Starting phenix.real_space_refine
on Thu Mar 13 09:49:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ria_19185/03_2025/8ria_19185.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ria_19185/03_2025/8ria_19185.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ria_19185/03_2025/8ria_19185.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ria_19185/03_2025/8ria_19185.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ria_19185/03_2025/8ria_19185.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ria_19185/03_2025/8ria_19185.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.028
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      36      5.16       5
     C    5642      2.51       5
     N    1464      2.21       5
     O    1644      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 8786
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 571, 4393
          Classifications: {'peptide': 571}
          Link IDs: {'PTRANS': 17, 'TRANS': 553}
    Chain: "B"
      Number of atoms: 4393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 571, 4393
          Classifications: {'peptide': 571}
          Link IDs: {'PTRANS': 17, 'TRANS': 553}
  Time building chain proxies: 5.23, per 1000 atoms: 0.60
  Number of scatterers: 8786
  At special positions: 0
  Unit cell: (75.57, 108.775, 135.11, 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      36     16.00
     O    1644      8.00
     N    1464      7.00
     C    5642      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.35
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2100

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 6 sheets defined
      69.8% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 23
    Processing helix  chain 'A' and resid 25 through 55
      Proline residue:  A  47  - end of helix
      removed outlier: 3.806A  pdb=" N   THR A  50 " --> pdb=" O   ILE A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 110
      removed outlier: 3.610A  pdb=" N   THR A  65 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 119
      removed outlier: 3.924A  pdb=" N   ASP A 116 " --> pdb=" O   VAL A 112 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   ALA A 119 " --> pdb=" O   PHE A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 163
      removed outlier: 3.788A  pdb=" N   VAL A 124 " --> pdb=" O   SER A 120 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   SER A 143 " --> pdb=" O   THR A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 210
      Proline residue:  A 175  - end of helix
      Proline residue:  A 183  - end of helix
    Processing helix  chain 'A' and resid 211 through 220
    Processing helix  chain 'A' and resid 221 through 276
      Proline residue:  A 252  - end of helix
    Processing helix  chain 'A' and resid 281 through 323
      removed outlier: 3.580A  pdb=" N   LEU A 288 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE A 294 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   MET A 295 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      Proline residue:  A 296  - end of helix
      removed outlier: 4.156A  pdb=" N   GLN A 299 " --> pdb=" O   MET A 295 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU A 307 " --> pdb=" O   PHE A 303 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   GLN A 308 " --> pdb=" O   PHE A 304 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU A 323 " --> pdb=" O   GLU A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 388
    Processing helix  chain 'A' and resid 409 through 417
      removed outlier: 3.506A  pdb=" N   TRP A 413 " --> pdb=" O   SER A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 438
      removed outlier: 4.317A  pdb=" N   ASN A 434 " --> pdb=" O   THR A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 455
    Processing helix  chain 'A' and resid 458 through 464
      removed outlier: 3.655A  pdb=" N   LEU A 464 " --> pdb=" O   PHE A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 496
    Processing helix  chain 'A' and resid 511 through 525
    Processing helix  chain 'A' and resid 537 through 542
    Processing helix  chain 'A' and resid 560 through 567
    Processing helix  chain 'A' and resid 571 through 580
    Processing helix  chain 'B' and resid 11 through 22
    Processing helix  chain 'B' and resid 25 through 57
      removed outlier: 3.752A  pdb=" N   LEU B  29 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ALA B  30 " --> pdb=" O   TYR B  26 " (cutoff:3.500A)
      Proline residue:  B  47  - end of helix
      removed outlier: 3.537A  pdb=" N   THR B  50 " --> pdb=" O   ILE B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 110
    Processing helix  chain 'B' and resid 112 through 117
      removed outlier: 4.394A  pdb=" N   ASP B 116 " --> pdb=" O   VAL B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 163
