N   SER B 421 " --> pdb=" O   ARG B 418 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 418 through 421'
    Processing helix  chain 'B' and resid 432 through 437
      removed outlier: 4.578A  pdb=" N   TRP B 437 " --> pdb=" O   HIS B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 467
    Processing helix  chain 'B' and resid 475 through 490
    Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 23
      removed outlier: 3.548A  pdb=" N   ALA A  40 " --> pdb=" O   THR A  31 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   LEU A  29 " --> pdb=" O   SER A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 190
      removed outlier: 5.916A  pdb=" N   VAL A 173 " --> pdb=" O   ARG A 164 " (cutoff:3.500A)
      removed outlier: 6.961A  pdb=" N   ARG A 164 " --> pdb=" O   VAL A 173 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ALA A 175 " --> pdb=" O   ALA A 162 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   LEU A 270 " --> pdb=" O   VAL A 266 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   VAL A 266 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 362 through 366
      removed outlier: 6.196A  pdb=" N   GLY A 422 " --> pdb=" O   PHE A 416 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 22 through 23
      removed outlier: 3.561A  pdb=" N   ALA B  40 " --> pdb=" O   THR B  31 " (cutoff:3.500A)
      removed outlier: 6.640A  pdb=" N   LEU B  29 " --> pdb=" O   SER B  42 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 190
      removed outlier: 5.719A  pdb=" N   VAL B 173 " --> pdb=" O   ARG B 164 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   ARG B 164 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ALA B 175 " --> pdb=" O   ALA B 162 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   LEU B 270 " --> pdb=" O   VAL B 266 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   VAL B 266 " --> pdb=" O   LEU B 270 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 362 through 366
      removed outlier: 7.162A  pdb=" N   ILE B 424 " --> pdb=" O   ARG B 415 " (cutoff:3.500A)
      removed outlier: 5.592A  pdb=" N   ARG B 415 " --> pdb=" O   ILE B 424 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   TRP B 426 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   ALA B 413 " --> pdb=" O   TRP B 426 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   ARG B 428 " --> pdb=" O   VAL B 411 " (cutoff:3.500A)
      removed outlier: 5.768A  pdb=" N   VAL B 411 " --> pdb=" O   ARG B 428 " (cutoff:3.500A)

    423 hydrogen bonds defined for protein.
    1185 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: 2.30

  Time building geometry restraints manager: 2.52 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1410
        1.32 -     1.44: 2081
        1.44 -     1.57: 4475
        1.57 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 8028
  Sorted by residual:
  bond pdb=" CB  MET B 154 "
       pdb=" CG  MET B 154 "
    ideal  model  delta    sigma   weight residual
    1.520  1.485  0.035 3.00e-02 1.11e+03 1.33e+00
  bond pdb=" CB  MET A 154 "
       pdb=" CG  MET A 154 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.26e+00
  bond pdb=" CB  ILE B 447 "
       pdb=" CG2 ILE B 447 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.20e+00
  bond pdb=" CG1 ILE A 294 "
       pdb=" CD1 ILE A 294 "
    ideal  model  delta    sigma   weight residual
    1.513  1.472  0.041 3.90e-02 6.57e+02 1.11e+00
  bond pdb=" CG1 ILE B 294 "
       pdb=" CD1 ILE B 294 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 9.93e-01
  ... (remaining 8023 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.62: 10415
        1.62 -     3.24: 430
        3.24 -     4.86: 54
        4.86 -     6.49: 9
        6.49 -     8.11: 4
  Bond angle restraints: 10912
  Sorted by residual:
  angle pdb=" CD  ARG A 453 "
        pdb=" NE  ARG A 453 "
        pdb=" CZ  ARG A 453 "
      ideal   model   delta    sigma   weight residual
     124.40  129.06   -4.66 1.40e+00 5.10e-01 1.11e+01
  angle pdb=" CB  ARG B 453 "
        pdb=" CG  ARG B 453 "
        pdb=" CD  ARG B 453 "
      ideal   model   delta    sigma   weight residual
     111.30  118.61   -7.31 2.30e+00 1.89e-01 1.01e+01
  angle pdb=" N   PRO B 452 "
        pdb=" CA  PRO B 452 "
        pdb=" C   PRO B 452 "
      ideal   model   delta    sigma   weight residual
     113.86  117.57   -3.71 1.25e+00 6.40e-01 8.83e+00
  angle pdb=" CG  ARG A 453 "
        pdb=" CD  ARG A 453 "
        pdb=" NE  ARG A 453 "
      ideal   model   delta    sigma   weight residual
     112.00  118.12   -6.12 2.20e+00 2.07e-01 7.75e+00
  angle pdb=" CB  MET A 154 "
        pdb=" CG  MET A 154 "
        pdb=" SD  MET A 154 "
      ideal   model   delta    sigma   weight residual
     112.70  104.59    8.11 3.00e+00 1.11e-01 7.30e+00
  ... (remaining 10907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.15: 4513
       17.15 -    34.31: 239
       34.31 -    51.46: 51
