Starting phenix.real_space_refine
on Wed Mar 12 04:00:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xja_33223/03_2025/7xja_33223.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xja_33223/03_2025/7xja_33223.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xja_33223/03_2025/7xja_33223.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xja_33223/03_2025/7xja_33223.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xja_33223/03_2025/7xja_33223.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xja_33223/03_2025/7xja_33223.cif"
  }
  resolution = 3.5
  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=   0.003
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      44      5.16       5
     C    4808      2.51       5
     N    1184      2.21       5
     O    1240      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7276
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3638
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 22, 'TRANS': 449}
    Chain: "B"
      Number of atoms: 3638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 472, 3638
          Classifications: {'peptide': 472}
          Link IDs: {'PTRANS': 22, 'TRANS': 449}
  Time building chain proxies: 5.25, per 1000 atoms: 0.72
  Number of scatterers: 7276
  At special positions: 0
  Unit cell: (80.413, 113.573, 79.584, 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      44     16.00
     O    1240      8.00
     N    1184      7.00
     C    4808      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: 1.87
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1744

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 3 sheets defined
      81.5% alpha, 1.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 89 through 126
    Processing helix  chain 'A' and resid 129 through 156
      Proline residue:  A 141  - end of helix
    Processing helix  chain 'A' and resid 157 through 160
    Processing helix  chain 'A' and resid 163 through 172
    Processing helix  chain 'A' and resid 176 through 180
    Processing helix  chain 'A' and resid 181 through 198
    Processing helix  chain 'A' and resid 204 through 225
    Processing helix  chain 'A' and resid 226 through 231
      removed outlier: 6.910A  pdb=" N   ILE A 229 " --> pdb=" O   PHE A 226 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   TYR A 230 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 253
      removed outlier: 3.609A  pdb=" N   PHE A 252 " --> pdb=" O   VAL A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 267
      removed outlier: 3.614A  pdb=" N   SER A 267 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 296
    Processing helix  chain 'A' and resid 317 through 319
      No H-bonds generated for 'chain 'A' and resid 317 through 319'
    Processing helix  chain 'A' and resid 320 through 352
      removed outlier: 3.514A  pdb=" N   GLN A 352 " --> pdb=" O   VAL A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 362
    Processing helix  chain 'A' and resid 364 through 378
      removed outlier: 3.556A  pdb=" N   ALA A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 386
      removed outlier: 3.726A  pdb=" N   GLN A 385 " --> pdb=" O   GLY A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 401
    Processing helix  chain 'A' and resid 419 through 425
    Processing helix  chain 'A' and resid 430 through 450
      removed outlier: 4.142A  pdb=" N   TRP A 444 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 481
    Processing helix  chain 'A' and resid 495 through 513
      removed outlier: 3.872A  pdb=" N   TYR A 499 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 526
      removed outlier: 4.425A  pdb=" N   VAL A 519 " --> pdb=" O   VAL A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 549
    Processing helix  chain 'A' and resid 551 through 560
    Processing helix  chain 'B' and resid 90 through 126
      removed outlier: 3.514A  pdb=" N   LEU B 126 " --> pdb=" O   MET B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 156
      Proline residue:  B 141  - end of helix
    Processing helix  chain 'B' and resid 157 through 160
    Processing helix  chain 'B' and resid 163 through 173
    Processing helix  chain 'B' and resid 176 through 180
    Processing helix  chain 'B' and resid 181 through 198
    Processing helix  chain 'B' and resid 204 through 225
      removed outlier: 3.854A  pdb=" N   LEU B 225 " --> pdb=" O   LYS B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 231
      removed outlier: 7.085A  pdb=" N   ILE B 229 " --> pdb=" O   PHE B 226 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   TYR B 230 " --> pdb=" O   GLY B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 253
      removed outlier: 3.647A  pdb=" N   PHE B 252 " --> pdb=" O   VAL B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 267
      removed outlier: 3.716A  pdb=" N   VAL B 259 " --> pdb=" O   PRO B 255 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER B 267 " --> pdb=" O   ILE B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 296
    Processing helix  chain 'B' and resid 317 through 319
      No H-bonds generated for 'chain 'B' and resid 317 through 319'
    Processing helix  chain 'B' and resid 320 through 352
    Processing helix  chain 'B' and resid 352 through 363
    Processing helix  chain 'B' and resid 364 through 378
      removed outlier: 3.574A  pdb=" N   ALA B 368 " --> pdb=" O   LEU B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 386
      removed outlier: 3.674A  pdb=" N   GLN B 385 " --> pdb=" O   GLY B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 401
    Processing helix  chain 'B' and resid 405 through 409
    Processing helix  chain 'B' and resid 419 through 425
    Processing helix  chain 'B' and resid 430 through 450
      removed outlier: 4.073A  pdb=" N   TRP B 444 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 481
    Processing helix  chain 'B' and resid 495 through 513
      removed outlier: 3.866A  pdb=" N   TYR B 499 " --> pdb=" O   VAL B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 516 through 526
    Processing helix  chain 'B' and resid 530 through 549
    Processing helix  chain 'B' and resid 551 through 560
    Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271
    Processing sheet with id=AA2, first strand: chain 'A' and resid 485 through 487
    Processing sheet with id=AA3, first strand: chain 'B' and resid 485 through 487

    569 hydrogen bonds defined for protein.