      removed outlier: 3.954A  pdb=" N   VAL B 124 " --> pdb=" O   SER B 120 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER B 143 " --> pdb=" O   THR B 139 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ILE B 146 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 210
      Proline residue:  B 175  - end of helix
      Proline residue:  B 183  - end of helix
    Processing helix  chain 'B' and resid 212 through 219
    Processing helix  chain 'B' and resid 221 through 275
      Proline residue:  B 252  - end of helix
    Processing helix  chain 'B' and resid 279 through 295
      removed outlier: 3.741A  pdb=" N   VAL B 284 " --> pdb=" O   ALA B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 323
      removed outlier: 4.551A  pdb=" N   GLN B 308 " --> pdb=" O   PHE B 304 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   LYS B 309 " --> pdb=" O   THR B 305 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   GLU B 323 " --> pdb=" O   GLU B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 388
    Processing helix  chain 'B' and resid 409 through 416
    Processing helix  chain 'B' and resid 431 through 438
      removed outlier: 4.202A  pdb=" N   ILE B 435 " --> pdb=" O   ILE B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 455
    Processing helix  chain 'B' and resid 456 through 461
      removed outlier: 3.853A  pdb=" N   PHE B 460 " --> pdb=" O   TYR B 456 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE B 461 " --> pdb=" O   ALA B 457 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 456 through 461'
    Processing helix  chain 'B' and resid 480 through 496
      removed outlier: 3.535A  pdb=" N   ASN B 496 " --> pdb=" O   ALA B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 524
    Processing helix  chain 'B' and resid 536 through 543
      removed outlier: 3.950A  pdb=" N   VAL B 540 " --> pdb=" O   ARG B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 562 through 571
      removed outlier: 3.681A  pdb=" N   ARG B 571 " --> pdb=" O   HIS B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 580
    Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 364
      removed outlier: 7.519A  pdb=" N   ALA A 362 " --> pdb=" O   ASP A 344 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   ASP A 344 " --> pdb=" O   ALA A 362 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   ILE A 364 " --> pdb=" O   GLN A 342 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   GLN A 342 " --> pdb=" O   ILE A 364 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 370 through 373
    Processing sheet with id=AA3, first strand: chain 'A' and resid 499 through 502
      removed outlier: 3.505A  pdb=" N   ILE A 531 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 360 through 364
      removed outlier: 7.396A  pdb=" N   ALA B 362 " --> pdb=" O   ASP B 344 " (cutoff:3.500A)
      removed outlier: 5.252A  pdb=" N   ASP B 344 " --> pdb=" O   ALA B 362 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   ILE B 364 " --> pdb=" O   GLN B 342 " (cutoff:3.500A)
      removed outlier: 5.304A  pdb=" N   GLN B 342 " --> pdb=" O   ILE B 364 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 499 through 502
      removed outlier: 6.470A  pdb=" N   THR B 370 " --> pdb=" O   VAL B 532 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   VAL B 369 " --> pdb=" O   GLN B 545 " (cutoff:3.500A)
      removed outlier: 8.292A  pdb=" N   LEU B 547 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   ALA B 371 " --> pdb=" O   LEU B 547 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   VAL B 549 " --> pdb=" O   ALA B 371 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   VAL B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   PHE B 548 " --> pdb=" O   THR B 555 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 429 through 430

    610 hydrogen bonds defined for protein.
    1812 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: 2.57

  Time building geometry restraints manager: 2.75 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1953
        1.33 -     1.45: 1743
        1.45 -     1.57: 5153
        1.57 -     1.69: 1
        1.69 -     1.81: 70
  Bond restraints: 8920
  Sorted by residual:
  bond pdb=" N   PRO B 497 "
       pdb=" CD  PRO B 497 "
    ideal  model  delta    sigma   weight residual
    1.473  1.609 -0.136 1.40e-02 5.10e+03 9.45e+01
  bond pdb=" N   ASN B  23 "
       pdb=" CA  ASN B  23 "
    ideal  model  delta    sigma   weight residual
    1.457  1.500 -0.043 1.41e-02 5.03e+03 9.37e+00
  bond pdb=" N   PRO B 465 "
       pdb=" CD  PRO B 465 "
    ideal  model  delta    sigma   weight residual
    1.473  1.508 -0.035 1.40e-02 5.10e+03 6.30e+00
  bond pdb=" CA  PRO A  24 "
       pdb=" C   PRO A  24 "
    ideal  model  delta    sigma   weight residual
    1.524  1.503  0.022 9.20e-03 1.18e+04 5.48e+00
