Starting phenix.real_space_refine
on Tue Mar 11 17:24:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vrl_21370/03_2025/6vrl_21370.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vrl_21370/03_2025/6vrl_21370.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vrl_21370/03_2025/6vrl_21370.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vrl_21370/03_2025/6vrl_21370.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vrl_21370/03_2025/6vrl_21370.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vrl_21370/03_2025/6vrl_21370.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.971
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 92 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     I       1     10.91       5
     S      34      5.16       5
     C    4045      2.51       5
     N     958      2.21       5
     O    1103      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6141
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 541, 4311
          Classifications: {'peptide': 541}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 23, 'TRANS': 517}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 100}
    Chain: "B"
      Number of atoms: 924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 924
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 5, 'TRANS': 111}
    Chain: "A"
      Number of atoms: 87
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 87
          Unusual residues: {'LMT': 1, 'NAG': 2, 'RFY': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 4.77, per 1000 atoms: 0.78
  Number of scatterers: 6141
  At special positions: 0
  Unit cell: (95.256, 104.328, 82.296, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     I       1     52.95
     S      34     16.00
     O    1103      8.00
     N     958      7.00
     C    4045      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  41 " - pdb=" SG  CYS B 115 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A 208 "
      " NAG A 702 " - " ASN A 217 "
  Time building additional restraints: 1.74
  Conformation dependent library (CDL) restraints added in 905.9 milliseconds
  

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1406

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 7 sheets defined
      53.8% alpha, 8.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 97
      removed outlier: 3.540A  pdb=" N   PHE A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 102
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 113 through 116
    Processing helix  chain 'A' and resid 117 through 128
    Processing helix  chain 'A' and resid 128 through 144
      removed outlier: 4.110A  pdb=" N   LEU A 132 " --> pdb=" O   GLY A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 158
    Processing helix  chain 'A' and resid 159 through 190
      removed outlier: 4.256A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ASN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   THR A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   MET A 180 " --> pdb=" O   TYR A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 235
    Processing helix  chain 'A' and resid 253 through 271
    Processing helix  chain 'A' and resid 273 through 285
      removed outlier: 3.721A  pdb=" N   LYS A 279 " --> pdb=" O   LYS A 275 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   VAL A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 300
      removed outlier: 3.665A  pdb=" N   ILE A 290 " --> pdb=" O   THR A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 314
      removed outlier: 4.080A  pdb=" N   VAL A 309 " --> pdb=" O   ALA A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 321
    Processing helix  chain 'A' and resid 322 through 338
      removed outlier: 4.094A  pdb=" N   TRP A 326 " --> pdb=" O   GLU A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 349
    Processing helix  chain 'A' and resid 356 through 390
      removed outlier: 3.531A  pdb=" N   ASP A 360 " --> pdb=" O   ASN A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 397
    Processing helix  chain 'A' and resid 403 through 408
    Processing helix  chain 'A' and resid 408 through 417
    Processing helix  chain 'A' and resid 419 through 454
      removed outlier: 4.039A  pdb=" N   PHE A 423 " --> pdb=" O   ALA A 419 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ASP A 437 " --> pdb=" O   THR A 433 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   SER A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 478
    Processing helix  chain 'A' and resid 479 through 481
      No H-bonds generated for 'chain 'A' and resid 479 through 481'
    Processing helix  chain 'A' and resid 484 through 496
      removed outlier: 3.832A  pdb=" N   VAL A 488 " --> pdb=" O   GLY A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 514
    Processing helix  chain 'A' and resid 517 through 530
    Processing helix  chain 'A' and resid 534 through 543
    Processing helix  chain 'A' and resid 543 through 557
    Processing helix  chain 'A' and resid 571 through 587
      removed outlier: 4.254A  pdb=" N   SER A 585 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   PHE A 586 " --> pdb=" O   GLY A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 596
    Processing helix  chain 'A' and resid 603 through 611
    Processing helix  chain 'B' and resid 81 through 84
      removed outlier: 4.011A  pdb=" N   LYS B  84 " --> pdb=" O   GLN B  81 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 81 through 84'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 564 through 565
      removed outlier: 3.666A  pdb=" N   LEU A 565 " --> pdb=" O   TYR A 568 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 24 through 26
    Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 41
    Processing sheet with id=AA4, first strand: chain 'C' and resid 73 through 74
      removed outlier: 6.797A  pdb=" N   TRP C  55 " --> pdb=" O   LEU C  67 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   TYR C  69 " --> pdb=" O   VAL C  53 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   VAL C  53 " --> pdb=" O   TYR C  69 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 22 through 25
    Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 39
      removed outlier: 3.811A  pdb=" N   VAL B  37 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU B 102 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ILE B  39 " --> pdb=" O   MET B 100 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   MET B 100 " --> pdb=" O   ILE B  39 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79
      removed outlier: 6.649A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   ASN B  69 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 6.978A  pdb=" N   MET B  53 " --> pdb=" O   ASN B  69 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   VAL B 112 " --> pdb=" O   GLN B  58 " (cutoff:3.500A)

    312 hydrogen bonds defined for protein.
