Starting phenix.real_space_refine
on Wed Mar  5 14:57:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zir_14738/03_2025/7zir_14738.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zir_14738/03_2025/7zir_14738.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zir_14738/03_2025/7zir_14738.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zir_14738/03_2025/7zir_14738.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zir_14738/03_2025/7zir_14738.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zir_14738/03_2025/7zir_14738.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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: 3
    Type Number    sf(0)   Gaussians
     C    1300      2.51       5
     N     325      2.21       5
     O     495      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 2120
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 414
          Classifications: {'peptide': 51}
          Link IDs: {'TRANS': 50}
    Chain: "C"
      Number of atoms: 11
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 11
          Classifications: {'water': 11}
          Link IDs: {None: 10}
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 8
          Classifications: {'water': 8}
          Link IDs: {None: 7}
    Chain: "E"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 12
          Classifications: {'water': 12}
          Link IDs: {None: 11}
    Chain: "D"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 10
          Classifications: {'water': 10}
          Link IDs: {None: 9}
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 9
          Classifications: {'water': 9}
          Link IDs: {None: 8}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 1.00, per 1000 atoms: 0.47
  Number of scatterers: 2120
  At special positions: 0
  Unit cell: (61.341, 64.897, 45.339, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     495      8.00
     N     325      7.00
     C    1300      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.23
  Conformation dependent library (CDL) restraints added in 264.5 milliseconds
  

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  380

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 27.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 347
      removed outlier: 6.743A  pdb=" N   TRP A 346 " --> pdb=" O   ASN B 347 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   TRP C 346 " --> pdb=" O   ASN D 347 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 353
      removed outlier: 6.597A  pdb=" N   ASN C 352 " --> pdb=" O   TYR B 353 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   ASN E 352 " --> pdb=" O   TYR D 353 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.459A  pdb=" N   TYR A 361 " --> pdb=" O   ASN B 362 " (cutoff:3.500A)
      removed outlier: 8.444A  pdb=" N   ASN D 362 " --> pdb=" O   GLY C 359 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   TYR C 361 " --> pdb=" O   ASN D 362 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 369 through 371
      removed outlier: 6.630A  pdb=" N   ASN A 370 " --> pdb=" O   TYR B 371 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   ASN C 370 " --> pdb=" O   TYR D 371 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 383
      removed outlier: 6.615A  pdb=" N   THR C 380 " --> pdb=" O   GLY B 381 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   ASN B 383 " --> pdb=" O   THR C 380 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   TYR C 382 " --> pdb=" O   ASN B 383 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   THR E 380 " --> pdb=" O   GLY D 381 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   ASN D 383 " --> pdb=" O   THR E 380 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   TYR E 382 " --> pdb=" O   ASN D 383 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 394
      removed outlier: 5.912A  pdb=" N   TYR A 389 " --> pdb=" O   GLY B 390 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   GLY B 392 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
      removed outlier: 9.391A  pdb=" N   GLN A 391 " --> pdb=" O   GLY B 392 " (cutoff:3.500A)
      removed outlier: 7.743A  pdb=" N   ALA B 394 " --> pdb=" O   GLN A 391 " (cutoff:3.500A)
      removed outlier: 9.406A  pdb=" N   TYR A 393 " --> pdb=" O   ALA B 394 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLN B 391 " --> pdb=" O   GLY C 390 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLY C 392 " --> pdb=" O   GLN B 391 " (cutoff:3.500A)
      removed outlier: 7.340A  pdb=" N   TYR B 393 " --> pdb=" O   GLY C 392 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   ALA C 394 " --> pdb=" O   TYR B 393 " (cutoff:3.500A)
      removed outlier: 5.842A  pdb=" N   TYR C 389 " --> pdb=" O   GLY D 390 " (cutoff:3.500A)
      removed outlier: 7.455A  pdb=" N   GLY D 392 " --> pdb=" O   TYR C 389 " (cutoff:3.500A)
      removed outlier: 9.414A  pdb=" N   GLN C 391 " --> pdb=" O   GLY D 392 " (cutoff:3.500A)
      removed outlier: 7.720A  pdb=" N   ALA D 394 " --> pdb=" O   GLN C 391 " (cutoff:3.500A)
      removed outlier: 9.469A  pdb=" N   TYR C 393 " --> pdb=" O   ALA D 394 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY E 392 " --> pdb=" O   GLN D 391 " (cutoff:3.500A)
      removed outlier: 7.271A  pdb=" N   TYR D 393 " --> pdb=" O   GLY E 392 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   ALA E 394 " --> pdb=" O   TYR D 393 " (cutoff:3.500A)