    1635 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: 2.12

  Time building geometry restraints manager: 2.20 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2238
        1.35 -     1.46: 1850
        1.46 -     1.58: 3298
        1.58 -     1.70: 0
        1.70 -     1.82: 74
  Bond restraints: 7460
  Sorted by residual:
  bond pdb=" CA  VAL A 175 "
       pdb=" CB  VAL A 175 "
    ideal  model  delta    sigma   weight residual
    1.530  1.541 -0.011 1.11e-02 8.12e+03 9.56e-01
  bond pdb=" N   PRO B 453 "
       pdb=" CA  PRO B 453 "
    ideal  model  delta    sigma   weight residual
    1.469  1.481 -0.012 1.28e-02 6.10e+03 9.45e-01
  bond pdb=" N   PRO A 453 "
       pdb=" CA  PRO A 453 "
    ideal  model  delta    sigma   weight residual
    1.469  1.481 -0.012 1.28e-02 6.10e+03 9.26e-01
  bond pdb=" CA  VAL B 175 "
       pdb=" CB  VAL B 175 "
    ideal  model  delta    sigma   weight residual
    1.530  1.540 -0.011 1.11e-02 8.12e+03 8.99e-01
  bond pdb=" CB  PRO A 381 "
       pdb=" CG  PRO A 381 "
    ideal  model  delta    sigma   weight residual
    1.492  1.447  0.045 5.00e-02 4.00e+02 8.13e-01
  ... (remaining 7455 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 9958
        1.74 -     3.49: 167
        3.49 -     5.23: 24
        5.23 -     6.97: 7
        6.97 -     8.72: 4
  Bond angle restraints: 10160
  Sorted by residual:
  angle pdb=" CB  MET B 167 "
        pdb=" CG  MET B 167 "
        pdb=" SD  MET B 167 "
      ideal   model   delta    sigma   weight residual
     112.70  103.98    8.72 3.00e+00 1.11e-01 8.44e+00
  angle pdb=" CB  MET A 167 "
        pdb=" CG  MET A 167 "
        pdb=" SD  MET A 167 "
      ideal   model   delta    sigma   weight residual
     112.70  104.08    8.62 3.00e+00 1.11e-01 8.26e+00
  angle pdb=" C   TYR B 230 "
        pdb=" N   GLU B 231 "
        pdb=" CA  GLU B 231 "
      ideal   model   delta    sigma   weight residual
     121.94  116.23    5.71 2.00e+00 2.50e-01 8.16e+00
  angle pdb=" CB  MET A 460 "
        pdb=" CG  MET A 460 "
        pdb=" SD  MET A 460 "
      ideal   model   delta    sigma   weight residual
     112.70  120.99   -8.29 3.00e+00 1.11e-01 7.63e+00
  angle pdb=" CB  MET B 360 "
        pdb=" CG  MET B 360 "
        pdb=" SD  MET B 360 "
      ideal   model   delta    sigma   weight residual
     112.70  120.21   -7.51 3.00e+00 1.11e-01 6.26e+00
  ... (remaining 10155 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.10: 3975
       16.10 -    32.21: 260
       32.21 -    48.31: 70
       48.31 -    64.41: 17
       64.41 -    80.52: 20
  Dihedral angle restraints: 4342
    sinusoidal: 1636
      harmonic: 2706
  Sorted by residual:
  dihedral pdb=" CG  ARG A 558 "
           pdb=" CD  ARG A 558 "
           pdb=" NE  ARG A 558 "
           pdb=" CZ  ARG A 558 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -138.50  -41.50     2      1.50e+01 4.44e-03 9.37e+00
  dihedral pdb=" CG  ARG B 558 "
           pdb=" CD  ARG B 558 "
           pdb=" NE  ARG B 558 "
           pdb=" CZ  ARG B 558 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -138.57  -41.43     2      1.50e+01 4.44e-03 9.34e+00
  dihedral pdb=" CG  ARG A 350 "
           pdb=" CD  ARG A 350 "
           pdb=" NE  ARG A 350 "
           pdb=" CZ  ARG A 350 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -138.90  -41.10     2      1.50e+01 4.44e-03 9.22e+00
  ... (remaining 4339 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 734
       0.029 -    0.057: 286
       0.057 -    0.086: 125
       0.086 -    0.114: 44
       0.114 -    0.143: 11
  Chirality restraints: 1200
  Sorted by residual:
  chirality pdb=" CA  GLU B 231 "
            pdb=" N   GLU B 231 "
            pdb=" C   GLU B 231 "
            pdb=" CB  GLU B 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.10e-01
  chirality pdb=" CA  PHE B 284 "
            pdb=" N   PHE B 284 "
            pdb=" C   PHE B 284 "
            pdb=" CB  PHE B 284 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.52e-01
  chirality pdb=" CA  VAL B 454 "
            pdb=" N   VAL B 454 "
            pdb=" C   VAL B 454 "
            pdb=" CB  VAL B 454 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.19e-01
  ... (remaining 1197 not shown)

  Planarity restraints: 1256
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 444 "   -0.019 2.00e-02 2.50e+03   1.45e-02 5.28e+00
        pdb=" CG  TRP A 444 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 444 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 444 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 444 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 444 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 444 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 444 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 444 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 444 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 444 "    0.012 2.00e-02 2.50e+03   1.25e-02 3.89e+00