    888 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.58

  Time building geometry restraints manager: 1.93 seconds

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

  Histogram of bond lengths:
        1.23 -     1.40: 2681
        1.40 -     1.58: 3595
        1.58 -     1.75: 0
        1.75 -     1.93: 49
        1.93 -     2.11: 1
  Bond restraints: 6326
  Sorted by residual:
  bond pdb=" C06 RFY A 704 "
       pdb=" C07 RFY A 704 "
    ideal  model  delta    sigma   weight residual
    1.511  1.576 -0.065 2.00e-02 2.50e+03 1.06e+01
  bond pdb=" C05 RFY A 704 "
       pdb=" C06 RFY A 704 "
    ideal  model  delta    sigma   weight residual
    1.543  1.493  0.050 2.00e-02 2.50e+03 6.30e+00
  bond pdb=" C17 RFY A 704 "
       pdb=" C18 RFY A 704 "
    ideal  model  delta    sigma   weight residual
    1.370  1.418 -0.048 2.00e-02 2.50e+03 5.81e+00
  bond pdb=" C19 RFY A 704 "
       pdb=" C20 RFY A 704 "
    ideal  model  delta    sigma   weight residual
    1.371  1.416 -0.045 2.00e-02 2.50e+03 5.11e+00
  bond pdb=" C01 RFY A 704 "
       pdb=" C06 RFY A 704 "
    ideal  model  delta    sigma   weight residual
    1.542  1.498  0.044 2.00e-02 2.50e+03 4.95e+00
  ... (remaining 6321 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 8430
        1.79 -     3.57: 150
        3.57 -     5.36: 25
        5.36 -     7.15: 10
        7.15 -     8.94: 4
  Bond angle restraints: 8619
  Sorted by residual:
  angle pdb=" N   VAL A 397 "
        pdb=" CA  VAL A 397 "
        pdb=" C   VAL A 397 "
      ideal   model   delta    sigma   weight residual
     113.42  109.33    4.09 1.17e+00 7.31e-01 1.22e+01
  angle pdb=" N   ARG B 121 "
        pdb=" CA  ARG B 121 "
        pdb=" C   ARG B 121 "
      ideal   model   delta    sigma   weight residual
     109.81  117.12   -7.31 2.21e+00 2.05e-01 1.09e+01
  angle pdb=" C2  LMT A 703 "
        pdb=" C3  LMT A 703 "
        pdb=" C4  LMT A 703 "
      ideal   model   delta    sigma   weight residual
     117.09  108.15    8.94 3.00e+00 1.11e-01 8.87e+00
  angle pdb=" C10 LMT A 703 "
        pdb=" C9  LMT A 703 "
        pdb=" C8  LMT A 703 "
      ideal   model   delta    sigma   weight residual
     116.03  107.32    8.71 3.00e+00 1.11e-01 8.43e+00
  angle pdb=" C   VAL B 120 "
        pdb=" N   ARG B 121 "
        pdb=" CA  ARG B 121 "
      ideal   model   delta    sigma   weight residual
     121.80  128.79   -6.99 2.44e+00 1.68e-01 8.20e+00
  ... (remaining 8614 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 3299
       17.53 -    35.07: 321
       35.07 -    52.60: 54
       52.60 -    70.14: 14
       70.14 -    87.67: 4
  Dihedral angle restraints: 3692
    sinusoidal: 1478
      harmonic: 2214
  Sorted by residual:
  dihedral pdb=" CA  ARG B 121 "
           pdb=" C   ARG B 121 "
           pdb=" N   PRO B 122 "
           pdb=" CA  PRO B 122 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  128.14   51.86     0      5.00e+00 4.00e-02 1.08e+02
  dihedral pdb=" CB  CYS A 200 "
           pdb=" SG  CYS A 200 "
           pdb=" SG  CYS A 209 "
           pdb=" CB  CYS A 209 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  133.61  -40.61     1      1.00e+01 1.00e-02 2.31e+01
  dihedral pdb=" CA  CYS A 209 "
           pdb=" C   CYS A 209 "
           pdb=" N   THR A 210 "
           pdb=" CA  THR A 210 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.28   18.72     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 3689 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 714
       0.042 -    0.083: 207
       0.083 -    0.125: 40
       0.125 -    0.166: 1
       0.166 -    0.208: 4
  Chirality restraints: 966
  Sorted by residual:
  chirality pdb=" C4' LMT A 703 "
            pdb=" C3' LMT A 703 "
            pdb=" C5' LMT A 703 "
            pdb=" O1B LMT A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.55   -2.76    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" C3B LMT A 703 "
            pdb=" C2B LMT A 703 "
            pdb=" C4B LMT A 703 "
            pdb=" O3B LMT A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50    2.29    0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" C5' LMT A 703 "
            pdb=" C4' LMT A 703 "
            pdb=" C6' LMT A 703 "
            pdb=" O5' LMT A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.30   -0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 963 not shown)

  Planarity restraints: 1050