    22 hydrogen bonds defined for protein.
    66 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: 0.45

  Time building geometry restraints manager: 1.32 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 360
        1.29 -     1.35: 315
        1.35 -     1.41: 565
        1.41 -     1.47: 275
        1.47 -     1.54: 635
  Bond restraints: 2150
  Sorted by residual:
  bond pdb=" CA  GLY E 357 "
       pdb=" C   GLY E 357 "
    ideal  model  delta    sigma   weight residual
    1.521  1.516  0.005 1.28e-02 6.10e+03 1.56e-01
  bond pdb=" CA  GLY C 357 "
       pdb=" C   GLY C 357 "
    ideal  model  delta    sigma   weight residual
    1.521  1.516  0.005 1.28e-02 6.10e+03 1.44e-01
  bond pdb=" CA  GLY B 357 "
       pdb=" C   GLY B 357 "
    ideal  model  delta    sigma   weight residual
    1.521  1.516  0.005 1.28e-02 6.10e+03 1.37e-01
  bond pdb=" C   GLY E 357 "
       pdb=" O   GLY E 357 "
    ideal  model  delta    sigma   weight residual
    1.231  1.235 -0.004 1.11e-02 8.12e+03 1.30e-01
  bond pdb=" C   GLY D 357 "
       pdb=" O   GLY D 357 "
    ideal  model  delta    sigma   weight residual
    1.231  1.235 -0.004 1.11e-02 8.12e+03 1.30e-01
  ... (remaining 2145 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.34: 2351
        0.34 -     0.67: 356
        0.67 -     1.01: 160
        1.01 -     1.34: 28
        1.34 -     1.68: 25
  Bond angle restraints: 2920
  Sorted by residual:
  angle pdb=" N   TYR E 384 "
        pdb=" CA  TYR E 384 "
        pdb=" C   TYR E 384 "
      ideal   model   delta    sigma   weight residual
     113.02  111.34    1.68 1.49e+00 4.50e-01 1.27e+00
  angle pdb=" N   TYR D 384 "
        pdb=" CA  TYR D 384 "
        pdb=" C   TYR D 384 "
      ideal   model   delta    sigma   weight residual
     113.02  111.34    1.68 1.49e+00 4.50e-01 1.27e+00
  angle pdb=" N   TYR B 384 "
        pdb=" CA  TYR B 384 "
        pdb=" C   TYR B 384 "
      ideal   model   delta    sigma   weight residual
     113.02  111.39    1.63 1.49e+00 4.50e-01 1.19e+00
  angle pdb=" N   TYR C 384 "
        pdb=" CA  TYR C 384 "
        pdb=" C   TYR C 384 "
      ideal   model   delta    sigma   weight residual
     113.02  111.40    1.62 1.49e+00 4.50e-01 1.19e+00
  angle pdb=" N   TYR A 384 "
        pdb=" CA  TYR A 384 "
        pdb=" C   TYR A 384 "
      ideal   model   delta    sigma   weight residual
     113.02  111.40    1.62 1.49e+00 4.50e-01 1.18e+00
  ... (remaining 2915 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.77: 1045
       15.77 -    31.53: 15
       31.53 -    47.30: 0
       47.30 -    63.06: 0
       63.06 -    78.83: 5
  Dihedral angle restraints: 1065
    sinusoidal: 365
      harmonic: 700
  Sorted by residual:
  dihedral pdb=" CB  GLN C 356 "
           pdb=" CG  GLN C 356 "
           pdb=" CD  GLN C 356 "
           pdb=" OE1 GLN C 356 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -78.83   78.83     2      3.00e+01 1.11e-03 5.13e+00
  dihedral pdb=" CB  GLN E 356 "
           pdb=" CG  GLN E 356 "
           pdb=" CD  GLN E 356 "
           pdb=" OE1 GLN E 356 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -78.82   78.82     2      3.00e+01 1.11e-03 5.13e+00
  dihedral pdb=" CB  GLN A 356 "
           pdb=" CG  GLN A 356 "
           pdb=" CD  GLN A 356 "
           pdb=" OE1 GLN A 356 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -78.78   78.78     2      3.00e+01 1.11e-03 5.13e+00
  ... (remaining 1062 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.013: 59
       0.013 -    0.025: 43
       0.025 -    0.038: 43
       0.038 -    0.050: 20
       0.050 -    0.063: 30
  Chirality restraints: 195
  Sorted by residual:
  chirality pdb=" CA  ALA B 364 "
            pdb=" N   ALA B 364 "
            pdb=" C   ALA B 364 "
            pdb=" CB  ALA B 364 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.55   -0.06 2.00e-01 2.50e+01 9.90e-02
  chirality pdb=" CA  GLN D 356 "
            pdb=" N   GLN D 356 "
            pdb=" C   GLN D 356 "
            pdb=" CB  GLN D 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.45    0.06 2.00e-01 2.50e+01 9.66e-02
  chirality pdb=" CA  ALA A 364 "
            pdb=" N   ALA A 364 "
            pdb=" C   ALA A 364 "
            pdb=" CB  ALA A 364 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.55   -0.06 2.00e-01 2.50e+01 9.61e-02
  ... (remaining 192 not shown)