       51.46 -    68.61: 14
       68.61 -    85.76: 9
  Dihedral angle restraints: 4826
    sinusoidal: 1994
      harmonic: 2832
  Sorted by residual:
  dihedral pdb=" CG  ARG A 453 "
           pdb=" CD  ARG A 453 "
           pdb=" NE  ARG A 453 "
           pdb=" CZ  ARG A 453 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00    5.38   84.62     2      1.50e+01 4.44e-03 2.11e+01
  dihedral pdb=" CA  ASP B  96 "
           pdb=" CB  ASP B  96 "
           pdb=" CG  ASP B  96 "
           pdb=" OD1 ASP B  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.23   53.23     1      2.00e+01 2.50e-03 9.63e+00
  dihedral pdb=" CG  ARG A 201 "
           pdb=" CD  ARG A 201 "
           pdb=" NE  ARG A 201 "
           pdb=" CZ  ARG A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -132.08   42.08     2      1.50e+01 4.44e-03 9.58e+00
  ... (remaining 4823 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 785
       0.038 -    0.075: 257
       0.075 -    0.113: 93
       0.113 -    0.150: 48
       0.150 -    0.188: 5
  Chirality restraints: 1188
  Sorted by residual:
  chirality pdb=" CA  PRO B 452 "
            pdb=" N   PRO B 452 "
            pdb=" C   PRO B 452 "
            pdb=" CB  PRO B 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.53    0.19 2.00e-01 2.50e+01 8.84e-01
  chirality pdb=" CA  PRO A 452 "
            pdb=" N   PRO A 452 "
            pdb=" C   PRO A 452 "
            pdb=" CB  PRO A 452 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.17 2.00e-01 2.50e+01 7.59e-01
  chirality pdb=" CA  ILE A 264 "
            pdb=" N   ILE A 264 "
            pdb=" C   ILE A 264 "
            pdb=" CB  ILE A 264 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.93e-01
  ... (remaining 1185 not shown)

  Planarity restraints: 1434
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 152 "    0.236 9.50e-02 1.11e+02   1.06e-01 8.43e+00
        pdb=" NE  ARG B 152 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 152 "    0.019 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 152 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 152 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 434 "    0.212 9.50e-02 1.11e+02   9.57e-02 7.46e+00
        pdb=" NE  ARG B 434 "   -0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 434 "    0.022 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 434 "   -0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 434 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 152 "   -0.211 9.50e-02 1.11e+02   9.49e-02 6.69e+00
        pdb=" NE  ARG A 152 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 152 "   -0.017 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 152 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 152 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1431 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2280
        2.83 -     3.35: 7229
        3.35 -     3.86: 12967
        3.86 -     4.38: 15202
        4.38 -     4.90: 26273
  Nonbonded interactions: 63951
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 178 "
            pdb=" O   LEU A 182 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" NH1 ARG B 178 "
            pdb=" O   LEU B 182 "
     model   vdw
     2.339 3.120
  nonbonded pdb=" NH1 ARG A 322 "
            pdb=" OD2 ASP A 488 "
     model   vdw
     2.369 3.120
  nonbonded pdb=" OG  SER A 399 "
            pdb=" OD1 ASP A 401 "
     model   vdw
     2.406 3.040
  nonbonded pdb=" OD1 ASP B 234 "
            pdb=" OG  SER B 236 "
     model   vdw
     2.411 3.040
  ... (remaining 63946 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: 0.04
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:             4.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.830
  Find NCS groups from input model:        0.260
  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:             0.010
  Load rotamer database and sin/cos tables:12.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8028  Z= 0.153
  Angle     :  0.735   8.108  10912  Z= 0.419
  Chirality :  0.048   0.188   1188
  Planarity :  0.010   0.106   1434
  Dihedral  : 11.993  85.765   3002
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  2.03 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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 (0.26), residues: 980
  helix:  0.76 (0.26), residues: 352
  sheet:  0.42 (0.40), residues: 166
  loop : -0.03 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP A  82 
 HIS   0.008   0.002   HIS A 167 
 PHE   0.020   0.003   PHE A 274 
 TYR   0.017   0.004   TYR B 163 
 ARG   0.024   0.003   ARG B 434 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14118 (  423)
  hydrogen bonds       : angle       7.11464 ( 1185)
  covalent geometry    : bond        0.00337 ( 8028)
  covalent geometry    : angle       0.73505 (10912)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 178