  bond pdb=" CA  ASP B 116 "
       pdb=" C   ASP B 116 "
    ideal  model  delta    sigma   weight residual
    1.522  1.491  0.031 1.38e-02 5.25e+03 5.04e+00
  ... (remaining 8915 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.69: 11933
        7.69 -    15.38: 90
       15.38 -    23.08: 34
       23.08 -    30.77: 11
       30.77 -    38.46: 4
  Bond angle restraints: 12072
  Sorted by residual:
  angle pdb=" N   PHE B 460 "
        pdb=" CA  PHE B 460 "
        pdb=" C   PHE B 460 "
      ideal   model   delta    sigma   weight residual
     112.89  150.29  -37.40 1.24e+00 6.50e-01 9.10e+02
  angle pdb=" N   ASN A 163 "
        pdb=" CA  ASN A 163 "
        pdb=" C   ASN A 163 "
      ideal   model   delta    sigma   weight residual
     109.24   74.83   34.41 1.67e+00 3.59e-01 4.24e+02
  angle pdb=" N   PHE A  57 "
        pdb=" CA  PHE A  57 "
        pdb=" C   PHE A  57 "
      ideal   model   delta    sigma   weight residual
     113.31  151.77  -38.46 2.04e+00 2.40e-01 3.55e+02
  angle pdb=" C   THR B  22 "
        pdb=" CA  THR B  22 "
        pdb=" CB  THR B  22 "
      ideal   model   delta    sigma   weight residual
     111.68   81.16   30.52 1.67e+00 3.59e-01 3.34e+02
  angle pdb=" N   TRP A 164 "
        pdb=" CA  TRP A 164 "
        pdb=" C   TRP A 164 "
      ideal   model   delta    sigma   weight residual
     112.04  136.11  -24.07 1.44e+00 4.82e-01 2.79e+02
  ... (remaining 12067 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.07: 4787
       16.07 -    32.15: 512
       32.15 -    48.22: 82
       48.22 -    64.29: 9
       64.29 -    80.37: 8
  Dihedral angle restraints: 5398
    sinusoidal: 2128
      harmonic: 3270
  Sorted by residual:
  dihedral pdb=" C   THR B  22 "
           pdb=" N   THR B  22 "
           pdb=" CA  THR B  22 "
           pdb=" CB  THR B  22 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00  -81.86  -40.14     0      2.50e+00 1.60e-01 2.58e+02
  dihedral pdb=" C   ASP B 510 "
           pdb=" N   ASP B 510 "
           pdb=" CA  ASP B 510 "
           pdb=" CB  ASP B 510 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -156.44   33.84     0      2.50e+00 1.60e-01 1.83e+02
  dihedral pdb=" C   ASP A 510 "
           pdb=" N   ASP A 510 "
           pdb=" CA  ASP A 510 "
           pdb=" CB  ASP A 510 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -150.97   28.37     0      2.50e+00 1.60e-01 1.29e+02
  ... (remaining 5395 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.283: 1426
       0.283 -    0.565: 21
       0.565 -    0.848: 7
       0.848 -    1.131: 3
       1.131 -    1.414: 5
  Chirality restraints: 1462
  Sorted by residual:
  chirality pdb=" CA  ASP B 510 "
            pdb=" N   ASP B 510 "
            pdb=" C   ASP B 510 "
            pdb=" CB  ASP B 510 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.10    1.41 2.00e-01 2.50e+01 5.00e+01
  chirality pdb=" CA  PHE A  57 "
            pdb=" N   PHE A  57 "
            pdb=" C   PHE A  57 "
            pdb=" CB  PHE A  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.10    1.41 2.00e-01 2.50e+01 4.95e+01
  chirality pdb=" CA  ASP A 510 "
            pdb=" N   ASP A 510 "
            pdb=" C   ASP A 510 "
            pdb=" CB  ASP A 510 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.32    1.19 2.00e-01 2.50e+01 3.55e+01
  ... (remaining 1459 not shown)

  Planarity restraints: 1514
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 496 "    0.131 5.00e-02 4.00e+02   1.89e-01 5.74e+01
        pdb=" N   PRO B 497 "   -0.327 5.00e-02 4.00e+02
        pdb=" CA  PRO B 497 "    0.112 5.00e-02 4.00e+02
        pdb=" CD  PRO B 497 "    0.084 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 464 "   -0.065 5.00e-02 4.00e+02   9.77e-02 1.53e+01
        pdb=" N   PRO B 465 "    0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO B 465 "   -0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO B 465 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B  23 "   -0.064 5.00e-02 4.00e+02   9.63e-02 1.48e+01
        pdb=" N   PRO B  24 "    0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO B  24 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO B  24 "   -0.057 5.00e-02 4.00e+02
  ... (remaining 1511 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 125
        2.52 -     3.11: 7804
        3.11 -     3.71: 14696
        3.71 -     4.30: 19355
        4.30 -     4.90: 29808
  Nonbonded interactions: 71788
  Sorted by model distance:
  nonbonded pdb=" O   HIS B 560 "
            pdb=" CG  HIS B 560 "
     model   vdw
     1.922 3.260
  nonbonded pdb=" O   THR B  22 "
            pdb=" CB  THR B  22 "
     model   vdw
     1.946 2.776
  nonbonded pdb=" O   ILE A 334 "
            pdb=" CG2 ILE A 334 "
     model   vdw
     1.964 3.460
  nonbonded pdb=" N   ASN A 163 "
            pdb=" O   ASN A 163 "