  Planarity restraints: 415
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 384 "    0.006 2.00e-02 2.50e+03   3.76e-03 2.82e-01
        pdb=" CG  TYR D 384 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 384 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 384 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 384 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 384 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 384 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR D 384 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 384 "    0.005 2.00e-02 2.50e+03   3.61e-03 2.60e-01
        pdb=" CG  TYR C 384 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 384 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 384 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 384 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 384 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 384 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR C 384 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 384 "    0.005 2.00e-02 2.50e+03   3.57e-03 2.54e-01
        pdb=" CG  TYR E 384 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 384 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 384 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 384 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 384 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 384 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR E 384 "    0.001 2.00e-02 2.50e+03
  ... (remaining 412 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 759
        2.83 -     3.35: 1424
        3.35 -     3.87: 3846
        3.87 -     4.38: 4784
        4.38 -     4.90: 7612
  Nonbonded interactions: 18425
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN C 356 "
            pdb=" O   HOH C 501 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" OE1 GLN D 356 "
            pdb=" O   HOH D 501 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" OE1 GLN A 356 "
            pdb=" O   HOH A 501 "
     model   vdw
     2.396 3.040
  nonbonded pdb=" OE1 GLN E 356 "
            pdb=" O   HOH E 501 "
     model   vdw
     2.467 3.040
  nonbonded pdb=" OE1 GLN B 356 "
            pdb=" O   HOH B 501 "
     model   vdw
     2.508 3.040
  ... (remaining 18420 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.360
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     10.450
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8781
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      :  0.002   0.007   2150  Z= 0.099
  Angle     :  0.336   1.678   2920  Z= 0.210
  Chirality :  0.032   0.063    195
  Planarity :  0.001   0.004    415
  Dihedral  :  9.018  78.827    685
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 1.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -3.82 (0.28), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.90 (0.22), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP E 346 
 PHE   0.001   0.000   PHE A 350 
 TYR   0.009   0.001   TYR D 384 