        pdb=" CG  TRP B 444 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 444 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 444 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 444 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 444 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 444 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 444 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 444 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 444 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 379 "   -0.026 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO B 380 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 380 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 380 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1253 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 271
        2.73 -     3.27: 7852
        3.27 -     3.81: 12578
        3.81 -     4.36: 13994
        4.36 -     4.90: 24526
  Nonbonded interactions: 59221
  Sorted by model distance:
  nonbonded pdb=" O   GLU B 166 "
            pdb=" OG1 THR B 169 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OE2 GLU A 320 "
            pdb=" OH  TYR A 499 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" OE2 GLU B 320 "
            pdb=" OH  TYR B 499 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   GLU A 166 "
            pdb=" OG1 THR A 169 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   ASP A 402 "
            pdb=" NH1 ARG A 471 "
     model   vdw
     2.284 3.120
  ... (remaining 59216 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.840
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.340
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
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   0.045   7460  Z= 0.170
  Angle     :  0.596   8.715  10160  Z= 0.332
  Chirality :  0.039   0.143   1200
  Planarity :  0.004   0.040   1256
  Dihedral  : 13.731  80.517   2598
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.28), residues: 940
  helix:  1.78 (0.20), residues: 692
  sheet:  None (None), residues: 0
  loop : -0.40 (0.41), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 444 
 HIS   0.012   0.002   HIS B 210 
 PHE   0.021   0.001   PHE B 147 
 TYR   0.016   0.001   TYR A 140 
 ARG   0.011   0.001   ARG B 277 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 279
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 LEU cc_start: 0.7116 (tt) cc_final: 0.6626 (pt)
REVERT: A  170 ILE cc_start: 0.9021 (mm) cc_final: 0.8773 (mm)
REVERT: A  288 ILE cc_start: 0.7953 (mm) cc_final: 0.7742 (mt)
REVERT: A  309 ARG cc_start: 0.6199 (ttp-170) cc_final: 0.5062 (mmt-90)
REVERT: A  374 ILE cc_start: 0.7585 (tt) cc_final: 0.7118 (mt)
REVERT: A  433 LEU cc_start: 0.7917 (tp) cc_final: 0.7463 (mt)
REVERT: A  515 VAL cc_start: 0.8225 (t) cc_final: 0.7969 (t)
REVERT: B  153 GLN cc_start: 0.7612 (tp40) cc_final: 0.7344 (tm-30)
REVERT: B  309 ARG cc_start: 0.5313 (mtm180) cc_final: 0.4758 (mmt-90)
REVERT: B  320 GLU cc_start: 0.6376 (mt-10) cc_final: 0.5887 (mt-10)
REVERT: B  433 LEU cc_start: 0.8048 (tp) cc_final: 0.7664 (mt)
REVERT: B  477 MET cc_start: 0.7560 (ttm) cc_final: 0.7334 (ttt)
REVERT: B  540 LEU cc_start: 0.8499 (mt) cc_final: 0.8255 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 279
  average time/residue: 0.1986
  time to fit residues: 72.9995
Evaluate side-chains
  179 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    0.0270
   chunk 71 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 44 optimal weight:    0.3980
   chunk 54 optimal weight:    2.9990
   chunk 85 optimal weight:    0.4980
   overall best weight:    0.7040

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

Flipped N/Q/H residues before XYZ refinement:
** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 425 ASN
A 542 ASN
A 546 GLN
B 542 ASN
B 546 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.185406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.155246 restraints weight = 9804.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.158689 restraints weight = 6446.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.161132 restraints weight = 4921.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7460  Z= 0.213
  Angle     :  0.582   8.146  10160  Z= 0.301
  Chirality :  0.042   0.192   1200
  Planarity :  0.005   0.040   1256
  Dihedral  :  3.563  14.796   1002
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 10.18 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.43 (0.28), residues: 940
  helix:  2.22 (0.19), residues: 700
  sheet:  None (None), residues: 0
  loop : -0.19 (0.46), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 444 
 HIS   0.005   0.002   HIS A 513 
 PHE   0.019   0.002   PHE A 185 