     model   vdw
     2.011 2.496
  nonbonded pdb=" O   LEU A 159 "
            pdb=" O   ASN A 163 "
     model   vdw
     2.020 3.040
  ... (remaining 71783 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: 0.05
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:             0.540
  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:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.830
  Find NCS groups from input model:        0.290
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.136   8920  Z= 0.382
  Angle     :  1.994  38.462  12072  Z= 1.215
  Chirality :  0.121   1.414   1462
  Planarity :  0.009   0.189   1514
  Dihedral  : 13.299  80.367   3298
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 29.52
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  : 10.28 %
    Favored  : 89.10 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.35 %
    Favored  : 98.44 %
  Cbeta Deviations :  4.19 %
  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: -1.40 (0.24), residues: 1138
  helix:  0.15 (0.18), residues: 753
  sheet: -0.27 (0.62), residues: 74
  loop : -3.81 (0.30), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP B 413 
 HIS   0.007   0.002   HIS A 141 
 PHE   0.038   0.003   PHE B  74 
 TYR   0.022   0.002   TYR B 289 
 ARG   0.010   0.001   ARG A 414 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 197
  time to evaluate  : 0.922 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 ASN cc_start: 0.9304 (m-40) cc_final: 0.9029 (m-40)
REVERT: A  205 LEU cc_start: 0.9660 (tp) cc_final: 0.9427 (tp)
REVERT: A  427 MET cc_start: 0.8340 (mpp) cc_final: 0.7817 (mpp)
REVERT: A  454 MET cc_start: 0.8265 (mmp) cc_final: 0.8060 (mpp)
REVERT: B  208 GLN cc_start: 0.9372 (tm-30) cc_final: 0.9053 (tm-30)
REVERT: B  225 GLU cc_start: 0.8799 (tp30) cc_final: 0.8191 (tp30)
REVERT: B  292 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8657 (tm-30)
REVERT: B  410 LEU cc_start: 0.9481 (tp) cc_final: 0.9251 (tp)
REVERT: B  413 TRP cc_start: 0.8416 (t60) cc_final: 0.8031 (t60)
  outliers start: 2
  outliers final: 1
  residues processed: 199
  average time/residue: 0.1726
  time to fit residues: 49.5519
Evaluate side-chains
  148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 147
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 29 optimal weight:    0.7980
   chunk 58 optimal weight:    6.9990
   chunk 46 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 34 optimal weight:   10.0000
   chunk 54 optimal weight:    0.0770
   chunk 66 optimal weight:    2.9990
   chunk 103 optimal weight:    8.9990
   overall best weight:    1.5744

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

Flipped N/Q/H residues before XYZ refinement:
A 163 ASN
A 272 GLN
A 338 HIS
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 416 HIS
** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 ASN
** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 519 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.125079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.084402 restraints weight = 25080.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.087172 restraints weight = 16096.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.089137 restraints weight = 11707.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.1498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8920  Z= 0.254
  Angle     :  0.816  12.372  12072  Z= 0.427
  Chirality :  0.046   0.297   1462
  Planarity :  0.007   0.078   1514
  Dihedral  :  5.935  28.490   1222
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 18.47
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.00 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  6.86 %
    Favored  : 92.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.25), residues: 1138
  helix:  0.73 (0.19), residues: 754
  sheet:  0.34 (0.67), residues: 63
  loop : -3.72 (0.29), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 413 
 HIS   0.007   0.002   HIS B 560 
 PHE   0.028   0.002   PHE B 460 
 TYR   0.018   0.002   TYR A 408 
 ARG   0.004   0.000   ARG B 536 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 202
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9486 (ttmt) cc_final: 0.9128 (tptm)
REVERT: A   91 ASN cc_start: 0.9246 (m-40) cc_final: 0.8996 (m-40)
REVERT: A  101 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8543 (mt-10)
REVERT: A  131 THR cc_start: 0.9356 (p) cc_final: 0.9075 (p)
REVERT: A  231 MET cc_start: 0.8917 (mpp) cc_final: 0.8709 (mpp)
REVERT: A  317 MET cc_start: 0.8926 (mmt) cc_final: 0.8535 (mmm)
REVERT: A  414 ARG cc_start: 0.9177 (tpp80) cc_final: 0.8789 (ttm-80)
REVERT: A  427 MET cc_start: 0.8198 (mpp) cc_final: 0.7642 (mpp)
REVERT: A  567 HIS cc_start: 0.7143 (t-90) cc_final: 0.6752 (p90)
REVERT: B  208 GLN cc_start: 0.9366 (tm-30) cc_final: 0.9139 (tm-30)