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.225 
Fit side-chains
REVERT: C  368 ASP cc_start: 0.7486 (p0) cc_final: 0.7214 (m-30)
REVERT: D  368 ASP cc_start: 0.7443 (p0) cc_final: 0.7158 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.2642
  time to fit residues: 8.2650
Evaluate side-chains
  24 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 6 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
C 352 ASN
C 386 ASN
D 386 ASN
B 386 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.109327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.070524 restraints weight = 2189.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 1.91
r_work: 0.2784 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2667 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9076
moved from start:          0.1600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.016   2150  Z= 0.267
  Angle     :  0.466   2.616   2920  Z= 0.284
  Chirality :  0.038   0.080    195
  Planarity :  0.002   0.006    415
  Dihedral  :  3.439  12.356    320
  Min Nonbonded Distance : 2.653

Molprobity Statistics.
  All-atom Clashscore : 0.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  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: -4.09 (0.25), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.11 (0.19), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP E 346 
 PHE   0.003   0.001   PHE B 350 
 TYR   0.014   0.002   TYR A 377 

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.224 
Fit side-chains
REVERT: C  368 ASP cc_start: 0.8079 (p0) cc_final: 0.7433 (m-30)
REVERT: D  355 ASP cc_start: 0.8340 (m-30) cc_final: 0.8069 (m-30)
REVERT: D  368 ASP cc_start: 0.8342 (p0) cc_final: 0.7784 (m-30)
REVERT: D  389 TYR cc_start: 0.6904 (m-80) cc_final: 0.6675 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.2739
  time to fit residues: 7.0875
Evaluate side-chains
  23 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0770
   chunk 16 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.9742

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

Flipped N/Q/H residues before XYZ refinement:
B 386 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.109561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.070472 restraints weight = 2202.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 1.94
r_work: 0.2792 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2676 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9078
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.011   2150  Z= 0.187
  Angle     :  0.409   2.208   2920  Z= 0.249
  Chirality :  0.036   0.071    195
  Planarity :  0.001   0.005    415
  Dihedral  :  3.379  11.658    320
  Min Nonbonded Distance : 2.657

Molprobity Statistics.
  All-atom Clashscore : 0.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  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: -3.93 (0.25), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.99 (0.19), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP E 346 
 PHE   0.003   0.001   PHE B 350 
 TYR   0.012   0.001   TYR A 377 

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.221 
Fit side-chains
REVERT: C  368 ASP cc_start: 0.8100 (p0) cc_final: 0.7445 (m-30)
REVERT: D  355 ASP cc_start: 0.8331 (m-30) cc_final: 0.8054 (m-30)
REVERT: D  368 ASP cc_start: 0.8278 (p0) cc_final: 0.7810 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.2833
  time to fit residues: 7.6196
Evaluate side-chains
  24 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    1.7188

-------------------------------------------------------------------------------
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 = 0.3516 r_free = 0.3516 target = 0.107959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.069417 restraints weight = 2171.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.2891 rms_B_bonded: 1.90
r_work: 0.2764 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2647 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9091
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.020   2150  Z= 0.332
  Angle     :  0.490   2.894   2920  Z= 0.297
  Chirality :  0.040   0.081    195
  Planarity :  0.002   0.007    415
  Dihedral  :  3.731  12.987    320
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 0.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.99 (0.25), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.03 (0.19), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 346 
 PHE   0.004   0.001   PHE B 350 
 TYR   0.015   0.002   TYR E 365 

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.235 
Fit side-chains
REVERT: C  368 ASP cc_start: 0.8039 (p0) cc_final: 0.7471 (m-30)
REVERT: D  355 ASP cc_start: 0.8338 (m-30) cc_final: 0.8116 (m-30)
REVERT: D  368 ASP cc_start: 0.8262 (p0) cc_final: 0.7779 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.2641
  time to fit residues: 7.1105
Evaluate side-chains
  24 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 0 optimal weight:    0.5980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 352 ASN
B 386 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.108395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.069780 restraints weight = 2213.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 1.93
r_work: 0.2772 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2656 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9087
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.014   2150  Z= 0.242
  Angle     :  0.439   2.534   2920  Z= 0.267
  Chirality :  0.038   0.073    195
  Planarity :  0.002   0.005    415
  Dihedral  :  3.610  12.457    320
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 0.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  4.44 %
    Favored  : 95.00 %
  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: -3.94 (0.25), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.00 (0.19), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 346 
 PHE   0.004   0.001   PHE B 350 
 TYR   0.012   0.001   TYR A 377 