 TYR   0.013   0.002   TYR B 340 
 ARG   0.004   0.001   ARG B 277 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 191
  time to evaluate  : 0.773 
Fit side-chains
REVERT: A  131 LEU cc_start: 0.7600 (tt) cc_final: 0.7135 (pt)
REVERT: A  309 ARG cc_start: 0.6541 (ttp-170) cc_final: 0.5386 (mmt-90)
REVERT: A  408 ARG cc_start: 0.4721 (mmp-170) cc_final: 0.4131 (tpp-160)
REVERT: B  108 MET cc_start: 0.7612 (mtt) cc_final: 0.7297 (mtp)
REVERT: B  170 ILE cc_start: 0.9055 (mm) cc_final: 0.8852 (mm)
REVERT: B  222 PHE cc_start: 0.6955 (t80) cc_final: 0.5064 (m-80)
REVERT: B  309 ARG cc_start: 0.5511 (mtm180) cc_final: 0.4949 (mmt-90)
REVERT: B  408 ARG cc_start: 0.3911 (mmm160) cc_final: 0.3473 (tpp-160)
REVERT: B  433 LEU cc_start: 0.8069 (tp) cc_final: 0.7834 (mt)
REVERT: B  483 ASP cc_start: 0.6489 (t70) cc_final: 0.6239 (t0)
  outliers start: 21
  outliers final: 14
  residues processed: 203
  average time/residue: 0.1874
  time to fit residues: 52.1055
Evaluate side-chains
  177 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 163
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  542 ASN
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  178 GLU
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  516 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN
** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 542 ASN
B 425 ASN
B 542 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.167795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.137323 restraints weight = 9930.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.140765 restraints weight = 6411.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.142968 restraints weight = 4910.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.4550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7460  Z= 0.319
  Angle     :  0.658   8.628  10160  Z= 0.347
  Chirality :  0.045   0.184   1200
  Planarity :  0.005   0.048   1256
  Dihedral  :  3.646  13.498   1002
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 12.53 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.28), residues: 940
  helix:  2.17 (0.19), residues: 704
  sheet:  None (None), residues: 0
  loop : -0.55 (0.44), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 444 
 HIS   0.006   0.002   HIS A 513 
 PHE   0.021   0.002   PHE B 208 
 TYR   0.016   0.002   TYR A 340 
 ARG   0.010   0.001   ARG A 290 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 172
  time to evaluate  : 0.782 
Fit side-chains
REVERT: A  158 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6717 (mt0)
REVERT: A  178 GLU cc_start: 0.7052 (pm20) cc_final: 0.6546 (pm20)
REVERT: A  222 PHE cc_start: 0.7150 (t80) cc_final: 0.4990 (m-10)
REVERT: A  309 ARG cc_start: 0.6753 (ttp-170) cc_final: 0.5344 (mmt-90)
REVERT: A  408 ARG cc_start: 0.5194 (mmp-170) cc_final: 0.4656 (tpp-160)
REVERT: A  439 ILE cc_start: 0.8203 (mm) cc_final: 0.7903 (mt)
REVERT: A  460 MET cc_start: 0.7908 (mmm) cc_final: 0.7629 (tpp)
REVERT: B  108 MET cc_start: 0.7887 (mtt) cc_final: 0.7607 (mtp)
REVERT: B  222 PHE cc_start: 0.6746 (t80) cc_final: 0.4947 (m-80)
REVERT: B  264 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7060 (mm-30)
REVERT: B  309 ARG cc_start: 0.5628 (mtm180) cc_final: 0.4679 (mmt-90)
REVERT: B  408 ARG cc_start: 0.4255 (mmm160) cc_final: 0.3780 (tpp-160)
REVERT: B  483 ASP cc_start: 0.6784 (t70) cc_final: 0.6479 (t0)
  outliers start: 21
  outliers final: 15
  residues processed: 187
  average time/residue: 0.1813
  time to fit residues: 45.5915
Evaluate side-chains
  168 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 152
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  158 GLN
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  476 SER
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  555 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 34 optimal weight:    0.4980
   chunk 44 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   chunk 52 optimal weight:    0.4980
   chunk 6 optimal weight:    0.4980
   chunk 62 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.169747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.139085 restraints weight = 9959.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.142332 restraints weight = 6571.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.144519 restraints weight = 5118.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.4908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7460  Z= 0.199
  Angle     :  0.556   9.795  10160  Z= 0.285
  Chirality :  0.042   0.172   1200
  Planarity :  0.004   0.042   1256
  Dihedral  :  3.439  12.485   1002
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.36 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.28), residues: 940
  helix:  2.35 (0.19), residues: 704
  sheet:  None (None), residues: 0