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 121 "   -0.044 5.00e-02 4.00e+02   6.70e-02 7.18e+00
        pdb=" N   PRO B 122 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO B 122 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 122 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 465 "   -0.010 2.00e-02 2.50e+03   1.97e-02 3.90e+00
        pdb=" C   PHE A 465 "    0.034 2.00e-02 2.50e+03
        pdb=" O   PHE A 465 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   VAL A 466 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 589 "    0.020 5.00e-02 4.00e+02   3.03e-02 1.47e+00
        pdb=" N   PRO A 590 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 590 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 590 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1047 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.72: 256
        2.72 -     3.28: 6880
        3.28 -     3.84: 11030
        3.84 -     4.40: 13024
        4.40 -     4.96: 22133
  Nonbonded interactions: 53323
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C  83 "
            pdb=" O   THR C  94 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" OG  SER B 110 "
            pdb=" O   LEU B 134 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" O   THR A 221 "
            pdb=" OG  SER A 224 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   ASP C 102 "
            pdb=" OH  TYR C 106 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   SER A 559 "
            pdb=" O6' LMT A 703 "
     model   vdw
     2.267 3.040
  ... (remaining 53318 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             2.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.740
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6910
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      :  0.004   0.065   6326  Z= 0.237
  Angle     :  0.633   8.936   8619  Z= 0.327
  Chirality :  0.040   0.208    966
  Planarity :  0.004   0.067   1048
  Dihedral  : 13.973  87.674   2277
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -3.12 (0.27), residues: 758
  helix: -0.96 (0.24), residues: 360
  sheet: -3.12 (0.42), residues: 99
  loop : -3.02 (0.32), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 151 
 HIS   0.001   0.000   HIS A 143 
 PHE   0.015   0.001   PHE A 311 
 TYR   0.013   0.001   TYR B 123 
 ARG   0.001   0.000   ARG B 121 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 TRP cc_start: 0.8013 (m100) cc_final: 0.7795 (m100)
REVERT: A  134 TYR cc_start: 0.7065 (t80) cc_final: 0.6847 (t80)
REVERT: A  135 MET cc_start: 0.7156 (ttm) cc_final: 0.6385 (ttm)
REVERT: A  136 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6434 (mm-30)
REVERT: A  151 TRP cc_start: 0.7689 (m100) cc_final: 0.7139 (m100)
REVERT: A  179 ILE cc_start: 0.8987 (mm) cc_final: 0.8532 (mt)
REVERT: A  234 ARG cc_start: 0.6268 (ttm-80) cc_final: 0.5843 (mtt-85)
REVERT: A  373 PHE cc_start: 0.8209 (t80) cc_final: 0.7918 (t80)
REVERT: A  408 ILE cc_start: 0.8773 (mt) cc_final: 0.8554 (mt)
REVERT: A  494 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6481 (mm-30)
REVERT: A  553 ILE cc_start: 0.9053 (pt) cc_final: 0.8831 (pt)
REVERT: C   47 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7393 (tm-30)
REVERT: C   67 LEU cc_start: 0.6982 (mm) cc_final: 0.6741 (mm)
REVERT: C  114 ILE cc_start: 0.8801 (pt) cc_final: 0.8581 (mp)
REVERT: B   42 LYS cc_start: 0.6139 (mttt) cc_final: 0.5449 (tptt)
REVERT: B   53 MET cc_start: 0.8867 (tpp) cc_final: 0.8515 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.1689
  time to fit residues: 46.1524
Evaluate side-chains
  148 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 38 optimal weight:    0.0050
   chunk 30 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0870
   chunk 22 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.5372

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

Flipped N/Q/H residues before XYZ refinement:
A 101 ASN
** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.184878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.168178 restraints weight = 10894.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.172215 restraints weight = 6691.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.175086 restraints weight = 4450.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6894
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6326  Z= 0.172
  Angle     :  0.622  10.165   8619  Z= 0.311
  Chirality :  0.041   0.245    966
  Planarity :  0.004   0.072   1048