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.239 
Fit side-chains
REVERT: C  368 ASP cc_start: 0.7978 (p0) cc_final: 0.7392 (m-30)
REVERT: D  355 ASP cc_start: 0.8344 (m-30) cc_final: 0.8112 (m-30)
REVERT: D  368 ASP cc_start: 0.8277 (p0) cc_final: 0.7720 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 23
  average time/residue: 0.3062
  time to fit residues: 7.8492
Evaluate side-chains
  23 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 17 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3529 r_free = 0.3529 target = 0.108506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.070103 restraints weight = 2187.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 1.91
r_work: 0.2781 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2665 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9090
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.012   2150  Z= 0.210
  Angle     :  0.423   2.429   2920  Z= 0.257
  Chirality :  0.037   0.073    195
  Planarity :  0.001   0.005    415
  Dihedral  :  3.568  12.493    320
  Min Nonbonded Distance : 2.652

Molprobity Statistics.
  All-atom Clashscore : 0.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  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: -3.86 (0.26), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.93 (0.20), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 346 
 PHE   0.004   0.001   PHE B 350 
 TYR   0.011   0.001   TYR A 377 

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.183 
Fit side-chains
REVERT: C  368 ASP cc_start: 0.7996 (p0) cc_final: 0.7483 (m-30)
REVERT: A  345 ASN cc_start: 0.7743 (t0) cc_final: 0.7495 (t0)
REVERT: D  355 ASP cc_start: 0.8365 (m-30) cc_final: 0.8143 (m-30)
REVERT: D  368 ASP cc_start: 0.8278 (p0) cc_final: 0.7778 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.2700
  time to fit residues: 7.2945
Evaluate side-chains
  24 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0980
   chunk 12 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
B 386 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.108238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.069746 restraints weight = 2223.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 1.93
r_work: 0.2775 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2659 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9094
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.013   2150  Z= 0.227
  Angle     :  0.433   2.476   2920  Z= 0.263
  Chirality :  0.037   0.073    195
  Planarity :  0.001   0.005    415
  Dihedral  :  3.616  12.473    320
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 0.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  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: -3.86 (0.26), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.94 (0.20), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 346 
 PHE   0.004   0.001   PHE B 350 
 TYR   0.012   0.001   TYR A 377 

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.252 
Fit side-chains
REVERT: C  368 ASP cc_start: 0.8000 (p0) cc_final: 0.7491 (m-30)
REVERT: A  345 ASN cc_start: 0.7800 (t0) cc_final: 0.7538 (t0)
REVERT: D  355 ASP cc_start: 0.8383 (m-30) cc_final: 0.8159 (m-30)
REVERT: D  368 ASP cc_start: 0.8291 (p0) cc_final: 0.7787 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.2808
  time to fit residues: 7.2342
Evaluate side-chains
  23 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 0 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 17 optimal weight:    4.9990
   chunk 7 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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 = 0.3516 r_free = 0.3516 target = 0.107761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.069250 restraints weight = 2265.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 1.94
r_work: 0.2760 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2642 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9102
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.017   2150  Z= 0.289
  Angle     :  0.463   2.747   2920  Z= 0.281
  Chirality :  0.039   0.076    195
  Planarity :  0.002   0.006    415
  Dihedral  :  3.754  12.955    320
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 0.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  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: -3.90 (0.26), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.96 (0.20), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 346 
 PHE   0.004   0.001   PHE B 350 
 TYR   0.013   0.002   TYR A 377 