  loop : -0.67 (0.43), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 444 
 HIS   0.005   0.002   HIS A 513 
 PHE   0.020   0.002   PHE A 314 
 TYR   0.023   0.002   TYR B 134 
 ARG   0.009   0.001   ARG A 273 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 162
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 ARG cc_start: 0.6547 (ttp-170) cc_final: 0.5163 (mmt-90)
REVERT: A  408 ARG cc_start: 0.5247 (mmp-170) cc_final: 0.4689 (tpp-160)
REVERT: A  460 MET cc_start: 0.7810 (mmm) cc_final: 0.7606 (tpp)
REVERT: B  108 MET cc_start: 0.7861 (mtt) cc_final: 0.7610 (mtp)
REVERT: B  222 PHE cc_start: 0.6608 (t80) cc_final: 0.4970 (m-80)
REVERT: B  264 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7079 (mm-30)
REVERT: B  309 ARG cc_start: 0.5499 (mtm180) cc_final: 0.4553 (mmt-90)
REVERT: B  408 ARG cc_start: 0.4189 (mmm160) cc_final: 0.3625 (tpp-160)
REVERT: B  483 ASP cc_start: 0.6647 (t70) cc_final: 0.6026 (m-30)
REVERT: B  557 ILE cc_start: 0.8098 (tp) cc_final: 0.7810 (tp)
  outliers start: 19
  outliers final: 12
  residues processed: 177
  average time/residue: 0.1827
  time to fit residues: 44.2780
Evaluate side-chains
  168 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 156
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  555 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 49 optimal weight:    0.5980
   chunk 75 optimal weight:    0.3980
   chunk 65 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.3804 r_free = 0.3804 target = 0.164759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.134425 restraints weight = 9973.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.137610 restraints weight = 6607.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.139696 restraints weight = 5152.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.5414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7460  Z= 0.249
  Angle     :  0.578  10.760  10160  Z= 0.299
  Chirality :  0.043   0.143   1200
  Planarity :  0.005   0.045   1256
  Dihedral  :  3.423  11.909   1002
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 15.40 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.28), residues: 940
  helix:  2.32 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -0.77 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 444 
 HIS   0.004   0.001   HIS A 513 
 PHE   0.021   0.002   PHE B 279 
 TYR   0.010   0.002   TYR A 492 
 ARG   0.004   0.001   ARG A 350 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 165
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 GLN cc_start: 0.7363 (mp10) cc_final: 0.6949 (mp10)
REVERT: A  309 ARG cc_start: 0.6647 (ttp-170) cc_final: 0.5153 (mmt-90)
REVERT: A  349 MET cc_start: 0.6927 (tpp) cc_final: 0.6316 (ttp)
REVERT: A  408 ARG cc_start: 0.5362 (mmp-170) cc_final: 0.4665 (tpp-160)
REVERT: A  425 ASN cc_start: 0.7679 (t0) cc_final: 0.7442 (m-40)
REVERT: B  108 MET cc_start: 0.7916 (mtt) cc_final: 0.7697 (mtp)
REVERT: B  222 PHE cc_start: 0.6679 (t80) cc_final: 0.4965 (m-80)
REVERT: B  264 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7105 (mm-30)
REVERT: B  309 ARG cc_start: 0.5741 (mtm180) cc_final: 0.4678 (mmt-90)
REVERT: B  348 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8225 (m)
REVERT: B  408 ARG cc_start: 0.4362 (mmm160) cc_final: 0.3792 (tpp-160)
REVERT: B  483 ASP cc_start: 0.6740 (t70) cc_final: 0.6118 (m-30)
REVERT: B  557 ILE cc_start: 0.8181 (tp) cc_final: 0.7938 (tp)
  outliers start: 23
  outliers final: 17
  residues processed: 181
  average time/residue: 0.1961
  time to fit residues: 47.2878
Evaluate side-chains
  167 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  516 SER
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  555 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B 527 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.159963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.129395 restraints weight = 10064.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.132419 restraints weight = 6810.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.134424 restraints weight = 5399.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.6019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   7460  Z= 0.297
  Angle     :  0.614   7.975  10160  Z= 0.321
  Chirality :  0.044   0.151   1200
  Planarity :  0.005   0.049   1256
  Dihedral  :  3.596  11.623   1002
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 16.58 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.27), residues: 940
  helix:  2.28 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -1.04 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 444 
 HIS   0.005   0.002   HIS B 210 
 PHE   0.031   0.002   PHE B 208 
 TYR   0.025   0.002   TYR B 134 
 ARG   0.004   0.001   ARG A 350 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 GLN cc_start: 0.7383 (mp10) cc_final: 0.6949 (mp10)