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 ASP cc_start: 0.7286 (t70) cc_final: 0.6880 (p0)
REVERT: A  394 ASN cc_start: 0.8018 (t0) cc_final: 0.7629 (t160)
REVERT: A  395 TRP cc_start: 0.7284 (t-100) cc_final: 0.7046 (t60)
REVERT: A  470 HIS cc_start: 0.7316 (m90) cc_final: 0.6840 (m90)
REVERT: B  228 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7259 (mm-30)
REVERT: B  314 LEU cc_start: 0.7674 (mt) cc_final: 0.7435 (mp)
REVERT: B  353 ASP cc_start: 0.7189 (m-30) cc_final: 0.6969 (m-30)
REVERT: B  430 GLU cc_start: 0.3794 (tt0) cc_final: 0.3572 (tt0)
  outliers start: 2
  outliers final: 1
  residues processed: 180
  average time/residue: 1.3039
  time to fit residues: 247.3118
Evaluate side-chains
  112 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    9.9990
   chunk 74 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 57 optimal weight:    0.6980
   chunk 88 optimal weight:    7.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  61 GLN
A  79 ASN
A 137 HIS
** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 433 HIS
B 137 HIS
B 278 HIS
B 391 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.189883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.135393 restraints weight = 9255.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 2.27
r_work: 0.3442 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3311 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8028  Z= 0.147
  Angle     :  0.574   7.940  10912  Z= 0.305
  Chirality :  0.045   0.172   1188
  Planarity :  0.004   0.039   1434
  Dihedral  :  6.964  86.649   1142
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  :  9.55 %
    Favored  : 87.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.44 (0.27), residues: 980
  helix:  1.79 (0.27), residues: 360
  sheet:  0.59 (0.41), residues: 162
  loop :  0.55 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 423 
 HIS   0.005   0.001   HIS B 391 
 PHE   0.013   0.002   PHE B 295 
 TYR   0.010   0.001   TYR B 163 
 ARG   0.004   0.001   ARG B  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04046 (  423)
  hydrogen bonds       : angle       5.49854 ( 1185)
  covalent geometry    : bond        0.00338 ( 8028)
  covalent geometry    : angle       0.57362 (10912)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.969 
Fit side-chains
REVERT: A  394 ASN cc_start: 0.8036 (t0) cc_final: 0.7647 (t160)
REVERT: A  395 TRP cc_start: 0.7238 (t-100) cc_final: 0.6808 (t60)
REVERT: A  440 LYS cc_start: 0.7684 (mttt) cc_final: 0.7415 (mtpt)
REVERT: A  465 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7162 (tt0)
REVERT: A  470 HIS cc_start: 0.7453 (m90) cc_final: 0.6960 (m170)
REVERT: B   43 GLU cc_start: 0.8105 (tt0) cc_final: 0.7717 (tp30)
REVERT: B   48 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7217 (tt)
REVERT: B  220 ARG cc_start: 0.7712 (mtm180) cc_final: 0.7156 (mmt180)
REVERT: B  228 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7367 (mm-30)
REVERT: B  353 ASP cc_start: 0.7032 (m-30) cc_final: 0.6610 (m-30)
REVERT: B  430 GLU cc_start: 0.3897 (tt0) cc_final: 0.3627 (tt0)
  outliers start: 28
  outliers final: 13
  residues processed: 141
  average time/residue: 1.2434
  time to fit residues: 185.7737
Evaluate side-chains
  115 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  392 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 5 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9980
   chunk 91 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 78 optimal weight:    0.4980
   chunk 22 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 16 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:
A  79 ASN
A 206 ASN
** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 391 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.189900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.134892 restraints weight = 9334.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 2.31
r_work: 0.3438 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8028  Z= 0.142
  Angle     :  0.525   5.329  10912  Z= 0.279
  Chirality :  0.044   0.172   1188
  Planarity :  0.004   0.043   1434
  Dihedral  :  6.821  89.827   1142
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 11.46 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.58 (0.27), residues: 980
  helix:  2.12 (0.26), residues: 360
  sheet:  0.60 (0.42), residues: 162
  loop :  0.45 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 423 
 HIS   0.008   0.001   HIS B 391 
 PHE   0.012   0.002   PHE B 295 
 TYR   0.009   0.002   TYR B 163 
 ARG   0.003   0.000   ARG B  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03737 (  423)
  hydrogen bonds       : angle       5.25560 ( 1185)
  covalent geometry    : bond        0.00336 ( 8028)
  covalent geometry    : angle       0.52549 (10912)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 109
  time to evaluate  : 0.877 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7712 (mp)