  Dihedral  :  7.263  77.857    961
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.23 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.30), residues: 758
  helix:  0.26 (0.26), residues: 363
  sheet: -2.56 (0.46), residues: 100
  loop : -2.44 (0.35), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 220 
 HIS   0.004   0.001   HIS C 111 
 PHE   0.018   0.001   PHE A 423 
 TYR   0.019   0.001   TYR B 123 
 ARG   0.005   0.000   ARG C 116 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 168
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6412 (mm-30)
REVERT: A  151 TRP cc_start: 0.7743 (m100) cc_final: 0.7089 (m100)
REVERT: A  240 HIS cc_start: 0.6981 (p90) cc_final: 0.6649 (m170)
REVERT: A  373 PHE cc_start: 0.8285 (t80) cc_final: 0.7831 (t80)
REVERT: A  388 GLU cc_start: 0.6769 (tm-30) cc_final: 0.6500 (tm-30)
REVERT: A  417 MET cc_start: 0.6414 (mtm) cc_final: 0.6028 (mtm)
REVERT: A  494 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6503 (mm-30)
REVERT: B   42 LYS cc_start: 0.6260 (mttt) cc_final: 0.5816 (tptt)
REVERT: B   53 MET cc_start: 0.8984 (tpp) cc_final: 0.8761 (tpt)
  outliers start: 16
  outliers final: 8
  residues processed: 170
  average time/residue: 0.1608
  time to fit residues: 36.9970
Evaluate side-chains
  148 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 140
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain B residue   79 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 12 optimal weight:    7.9990
   chunk 61 optimal weight:    7.9990
   chunk 70 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   chunk 43 optimal weight:    7.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 368 ASN
A 562 GLN
** C  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  24 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.178830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.161951 restraints weight = 10911.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.165098 restraints weight = 6598.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.168379 restraints weight = 4747.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.4085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   6326  Z= 0.286
  Angle     :  0.697  11.131   8619  Z= 0.351
  Chirality :  0.044   0.226    966
  Planarity :  0.005   0.074   1048
  Dihedral  :  7.537  79.782    961
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 15.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 20.46 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -1.42 (0.30), residues: 758
  helix:  0.54 (0.27), residues: 356
  sheet: -2.75 (0.45), residues: 105
  loop : -2.06 (0.37), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 220 
 HIS   0.008   0.002   HIS C 111 
 PHE   0.018   0.002   PHE A 423 
 TYR   0.024   0.002   TYR A 134 
 ARG   0.006   0.000   ARG A 234 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6635 (mm-30)
REVERT: A  492 LEU cc_start: 0.8256 (mt) cc_final: 0.7976 (mt)
REVERT: A  494 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6702 (mm-30)
REVERT: C  101 GLU cc_start: 0.7094 (tp30) cc_final: 0.6823 (tp30)
REVERT: B   42 LYS cc_start: 0.6391 (mttt) cc_final: 0.5899 (tptt)
REVERT: B   53 MET cc_start: 0.9057 (tpp) cc_final: 0.8802 (tpt)
  outliers start: 20
  outliers final: 16
  residues processed: 154
  average time/residue: 0.1605
  time to fit residues: 33.4577
Evaluate side-chains
  150 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  311 PHE
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  611 SER
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   79 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 55 optimal weight:    7.9990
   chunk 57 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 416 ASN
** C  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.186089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.168745 restraints weight = 10542.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.172744 restraints weight = 6418.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.175659 restraints weight = 4350.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.4169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6974
moved from start:          0.2900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6326  Z= 0.182
  Angle     :  0.626  11.990   8619  Z= 0.313
  Chirality :  0.041   0.208    966
  Planarity :  0.004   0.073   1048
  Dihedral  :  7.372  80.683    961
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 23.54 %