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.227 
Fit side-chains
REVERT: C  368 ASP cc_start: 0.7990 (p0) cc_final: 0.7471 (m-30)
REVERT: A  345 ASN cc_start: 0.7812 (t0) cc_final: 0.7539 (t0)
REVERT: D  355 ASP cc_start: 0.8388 (m-30) cc_final: 0.8183 (m-30)
REVERT: D  368 ASP cc_start: 0.8294 (p0) cc_final: 0.7760 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.2824
  time to fit residues: 7.2623
Evaluate side-chains
  23 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 14 optimal weight:    0.1980
   chunk 23 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 1 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   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 = 0.3536 r_free = 0.3536 target = 0.108949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.070365 restraints weight = 2243.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 1.94
r_work: 0.2788 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2672 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9084
moved from start:          0.2113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.009   2150  Z= 0.142
  Angle     :  0.390   2.052   2920  Z= 0.237
  Chirality :  0.036   0.069    195
  Planarity :  0.001   0.004    415
  Dihedral  :  3.467  11.993    320
  Min Nonbonded Distance : 2.663

Molprobity Statistics.
  All-atom Clashscore : 0.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  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: -3.81 (0.27), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.89 (0.21), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 346 
 PHE   0.003   0.001   PHE B 350 
 TYR   0.010   0.001   TYR A 377 

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.231 
Fit side-chains
REVERT: C  368 ASP cc_start: 0.8033 (p0) cc_final: 0.7497 (m-30)
REVERT: A  345 ASN cc_start: 0.7768 (t0) cc_final: 0.7521 (t0)
REVERT: D  355 ASP cc_start: 0.8360 (m-30) cc_final: 0.8115 (m-30)
REVERT: D  368 ASP cc_start: 0.8267 (p0) cc_final: 0.7796 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.2879
  time to fit residues: 7.7110
Evaluate side-chains
  24 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
B 386 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.108372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.069804 restraints weight = 2257.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 1.94
r_work: 0.2776 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2660 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9095
moved from start:          0.2126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.013   2150  Z= 0.214
  Angle     :  0.427   2.473   2920  Z= 0.259
  Chirality :  0.037   0.074    195
  Planarity :  0.001   0.005    415
  Dihedral  :  3.603  12.406    320
  Min Nonbonded Distance : 2.656

Molprobity Statistics.
  All-atom Clashscore : 0.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  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: -3.84 (0.27), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.20), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 346 
 PHE   0.004   0.001   PHE B 350 
 TYR   0.012   0.001   TYR A 377 

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

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

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  490 Ramachandran restraints generated.
    245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.232 
Fit side-chains
REVERT: C  368 ASP cc_start: 0.8043 (p0) cc_final: 0.7502 (m-30)
REVERT: A  345 ASN cc_start: 0.7758 (t0) cc_final: 0.7476 (t0)
REVERT: D  355 ASP cc_start: 0.8396 (m-30) cc_final: 0.8175 (m-30)
REVERT: D  368 ASP cc_start: 0.8281 (p0) cc_final: 0.7799 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.2803
  time to fit residues: 7.2082
Evaluate side-chains
  23 residues out of total 180 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 25
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3533 r_free = 0.3533 target = 0.108602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.070166 restraints weight = 2216.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 1.92
r_work: 0.2785 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2669 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9089
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.012   2150  Z= 0.191
  Angle     :  0.412   2.338   2920  Z= 0.250
  Chirality :  0.037   0.072    195
  Planarity :  0.001   0.005    415
  Dihedral  :  3.558  12.318    320
  Min Nonbonded Distance : 2.657

Molprobity Statistics.
  All-atom Clashscore : 0.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  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: -3.82 (0.27), residues: 245
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.90 (0.21), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 346 
 PHE   0.004   0.001   PHE B 350 
 TYR   0.011   0.001   TYR A 377 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1863.22 seconds
wall clock time: 32 minutes 40.65 seconds (1960.65 seconds total)