REVERT: A  219 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.5944 (mmt)
REVERT: A  231 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6877 (mm-30)
REVERT: A  395 TRP cc_start: 0.7236 (t-100) cc_final: 0.6733 (t60)
REVERT: A  440 LYS cc_start: 0.7695 (mttt) cc_final: 0.7398 (mtpt)
REVERT: A  465 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7155 (tt0)
REVERT: B   43 GLU cc_start: 0.8130 (tt0) cc_final: 0.7748 (tp30)
REVERT: B   48 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7214 (tt)
REVERT: B  135 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8153 (mp10)
REVERT: B  220 ARG cc_start: 0.7697 (mtm180) cc_final: 0.7112 (mmt180)
REVERT: B  228 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7422 (mm-30)
REVERT: B  353 ASP cc_start: 0.6949 (m-30) cc_final: 0.6524 (m-30)
REVERT: B  430 GLU cc_start: 0.3953 (tt0) cc_final: 0.3682 (tt0)
  outliers start: 32
  outliers final: 15
  residues processed: 131
  average time/residue: 1.1255
  time to fit residues: 156.9772
Evaluate side-chains
  119 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  246 ILE
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  135 GLN
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  391 HIS
Chi-restraints excluded: chain B residue  392 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 82 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 34 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0980
   chunk 33 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 206 ASN
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.190072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.141440 restraints weight = 9265.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3649 rms_B_bonded: 2.19
r_work: 0.3445 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8028  Z= 0.135
  Angle     :  0.529  10.642  10912  Z= 0.273
  Chirality :  0.044   0.167   1188
  Planarity :  0.004   0.038   1434
  Dihedral  :  6.710  86.200   1142
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 13.84 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.62 (0.27), residues: 980
  helix:  2.26 (0.26), residues: 360
  sheet:  0.55 (0.42), residues: 162
  loop :  0.40 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 426 
 HIS   0.008   0.001   HIS B 391 
 PHE   0.011   0.002   PHE B 295 
 TYR   0.009   0.001   TYR B 286 
 ARG   0.003   0.000   ARG A 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03602 (  423)
  hydrogen bonds       : angle       5.13120 ( 1185)
  covalent geometry    : bond        0.00318 ( 8028)
  covalent geometry    : angle       0.52859 (10912)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 104
  time to evaluate  : 0.937 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7648 (mp)
REVERT: A  395 TRP cc_start: 0.7128 (t-100) cc_final: 0.6571 (t60)
REVERT: A  440 LYS cc_start: 0.7732 (mttt) cc_final: 0.7443 (mtpt)
REVERT: A  465 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7180 (tt0)
REVERT: B   43 GLU cc_start: 0.8083 (tt0) cc_final: 0.7712 (tp30)
REVERT: B   88 THR cc_start: 0.8750 (t) cc_final: 0.8429 (p)
REVERT: B  135 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8211 (mp10)
REVERT: B  220 ARG cc_start: 0.7700 (mtm180) cc_final: 0.7140 (mmt180)
REVERT: B  228 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7424 (mm-30)
REVERT: B  353 ASP cc_start: 0.7097 (m-30) cc_final: 0.6662 (m-30)
REVERT: B  430 GLU cc_start: 0.4000 (tt0) cc_final: 0.3703 (tt0)
  outliers start: 31
  outliers final: 13
  residues processed: 123
  average time/residue: 1.1113
  time to fit residues: 145.5210
Evaluate side-chains
  118 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  135 GLN
Chi-restraints excluded: chain B residue  186 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 52 optimal weight:    1.9990
   chunk 90 optimal weight:    9.9990
   chunk 1 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 59 optimal weight:    0.1980
   chunk 18 optimal weight:    0.8980
   chunk 96 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 226 ASN
B 188 GLN
B 391 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.191179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.134396 restraints weight = 9100.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3601 rms_B_bonded: 2.28
r_work: 0.3471 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3337 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8028  Z= 0.128
  Angle     :  0.532  16.993  10912  Z= 0.270
  Chirality :  0.043   0.166   1188
  Planarity :  0.004   0.036   1434
  Dihedral  :  6.592  80.310   1142
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 14.68 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.67 (0.27), residues: 980
  helix:  2.34 (0.26), residues: 360
  sheet:  0.54 (0.43), residues: 162
  loop :  0.42 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 426 
 HIS   0.005   0.001   HIS B 391 
 PHE   0.010   0.001   PHE B 295 