    Favored  : 73.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -1.13 (0.31), residues: 758
  helix:  0.77 (0.27), residues: 355
  sheet: -2.38 (0.46), residues: 100
  loop : -1.99 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 220 
 HIS   0.003   0.001   HIS C 111 
 PHE   0.023   0.001   PHE A 521 
 TYR   0.028   0.001   TYR A 134 
 ARG   0.003   0.000   ARG C  81 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6693 (mm-30)
REVERT: A  492 LEU cc_start: 0.8223 (mt) cc_final: 0.7947 (mt)
REVERT: A  494 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6545 (mm-30)
REVERT: C  101 GLU cc_start: 0.7309 (tp30) cc_final: 0.7036 (tp30)
REVERT: B   42 LYS cc_start: 0.6205 (mttt) cc_final: 0.5748 (tptt)
  outliers start: 18
  outliers final: 13
  residues processed: 150
  average time/residue: 0.1628
  time to fit residues: 33.0771
Evaluate side-chains
  147 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 134
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   79 TYR
Chi-restraints excluded: chain B residue  136 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 64 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 70 optimal weight:   10.0000
   chunk 66 optimal weight:   10.0000
   chunk 69 optimal weight:    6.9990
   chunk 25 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 9 optimal weight:    8.9990
   overall best weight:    2.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 416 ASN
A 562 GLN
** C  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.181438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.164187 restraints weight = 10677.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.168032 restraints weight = 6544.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.170937 restraints weight = 4462.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.4139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.3287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   6326  Z= 0.294
  Angle     :  0.703  10.841   8619  Z= 0.355
  Chirality :  0.044   0.238    966
  Planarity :  0.004   0.076   1048
  Dihedral  :  7.312  80.507    961
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 15.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 23.69 %
    Favored  : 71.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -1.34 (0.30), residues: 758
  helix:  0.54 (0.27), residues: 358
  sheet: -2.53 (0.44), residues: 105
  loop : -2.00 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B  55 
 HIS   0.006   0.002   HIS C 111 
 PHE   0.016   0.002   PHE A 521 
 TYR   0.027   0.002   TYR A 134 
 ARG   0.006   0.001   ARG C  81 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 135
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6816 (mm-30)
REVERT: A  492 LEU cc_start: 0.8277 (mt) cc_final: 0.8012 (mt)
REVERT: A  494 GLU cc_start: 0.7486 (mm-30) cc_final: 0.6714 (mm-30)
REVERT: C  101 GLU cc_start: 0.7424 (tp30) cc_final: 0.7189 (tp30)
REVERT: B   42 LYS cc_start: 0.6285 (mttt) cc_final: 0.5866 (tptt)
REVERT: B   58 GLN cc_start: 0.5228 (OUTLIER) cc_final: 0.4431 (tp40)
  outliers start: 30
  outliers final: 23
  residues processed: 151
  average time/residue: 0.1459
  time to fit residues: 30.6703
Evaluate side-chains
  155 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 131
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  611 SER
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   68 ILE
Chi-restraints excluded: chain C residue  111 HIS
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   58 GLN
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   79 TYR
Chi-restraints excluded: chain B residue  134 LEU
Chi-restraints excluded: chain B residue  136 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 6 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 24 optimal weight:    0.2980
   chunk 26 optimal weight:    0.0010
   chunk 71 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 16 optimal weight:    7.9990
   overall best weight:    0.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 416 ASN
** C  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.186625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.168761 restraints weight = 10373.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.173025 restraints weight = 6269.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.175981 restraints weight = 4158.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.4176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.3366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6326  Z= 0.189
  Angle     :  0.644  10.093   8619  Z= 0.323