REVERT: A  309 ARG cc_start: 0.6751 (ttp-170) cc_final: 0.5270 (mmt-90)
REVERT: A  349 MET cc_start: 0.7127 (tpp) cc_final: 0.6600 (ttp)
REVERT: A  385 GLN cc_start: 0.8335 (pp30) cc_final: 0.8105 (pt0)
REVERT: A  408 ARG cc_start: 0.5569 (mmp-170) cc_final: 0.4825 (tpp-160)
REVERT: A  425 ASN cc_start: 0.7727 (t0) cc_final: 0.7435 (m-40)
REVERT: A  523 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7638 (mt-10)
REVERT: B  108 MET cc_start: 0.7987 (mtt) cc_final: 0.7756 (mtp)
REVERT: B  222 PHE cc_start: 0.6366 (t80) cc_final: 0.5163 (m-10)
REVERT: B  264 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7334 (mm-30)
REVERT: B  309 ARG cc_start: 0.5800 (mtm180) cc_final: 0.4733 (mmt-90)
REVERT: B  320 GLU cc_start: 0.7061 (mt-10) cc_final: 0.5907 (mt-10)
REVERT: B  348 VAL cc_start: 0.8694 (t) cc_final: 0.8268 (m)
REVERT: B  408 ARG cc_start: 0.4418 (mmm160) cc_final: 0.3819 (tpp-160)
REVERT: B  483 ASP cc_start: 0.6799 (t70) cc_final: 0.6206 (m-30)
REVERT: B  557 ILE cc_start: 0.8119 (tp) cc_final: 0.7899 (tp)
  outliers start: 25
  outliers final: 21
  residues processed: 183
  average time/residue: 0.2020
  time to fit residues: 49.2009
Evaluate side-chains
  178 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 157
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  208 PHE
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  215 CYS
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  555 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 87 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 0 optimal weight:    4.9990
   chunk 86 optimal weight:    0.4980
   chunk 56 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3774 r_free = 0.3774 target = 0.162343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.132512 restraints weight = 10043.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.135670 restraints weight = 6658.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.137751 restraints weight = 5200.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.6202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7460  Z= 0.214
  Angle     :  0.586  10.418  10160  Z= 0.303
  Chirality :  0.042   0.216   1200
  Planarity :  0.005   0.045   1256
  Dihedral  :  3.478  11.227   1002
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 18.80 %
    Favored  : 78.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.28), residues: 940
  helix:  2.41 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -1.16 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 444 
 HIS   0.004   0.002   HIS B 210 
 PHE   0.019   0.002   PHE A 279 
 TYR   0.008   0.001   TYR A 140 
 ARG   0.005   0.000   ARG A 350 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 165
  time to evaluate  : 0.859 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 GLN cc_start: 0.7361 (mp10) cc_final: 0.7031 (mp10)
REVERT: A  309 ARG cc_start: 0.6655 (ttp-170) cc_final: 0.5208 (mmt-90)
REVERT: A  385 GLN cc_start: 0.8336 (pp30) cc_final: 0.8090 (pt0)
REVERT: A  408 ARG cc_start: 0.5540 (mmp-170) cc_final: 0.4572 (tpp-160)
REVERT: A  425 ASN cc_start: 0.7739 (t0) cc_final: 0.7468 (m-40)
REVERT: B  108 MET cc_start: 0.7931 (mtt) cc_final: 0.7726 (mtp)
REVERT: B  222 PHE cc_start: 0.6697 (t80) cc_final: 0.5174 (m-10)
REVERT: B  264 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7248 (mm-30)
REVERT: B  309 ARG cc_start: 0.5854 (OUTLIER) cc_final: 0.4545 (mmt-90)
REVERT: B  320 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6150 (mt-10)
REVERT: B  348 VAL cc_start: 0.8660 (t) cc_final: 0.8302 (m)
REVERT: B  408 ARG cc_start: 0.4365 (mmm160) cc_final: 0.3852 (tpp-160)
REVERT: B  483 ASP cc_start: 0.6696 (t70) cc_final: 0.6184 (m-30)
REVERT: B  557 ILE cc_start: 0.8125 (tp) cc_final: 0.7885 (tp)
  outliers start: 23
  outliers final: 17
  residues processed: 182
  average time/residue: 0.2072
  time to fit residues: 49.9053
Evaluate side-chains
  177 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 159
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  405 THR
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  555 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0970
   chunk 92 optimal weight:    0.6980
   chunk 78 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   overall best weight:    0.6378

-------------------------------------------------------------------------------
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 = 0.3778 r_free = 0.3778 target = 0.162616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.132865 restraints weight = 10210.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.135977 restraints weight = 6775.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.137998 restraints weight = 5316.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.6372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7460  Z= 0.205
  Angle     :  0.587   9.705  10160  Z= 0.301