 TYR   0.010   0.001   TYR A  58 
 ARG   0.004   0.000   ARG A 113 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03487 (  423)
  hydrogen bonds       : angle       5.05799 ( 1185)
  covalent geometry    : bond        0.00302 ( 8028)
  covalent geometry    : angle       0.53153 (10912)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 101
  time to evaluate  : 0.929 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7669 (mp)
REVERT: A   73 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7144 (tm-30)
REVERT: A  219 MET cc_start: 0.6683 (OUTLIER) cc_final: 0.5963 (mmt)
REVERT: A  395 TRP cc_start: 0.7122 (t-100) cc_final: 0.6525 (t60)
REVERT: A  465 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7351 (tt0)
REVERT: B   43 GLU cc_start: 0.8127 (tt0) cc_final: 0.7746 (tp30)
REVERT: B   88 THR cc_start: 0.8696 (t) cc_final: 0.8425 (p)
REVERT: B  135 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8261 (mp10)
REVERT: B  220 ARG cc_start: 0.7738 (mtm180) cc_final: 0.7242 (mmt180)
REVERT: B  353 ASP cc_start: 0.7253 (m-30) cc_final: 0.6832 (m-30)
  outliers start: 34
  outliers final: 13
  residues processed: 124
  average time/residue: 1.1245
  time to fit residues: 148.5703
Evaluate side-chains
  112 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  492 LEU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  135 GLN
Chi-restraints excluded: chain B residue  186 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 76 optimal weight:    0.5980
   chunk 73 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 51 optimal weight:    0.5980
   chunk 84 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0980
   chunk 82 optimal weight:    5.9990
   chunk 91 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
B 188 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.191734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.135327 restraints weight = 9170.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.3609 rms_B_bonded: 2.30
r_work: 0.3477 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8028  Z= 0.121
  Angle     :  0.537  13.933  10912  Z= 0.272
  Chirality :  0.043   0.175   1188
  Planarity :  0.004   0.034   1434
  Dihedral  :  6.503  75.084   1142
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 16.23 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.69 (0.27), residues: 980
  helix:  2.39 (0.27), residues: 360
  sheet:  0.54 (0.43), residues: 162
  loop :  0.40 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 426 
 HIS   0.008   0.001   HIS A  93 
 PHE   0.009   0.001   PHE B 295 
 TYR   0.010   0.001   TYR B 286 
 ARG   0.006   0.000   ARG A  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03473 (  423)
  hydrogen bonds       : angle       4.97497 ( 1185)
  covalent geometry    : bond        0.00283 ( 8028)
  covalent geometry    : angle       0.53679 (10912)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 98
  time to evaluate  : 0.880 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7628 (mp)
REVERT: A   46 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7593 (tp40)
REVERT: A   73 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7073 (tm-30)
REVERT: A  219 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.5957 (mmt)
REVERT: A  395 TRP cc_start: 0.7069 (t-100) cc_final: 0.6494 (t60)
REVERT: A  465 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7350 (tt0)
REVERT: B   43 GLU cc_start: 0.8108 (tt0) cc_final: 0.7733 (tp30)
REVERT: B   88 THR cc_start: 0.8659 (t) cc_final: 0.8388 (p)
REVERT: B  135 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8260 (mp10)
REVERT: B  220 ARG cc_start: 0.7673 (mtm180) cc_final: 0.7250 (mmt180)
REVERT: B  353 ASP cc_start: 0.7315 (m-30) cc_final: 0.6878 (m-30)
  outliers start: 28
  outliers final: 13
  residues processed: 119
  average time/residue: 1.0445
  time to fit residues: 132.9332
Evaluate side-chains
  114 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 96
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   62 GLU
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  135 GLN
Chi-restraints excluded: chain B residue  186 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 66 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 75 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0870
   chunk 34 optimal weight:    5.9990
   chunk 59 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 86 optimal weight:    0.5980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
A 277 HIS
B 188 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.192669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.134021 restraints weight = 9154.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 2.36
r_work: 0.3498 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3366 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8028  Z= 0.120
  Angle     :  0.509  10.459  10912  Z= 0.262
  Chirality :  0.043   0.185   1188