  Chirality :  0.043   0.316    966
  Planarity :  0.004   0.074   1048
  Dihedral  :  6.684  77.569    961
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 26.00 %
    Favored  : 71.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    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: -1.03 (0.30), residues: 758
  helix:  0.73 (0.27), residues: 355
  sheet: -2.18 (0.45), residues: 100
  loop : -1.84 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 103 
 HIS   0.004   0.001   HIS C 111 
 PHE   0.018   0.001   PHE A 428 
 TYR   0.021   0.001   TYR A 134 
 ARG   0.004   0.000   ARG C  81 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 135
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6881 (mm-30)
REVERT: A  417 MET cc_start: 0.6433 (mtm) cc_final: 0.5580 (mtm)
REVERT: A  494 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6511 (mm-30)
REVERT: A  528 MET cc_start: 0.6726 (mtp) cc_final: 0.6417 (mtp)
REVERT: B   42 LYS cc_start: 0.6272 (mttt) cc_final: 0.5757 (tptt)
  outliers start: 18
  outliers final: 14
  residues processed: 145
  average time/residue: 0.1483
  time to fit residues: 29.8728
Evaluate side-chains
  141 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   79 TYR
Chi-restraints excluded: chain B residue  136 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 50 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   chunk 63 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 416 ASN
** C  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 109 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.185018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.167275 restraints weight = 10553.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.171438 restraints weight = 6382.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.174504 restraints weight = 4239.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.4167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7034
moved from start:          0.3547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6326  Z= 0.208
  Angle     :  0.665  12.501   8619  Z= 0.331
  Chirality :  0.042   0.281    966
  Planarity :  0.004   0.073   1048
  Dihedral  :  6.575  77.259    961
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 26.77 %
    Favored  : 69.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.30), residues: 758
  helix:  0.75 (0.27), residues: 356
  sheet: -2.06 (0.45), residues: 99
  loop : -1.75 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP A 103 
 HIS   0.004   0.001   HIS C 111 
 PHE   0.027   0.001   PHE A 521 
 TYR   0.024   0.002   TYR A 134 
 ARG   0.007   0.000   ARG C 116 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6880 (mm-30)
REVERT: A  494 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6520 (mm-30)
REVERT: B   42 LYS cc_start: 0.6336 (mttt) cc_final: 0.5862 (tptp)
REVERT: B   58 GLN cc_start: 0.5199 (OUTLIER) cc_final: 0.4527 (tp40)
  outliers start: 25
  outliers final: 21
  residues processed: 147
  average time/residue: 0.1551
  time to fit residues: 31.4120
Evaluate side-chains
  149 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  611 SER
Chi-restraints excluded: chain C residue   68 ILE
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   58 GLN
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   79 TYR
Chi-restraints excluded: chain B residue  136 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9990
   chunk 9 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 38 optimal weight:    0.0030
   chunk 1 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.9996

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 416 ASN
A 520 GLN
** C  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  99 GLN
C 109 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.186213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.169260 restraints weight = 10488.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.172088 restraints weight = 6421.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.175598 restraints weight = 4619.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.4201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6998
moved from start:          0.3673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6326  Z= 0.192
  Angle     :  0.659  10.196   8619  Z= 0.328