  Chirality :  0.042   0.228   1200
  Planarity :  0.004   0.042   1256
  Dihedral  :  3.411  11.362   1002
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 19.71 %
    Favored  : 77.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.28), residues: 940
  helix:  2.45 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -1.17 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 444 
 HIS   0.004   0.002   HIS B 210 
 PHE   0.027   0.002   PHE A 279 
 TYR   0.025   0.002   TYR A 134 
 ARG   0.004   0.000   ARG B 350 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 167
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 GLN cc_start: 0.7340 (mp10) cc_final: 0.7112 (mp10)
REVERT: A  309 ARG cc_start: 0.6474 (ttp-170) cc_final: 0.5089 (mmt-90)
REVERT: A  348 VAL cc_start: 0.8436 (t) cc_final: 0.8020 (m)
REVERT: A  385 GLN cc_start: 0.8316 (pp30) cc_final: 0.8077 (pt0)
REVERT: A  408 ARG cc_start: 0.5622 (mmp-170) cc_final: 0.4684 (tpp-160)
REVERT: A  425 ASN cc_start: 0.7750 (t0) cc_final: 0.7483 (m-40)
REVERT: B  108 MET cc_start: 0.7929 (mtt) cc_final: 0.7728 (mtp)
REVERT: B  222 PHE cc_start: 0.6722 (t80) cc_final: 0.5070 (m-10)
REVERT: B  309 ARG cc_start: 0.5858 (mtm180) cc_final: 0.4540 (mmp80)
REVERT: B  320 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6155 (mt-10)
REVERT: B  348 VAL cc_start: 0.8662 (t) cc_final: 0.8297 (m)
REVERT: B  408 ARG cc_start: 0.4490 (mmm160) cc_final: 0.3912 (tpp-160)
REVERT: B  483 ASP cc_start: 0.6666 (t70) cc_final: 0.6203 (m-30)
REVERT: B  535 MET cc_start: 0.7706 (mmt) cc_final: 0.7358 (mmt)
REVERT: B  557 ILE cc_start: 0.8135 (tp) cc_final: 0.7930 (tp)
  outliers start: 23
  outliers final: 21
  residues processed: 184
  average time/residue: 0.1984
  time to fit residues: 48.4974
Evaluate side-chains
  184 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 163
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  398 VAL
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  405 THR
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  555 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 82 optimal weight:    0.5980
   chunk 53 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 79 optimal weight:    7.9990
   chunk 88 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0980
   chunk 23 optimal weight:    0.0570
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.4298

-------------------------------------------------------------------------------
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 = 0.3796 r_free = 0.3796 target = 0.163868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.133830 restraints weight = 10151.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.136971 restraints weight = 6760.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.139044 restraints weight = 5301.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.6440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7460  Z= 0.192
  Angle     :  0.599  10.583  10160  Z= 0.302
  Chirality :  0.042   0.213   1200
  Planarity :  0.004   0.041   1256
  Dihedral  :  3.356  12.404   1002
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 20.10 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.28), residues: 940
  helix:  2.48 (0.19), residues: 694
  sheet:  None (None), residues: 0
  loop : -1.16 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 444 
 HIS   0.004   0.002   HIS A 513 
 PHE   0.028   0.002   PHE A 279 
 TYR   0.009   0.001   TYR B 134 
 ARG   0.006   0.000   ARG A 350 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 176
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 ARG cc_start: 0.6363 (ttp-170) cc_final: 0.4960 (mmt-90)
REVERT: A  348 VAL cc_start: 0.8420 (t) cc_final: 0.8068 (m)
REVERT: A  385 GLN cc_start: 0.8315 (pp30) cc_final: 0.8104 (pt0)
REVERT: A  408 ARG cc_start: 0.5509 (mmp-170) cc_final: 0.4630 (tpp-160)
REVERT: A  425 ASN cc_start: 0.7714 (t0) cc_final: 0.7483 (m-40)
REVERT: B  108 MET cc_start: 0.7929 (mtt) cc_final: 0.7729 (mtp)
REVERT: B  222 PHE cc_start: 0.6723 (t80) cc_final: 0.5088 (m-10)
REVERT: B  309 ARG cc_start: 0.5859 (mtm180) cc_final: 0.4791 (mmt-90)
REVERT: B  320 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6114 (mt-10)
REVERT: B  348 VAL cc_start: 0.8652 (t) cc_final: 0.8269 (m)
REVERT: B  363 ARG cc_start: 0.4743 (ptp90) cc_final: 0.4253 (ptp-170)
REVERT: B  408 ARG cc_start: 0.4494 (mmm160) cc_final: 0.4086 (tpm170)
REVERT: B  483 ASP cc_start: 0.6573 (t70) cc_final: 0.6179 (m-30)
REVERT: B  535 MET cc_start: 0.7681 (mmt) cc_final: 0.7413 (mmt)
REVERT: B  557 ILE cc_start: 0.8125 (tp) cc_final: 0.7919 (tp)
  outliers start: 19
  outliers final: 19
  residues processed: 190
  average time/residue: 0.2036
  time to fit residues: 51.1568
Evaluate side-chains
  183 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 164