  Planarity :  0.004   0.033   1434
  Dihedral  :  6.438  70.159   1142
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 16.23 %
    Favored  : 80.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.71 (0.28), residues: 980
  helix:  2.46 (0.27), residues: 360
  sheet:  0.50 (0.44), residues: 162
  loop :  0.38 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 426 
 HIS   0.006   0.001   HIS A  93 
 PHE   0.009   0.001   PHE B 295 
 TYR   0.010   0.001   TYR B 286 
 ARG   0.005   0.000   ARG B 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03417 (  423)
  hydrogen bonds       : angle       4.91847 ( 1185)
  covalent geometry    : bond        0.00281 ( 8028)
  covalent geometry    : angle       0.50873 (10912)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 98
  time to evaluate  : 1.144 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7662 (mp)
REVERT: A   46 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7630 (tp40)
REVERT: A   73 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7102 (tm-30)
REVERT: A  219 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.5926 (mmt)
REVERT: A  395 TRP cc_start: 0.7015 (t-100) cc_final: 0.6552 (t60)
REVERT: A  465 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7349 (tt0)
REVERT: B   43 GLU cc_start: 0.8057 (tt0) cc_final: 0.7770 (tp30)
REVERT: B   88 THR cc_start: 0.8631 (t) cc_final: 0.8390 (p)
REVERT: B  135 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8273 (mp10)
REVERT: B  220 ARG cc_start: 0.7717 (mtm180) cc_final: 0.7312 (mmt180)
REVERT: B  353 ASP cc_start: 0.7338 (m-30) cc_final: 0.6932 (m-30)
REVERT: B  358 MET cc_start: 0.6845 (ttt) cc_final: 0.6610 (tmm)
REVERT: B  443 LYS cc_start: 0.7253 (mmtm) cc_final: 0.6785 (mptt)
REVERT: B  485 LEU cc_start: 0.8366 (tt) cc_final: 0.8144 (tt)
  outliers start: 30
  outliers final: 13
  residues processed: 119
  average time/residue: 1.1116
  time to fit residues: 141.4909
Evaluate side-chains
  113 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   43 GLU
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  393 ASP
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  135 GLN
Chi-restraints excluded: chain B residue  186 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 79 optimal weight:    0.6980
   chunk 96 optimal weight:    0.0980
   chunk 4 optimal weight:    0.9980
   chunk 68 optimal weight:    0.3980
   chunk 59 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 72 optimal weight:    0.0170
   chunk 93 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.3618

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

Flipped N/Q/H residues before XYZ refinement:
A 226 ASN
B 188 GLN
B 391 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.193607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.136335 restraints weight = 9226.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 2.40
r_work: 0.3483 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3346 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.3300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   8028  Z= 0.103
  Angle     :  0.511  12.543  10912  Z= 0.262
  Chirality :  0.043   0.196   1188
  Planarity :  0.003   0.031   1434
  Dihedral  :  6.349  63.844   1142
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 17.66 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.74 (0.27), residues: 980
  helix:  2.52 (0.26), residues: 362
  sheet:  0.55 (0.44), residues: 162
  loop :  0.34 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 426 
 HIS   0.010   0.001   HIS B 391 
 PHE   0.008   0.001   PHE B 274 
 TYR   0.010   0.001   TYR B 286 
 ARG   0.003   0.000   ARG A  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03276 (  423)
  hydrogen bonds       : angle       4.80065 ( 1185)
  covalent geometry    : bond        0.00238 ( 8028)
  covalent geometry    : angle       0.51089 (10912)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.868 
Fit side-chains
REVERT: A   43 GLU cc_start: 0.7881 (pt0) cc_final: 0.7633 (pt0)
REVERT: A   46 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7582 (tp40)
REVERT: A   73 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7058 (tm-30)
REVERT: A  219 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.5960 (mmt)
REVERT: A  395 TRP cc_start: 0.6939 (t-100) cc_final: 0.6424 (t60)
REVERT: A  465 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7432 (tt0)
REVERT: B   43 GLU cc_start: 0.8058 (tt0) cc_final: 0.7707 (tp30)
REVERT: B   88 THR cc_start: 0.8606 (t) cc_final: 0.8364 (p)
REVERT: B  101 SER cc_start: 0.8948 (OUTLIER) cc_final: 0.8686 (m)
REVERT: B  220 ARG cc_start: 0.7622 (mtm180) cc_final: 0.7191 (mmt180)
REVERT: B  318 SER cc_start: 0.8435 (OUTLIER) cc_final: 0.8225 (m)
REVERT: B  353 ASP cc_start: 0.7378 (m-30) cc_final: 0.6957 (m-30)
REVERT: B  443 LYS cc_start: 0.7274 (mmtm) cc_final: 0.6863 (mptt)
REVERT: B  485 LEU cc_start: 0.8349 (tt) cc_final: 0.8140 (tt)