  Chirality :  0.042   0.274    966
  Planarity :  0.004   0.073   1048
  Dihedral  :  6.412  77.285    961
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 26.62 %
    Favored  : 69.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.85 (0.30), residues: 758
  helix:  0.79 (0.27), residues: 356
  sheet: -1.85 (0.46), residues: 99
  loop : -1.72 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 541 
 HIS   0.003   0.001   HIS C 111 
 PHE   0.020   0.001   PHE A 428 
 TYR   0.023   0.001   TYR A 134 
 ARG   0.009   0.001   ARG C  81 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6782 (mm-30)
REVERT: A  180 MET cc_start: 0.7994 (mmp) cc_final: 0.7523 (mmm)
REVERT: A  494 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6477 (mm-30)
REVERT: C   74 ARG cc_start: 0.7009 (ptt-90) cc_final: 0.6769 (ptp90)
REVERT: C   99 GLN cc_start: 0.6447 (OUTLIER) cc_final: 0.6209 (mp10)
REVERT: B   42 LYS cc_start: 0.6292 (mttt) cc_final: 0.5878 (tptp)
REVERT: B   58 GLN cc_start: 0.5122 (OUTLIER) cc_final: 0.4472 (tp40)
REVERT: B  109 ASP cc_start: 0.7597 (p0) cc_final: 0.7393 (m-30)
  outliers start: 26
  outliers final: 21
  residues processed: 153
  average time/residue: 0.1532
  time to fit residues: 33.0198
Evaluate side-chains
  153 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 TRP
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  611 SER
Chi-restraints excluded: chain C residue   99 GLN
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   58 GLN
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   79 TYR
Chi-restraints excluded: chain B residue   90 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 57 optimal weight:    5.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 416 ASN
** C  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  99 GLN
C 109 GLN
** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.182998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.165434 restraints weight = 10492.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.169258 restraints weight = 6343.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.172374 restraints weight = 4424.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.4141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.3758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6326  Z= 0.245
  Angle     :  0.712  12.921   8619  Z= 0.354
  Chirality :  0.044   0.259    966
  Planarity :  0.004   0.074   1048
  Dihedral  :  6.544  77.343    961
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 15.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 26.92 %
    Favored  : 68.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.30), residues: 758
  helix:  0.69 (0.27), residues: 355
  sheet: -2.18 (0.45), residues: 100
  loop : -1.61 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 541 
 HIS   0.004   0.001   HIS C 111 
 PHE   0.026   0.002   PHE A 440 
 TYR   0.025   0.002   TYR A 134 
 ARG   0.005   0.000   ARG C 116 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 132
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6916 (mm-30)
REVERT: A  180 MET cc_start: 0.8071 (mmp) cc_final: 0.7696 (mmm)
REVERT: A  388 GLU cc_start: 0.6915 (tm-30) cc_final: 0.6713 (tm-30)
REVERT: A  494 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6540 (mm-30)
REVERT: C   74 ARG cc_start: 0.7073 (ptt-90) cc_final: 0.6785 (ptp90)
REVERT: C   99 GLN cc_start: 0.6564 (OUTLIER) cc_final: 0.6222 (mp10)
REVERT: B   42 LYS cc_start: 0.6414 (mttt) cc_final: 0.5892 (tptp)
REVERT: B   58 GLN cc_start: 0.5256 (OUTLIER) cc_final: 0.4552 (tp40)
  outliers start: 30
  outliers final: 28
  residues processed: 151
  average time/residue: 0.1498
  time to fit residues: 32.0382
Evaluate side-chains
  157 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 TRP
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  611 SER
Chi-restraints excluded: chain C residue   68 ILE
Chi-restraints excluded: chain C residue   99 GLN
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   46 TYR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   58 GLN
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   79 TYR
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  136 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 57 optimal weight:    8.9990
   chunk 73 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 17 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 391 ASN
A 416 ASN
** C  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  99 GLN
C 109 GLN
** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.186607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.168931 restraints weight = 10617.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.173116 restraints weight = 6386.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.176222 restraints weight = 4238.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6994
moved from start:          0.3827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6326  Z= 0.193
  Angle     :  0.688  12.057   8619  Z= 0.342
  Chirality :  0.043   0.262    966
  Planarity :  0.004   0.075   1048
  Dihedral  :  6.390  77.250    961
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 14.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 26.77 %
    Favored  : 68.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.30), residues: 758
  helix:  0.77 (0.27), residues: 356
  sheet: -2.03 (0.45), residues: 101
  loop : -1.59 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.001   TRP A 541 
 HIS   0.004   0.001   HIS C 111 
 PHE   0.026   0.002   PHE A 440 
 TYR   0.020   0.001   TYR A 134 
 ARG   0.004   0.000   ARG C  81 

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6832 (mm-30)
REVERT: A  180 MET cc_start: 0.8010 (mmp) cc_final: 0.7613 (mmm)
REVERT: A  475 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.8105 (m-80)
REVERT: A  494 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6462 (mm-30)
REVERT: C   74 ARG cc_start: 0.6951 (ptt-90) cc_final: 0.6704 (ptp90)
REVERT: C   99 GLN cc_start: 0.6427 (OUTLIER) cc_final: 0.6214 (mp10)
REVERT: B   42 LYS cc_start: 0.6216 (mttt) cc_final: 0.5731 (tptt)
REVERT: B   58 GLN cc_start: 0.5142 (OUTLIER) cc_final: 0.4490 (tp40)
  outliers start: 30
  outliers final: 25
  residues processed: 158
  average time/residue: 0.1394
  time to fit residues: 30.9882
Evaluate side-chains
  159 residues out of total 652 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 131
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 TRP
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  206 THR
Chi-restraints excluded: chain A residue  209 CYS
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  323 THR
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  391 ASN
Chi-restraints excluded: chain A residue  465 PHE
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  548 PHE
Chi-restraints excluded: chain A residue  611 SER
Chi-restraints excluded: chain C residue   99 GLN
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   46 TYR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   58 GLN
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   79 TYR
Chi-restraints excluded: chain B residue   90 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 65 optimal weight:    6.9990
   chunk 55 optimal weight:    8.9990
   chunk 47 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 62 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0980
   chunk 18 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 391 ASN
A 416 ASN
** C  57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 109 GLN
** C 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.186718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.170222 restraints weight = 9948.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.174026 restraints weight = 6192.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.176774 restraints weight = 4213.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.4187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.3894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.144   6326  Z= 0.374
  Angle     :  1.181  59.119   8619  Z= 0.686
  Chirality :  0.047   0.516    966
  Planarity :  0.007   0.163   1048
  Dihedral  :  6.407  77.247    961
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 18.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 26.77 %
    Favored  : 68.46 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.14 %
    Twisted Proline : 3.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.30), residues: 758
  helix:  0.78 (0.27), residues: 356
  sheet: -2.08 (0.44), residues: 101
  loop : -1.60 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.002   TRP A 541 
 HIS   0.007   0.001   HIS A 223 
 PHE   0.022   0.002   PHE A 440 
 TYR   0.072   0.002   TYR A 350 
 ARG   0.004   0.000   ARG A  79 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2224.24 seconds
wall clock time: 39 minutes 32.83 seconds (2372.83 seconds total)