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  420 THR
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  557 ILE
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  405 THR
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  555 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 63 optimal weight:    6.9990
   chunk 71 optimal weight:    3.9990
   chunk 87 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    1.5784

-------------------------------------------------------------------------------
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 = 0.3714 r_free = 0.3714 target = 0.156775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.127202 restraints weight = 10408.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.130185 restraints weight = 6889.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.132191 restraints weight = 5382.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.6910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   7460  Z= 0.320
  Angle     :  0.680   9.437  10160  Z= 0.351
  Chirality :  0.047   0.294   1200
  Planarity :  0.005   0.048   1256
  Dihedral  :  3.637  12.840   1002
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 18.80 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.28), residues: 940
  helix:  2.06 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.44 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 295 
 HIS   0.004   0.002   HIS B 210 
 PHE   0.028   0.002   PHE B 208 
 TYR   0.025   0.002   TYR B 134 
 ARG   0.005   0.001   ARG A 350 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 153
  time to evaluate  : 0.754 
Fit side-chains
REVERT: A  309 ARG cc_start: 0.6494 (ttp-170) cc_final: 0.5064 (mmt-90)
REVERT: A  348 VAL cc_start: 0.8515 (t) cc_final: 0.8171 (m)
REVERT: A  385 GLN cc_start: 0.8396 (pp30) cc_final: 0.8152 (pt0)
REVERT: A  425 ASN cc_start: 0.7739 (t0) cc_final: 0.7455 (m-40)
REVERT: B  108 MET cc_start: 0.7990 (mtt) cc_final: 0.7777 (mtp)
REVERT: B  222 PHE cc_start: 0.6938 (t80) cc_final: 0.5251 (m-10)
REVERT: B  264 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7287 (mm-30)
REVERT: B  309 ARG cc_start: 0.5862 (OUTLIER) cc_final: 0.4582 (mmt-90)
REVERT: B  348 VAL cc_start: 0.8697 (t) cc_final: 0.8336 (m)
REVERT: B  408 ARG cc_start: 0.4623 (mmm160) cc_final: 0.3863 (tpp-160)
REVERT: B  483 ASP cc_start: 0.6781 (t70) cc_final: 0.6297 (m-30)
REVERT: B  535 MET cc_start: 0.7672 (mmt) cc_final: 0.7372 (mmt)
  outliers start: 26
  outliers final: 19
  residues processed: 171
  average time/residue: 0.2037
  time to fit residues: 46.3878
Evaluate side-chains
  177 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 157
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  160 VAL
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  421 SER
Chi-restraints excluded: chain A residue  431 VAL
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain B residue   92 ILE
Chi-restraints excluded: chain B residue  160 VAL
Chi-restraints excluded: chain B residue  208 PHE
Chi-restraints excluded: chain B residue  303 THR
Chi-restraints excluded: chain B residue  309 ARG
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  369 LEU
Chi-restraints excluded: chain B residue  405 THR
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  516 SER
Chi-restraints excluded: chain B residue  555 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0370
   chunk 12 optimal weight:    0.7980
   chunk 40 optimal weight:    6.9990
   chunk 65 optimal weight:    0.4980
   chunk 70 optimal weight:    2.9990
   chunk 92 optimal weight:    0.7980
   chunk 75 optimal weight:    0.7980
   chunk 83 optimal weight:    0.6980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
A 274 ASN
B 393 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.161672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.131205 restraints weight = 10100.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.134475 restraints weight = 6606.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.136613 restraints weight = 5123.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.6910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7460  Z= 0.207
  Angle     :  0.627  12.905  10160  Z= 0.316
  Chirality :  0.044   0.368   1200
  Planarity :  0.005   0.042   1256
  Dihedral  :  3.503  13.141   1002
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 20.37 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.28), residues: 940
  helix:  2.22 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.44 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 444 
 HIS   0.004   0.001   HIS A 513 
 PHE   0.028   0.002   PHE A 279 
 TYR   0.009   0.001   TYR B 134 
 ARG   0.005   0.000   ARG A 350 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2551.70 seconds
wall clock time: 45 minutes 21.99 seconds (2721.99 seconds total)