  outliers start: 21
  outliers final: 12
  residues processed: 114
  average time/residue: 1.1276
  time to fit residues: 137.2317
Evaluate side-chains
  107 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  154 MET
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  318 SER
Chi-restraints excluded: chain B residue  391 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 74 optimal weight:    0.0770
   chunk 69 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 59 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 78 optimal weight:    0.6980
   chunk 28 optimal weight:    0.4980
   chunk 86 optimal weight:    0.9980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
** B  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 GLN
B 308 GLN
** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.192732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.135638 restraints weight = 9298.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 2.38
r_work: 0.3471 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3335 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.3350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8028  Z= 0.123
  Angle     :  0.533  15.027  10912  Z= 0.270
  Chirality :  0.043   0.205   1188
  Planarity :  0.004   0.052   1434
  Dihedral  :  6.280  61.846   1140
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.62 %
    Favored  : 79.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.72 (0.27), residues: 980
  helix:  2.42 (0.26), residues: 362
  sheet:  0.66 (0.42), residues: 172
  loop :  0.36 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 423 
 HIS   0.015   0.001   HIS B 391 
 PHE   0.009   0.001   PHE B 295 
 TYR   0.026   0.002   TYR A 190 
 ARG   0.013   0.000   ARG A  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03406 (  423)
  hydrogen bonds       : angle       4.83331 ( 1185)
  covalent geometry    : bond        0.00290 ( 8028)
  covalent geometry    : angle       0.53265 (10912)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.947 
Fit side-chains
REVERT: A   43 GLU cc_start: 0.7878 (pt0) cc_final: 0.7631 (pt0)
REVERT: A   46 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7575 (tp40)
REVERT: A   73 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7054 (tm-30)
REVERT: A  219 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.5952 (mmt)
REVERT: A  395 TRP cc_start: 0.6956 (t-100) cc_final: 0.6447 (t60)
REVERT: A  465 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7424 (tt0)
REVERT: B   43 GLU cc_start: 0.8074 (tt0) cc_final: 0.7690 (tp30)
REVERT: B   88 THR cc_start: 0.8625 (t) cc_final: 0.8379 (p)
REVERT: B  220 ARG cc_start: 0.7613 (mtm180) cc_final: 0.7146 (mmt180)
REVERT: B  318 SER cc_start: 0.8445 (t) cc_final: 0.8244 (m)
REVERT: B  443 LYS cc_start: 0.7177 (mmtm) cc_final: 0.6721 (mptt)
REVERT: B  485 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8130 (tt)
  outliers start: 20
  outliers final: 11
  residues processed: 107
  average time/residue: 1.1579
  time to fit residues: 131.9121
Evaluate side-chains
  108 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  485 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0970
   chunk 64 optimal weight:    0.0060
   chunk 60 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 68 optimal weight:    0.3980
   chunk 52 optimal weight:    0.2980
   chunk 22 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.3394

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

Flipped N/Q/H residues before XYZ refinement:
** B  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 GLN
B 391 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.193732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.142640 restraints weight = 9165.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 2.38
r_work: 0.3488 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.3460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   8028  Z= 0.104
  Angle     :  0.529  16.793  10912  Z= 0.267
  Chirality :  0.043   0.213   1188
  Planarity :  0.003   0.030   1434
  Dihedral  :  6.254  58.237   1140
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 18.62 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.80 (0.27), residues: 980
  helix:  2.49 (0.26), residues: 362
  sheet:  0.70 (0.42), residues: 172
  loop :  0.39 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 423 
 HIS   0.009   0.001   HIS B 391 
 PHE   0.008   0.001   PHE B 274 
 TYR   0.024   0.001   TYR A 190 
 ARG   0.006   0.000   ARG B 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03260 (  423)
  hydrogen bonds       : angle       4.75793 ( 1185)
  covalent geometry    : bond        0.00238 ( 8028)
  covalent geometry    : angle       0.52870 (10912)

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

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

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1960 Ramachandran restraints generated.
    980 Oldfield, 0 Emsley, 980 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.934 
Fit side-chains
REVERT: A    9 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7539 (mp)
REVERT: A   43 GLU cc_start: 0.7836 (pt0) cc_final: 0.7596 (pt0)
REVERT: A   46 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7559 (tp40)
REVERT: A   70 ARG cc_start: 0.8364 (ttp-110) cc_final: 0.8044 (mtm-85)
REVERT: A   73 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7067 (tm-30)
REVERT: A  111 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8052 (mt-10)
REVERT: A  219 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6013 (mmt)
REVERT: A  395 TRP cc_start: 0.6958 (t-100) cc_final: 0.6422 (t60)
REVERT: A  465 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7449 (tt0)
REVERT: B   43 GLU cc_start: 0.8075 (tt0) cc_final: 0.7688 (tp30)
REVERT: B   88 THR cc_start: 0.8603 (t) cc_final: 0.8361 (p)
REVERT: B  101 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8713 (m)
REVERT: B  220 ARG cc_start: 0.7591 (mtm180) cc_final: 0.7152 (mmt180)
REVERT: B  443 LYS cc_start: 0.7175 (mmtm) cc_final: 0.6784 (mptt)
REVERT: B  485 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8176 (tt)
  outliers start: 21
  outliers final: 11
  residues processed: 109
  average time/residue: 1.1383
  time to fit residues: 132.4108
Evaluate side-chains
  108 residues out of total 838 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   46 GLN
Chi-restraints excluded: chain A residue  219 MET
Chi-restraints excluded: chain A residue  230 ASN
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   54 SER
Chi-restraints excluded: chain B residue   67 GLU
Chi-restraints excluded: chain B residue  101 SER
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  391 HIS
Chi-restraints excluded: chain B residue  485 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 96 optimal weight:    0.8980
   chunk 19 optimal weight:    0.3980
   chunk 60 optimal weight:    3.9990
   chunk 63 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9980
   chunk 90 optimal weight:    6.9990
   chunk 21 optimal weight:    0.0970
   chunk 13 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** B  18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 GLN
B 391 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.192974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.142763 restraints weight = 9159.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 2.18
r_work: 0.3491 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3359 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.3466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8028  Z= 0.122
  Angle     :  0.533  16.706  10912  Z= 0.269
  Chirality :  0.043   0.212   1188
  Planarity :  0.004   0.032   1434
  Dihedral  :  6.272  57.315   1140
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 18.97 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.75 (0.27), residues: 980
  helix:  2.44 (0.26), residues: 362
  sheet:  0.69 (0.42), residues: 172
  loop :  0.37 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 423 
 HIS   0.009   0.001   HIS B 391 
 PHE   0.009   0.001   PHE B 295 
 TYR   0.030   0.002   TYR A 190 
 ARG   0.007   0.000   ARG B 321 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03392 (  423)
  hydrogen bonds       : angle       4.79366 ( 1185)
  covalent geometry    : bond        0.00287 ( 8028)
  covalent geometry    : angle       0.53289 (10912)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7171.16 seconds
wall clock time: 122 minutes 20.41 seconds (7340.41 seconds total)