REVERT: B  225 GLU cc_start: 0.8825 (tp30) cc_final: 0.8134 (tp30)
REVERT: B  413 TRP cc_start: 0.8268 (t60) cc_final: 0.8042 (t60)
REVERT: B  500 LEU cc_start: 0.9242 (tp) cc_final: 0.9027 (tp)
REVERT: B  501 MET cc_start: 0.9345 (ppp) cc_final: 0.9057 (ppp)
  outliers start: 4
  outliers final: 1
  residues processed: 205
  average time/residue: 0.1784
  time to fit residues: 53.0046
Evaluate side-chains
  154 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 92 optimal weight:   20.0000
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 110 optimal weight:   40.0000
   chunk 9 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.125768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.086038 restraints weight = 25505.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.088954 restraints weight = 16216.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.091036 restraints weight = 11668.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8920  Z= 0.222
  Angle     :  0.760  11.717  12072  Z= 0.397
  Chirality :  0.046   0.246   1462
  Planarity :  0.006   0.074   1514
  Dihedral  :  5.754  34.130   1222
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 17.69
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  8.35 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  6.13 %
    Favored  : 93.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -0.54 (0.25), residues: 1138
  helix:  0.90 (0.18), residues: 757
  sheet:  0.31 (0.67), residues: 63
  loop : -3.75 (0.29), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 413 
 HIS   0.004   0.001   HIS B 141 
 PHE   0.022   0.002   PHE B 304 
 TYR   0.017   0.002   TYR B 408 
 ARG   0.008   0.000   ARG B 345 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 197
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9181 (tttt) cc_final: 0.8813 (ttmt)
REVERT: A   91 ASN cc_start: 0.9182 (m-40) cc_final: 0.8944 (m-40)
REVERT: A  101 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8413 (tt0)
REVERT: A  414 ARG cc_start: 0.9109 (tpp80) cc_final: 0.8487 (ttm110)
REVERT: A  427 MET cc_start: 0.8201 (mpp) cc_final: 0.7640 (mpp)
REVERT: A  567 HIS cc_start: 0.7088 (t-90) cc_final: 0.6686 (p90)
REVERT: B  208 GLN cc_start: 0.9484 (tm-30) cc_final: 0.9084 (tm-30)
REVERT: B  217 LYS cc_start: 0.9347 (tptt) cc_final: 0.8782 (tptt)
REVERT: B  225 GLU cc_start: 0.8833 (tp30) cc_final: 0.8100 (tp30)
REVERT: B  413 TRP cc_start: 0.8271 (t60) cc_final: 0.7987 (t60)
REVERT: B  454 MET cc_start: 0.8647 (mmp) cc_final: 0.8428 (mmm)
REVERT: B  485 GLN cc_start: 0.9025 (pp30) cc_final: 0.8712 (pp30)
  outliers start: 2
  outliers final: 0
  residues processed: 198
  average time/residue: 0.1795
  time to fit residues: 51.1427
Evaluate side-chains
  155 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 2 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9980
   chunk 93 optimal weight:   50.0000
   chunk 56 optimal weight:   20.0000
   chunk 107 optimal weight:    8.9990
   chunk 80 optimal weight:    7.9990
   chunk 67 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   overall best weight:    2.5784

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

Flipped N/Q/H residues before XYZ refinement:
** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 HIS
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 ASN
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 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 = 0.3977 r_free = 0.3977 target = 0.125080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.083967 restraints weight = 25546.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.086754 restraints weight = 16508.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.088737 restraints weight = 12035.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.2219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8920  Z= 0.271
  Angle     :  0.781  12.350  12072  Z= 0.410
  Chirality :  0.045   0.247   1462
  Planarity :  0.006   0.074   1514
  Dihedral  :  5.690  36.048   1222
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 18.69
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  8.44 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.99 %
    Favored  : 94.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -0.64 (0.25), residues: 1138
  helix:  0.81 (0.18), residues: 755
  sheet:  0.01 (0.66), residues: 63
  loop : -3.63 (0.29), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 104 
 HIS   0.005   0.001   HIS A 535 
 PHE   0.056   0.003   PHE A 384 
 TYR   0.015   0.002   TYR A 408 
 ARG   0.008   0.000   ARG B 345 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 193
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9130 (tttt) cc_final: 0.8737 (tppt)
REVERT: A   91 ASN cc_start: 0.9256 (m-40) cc_final: 0.9028 (m-40)
REVERT: A  101 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8481 (tt0)
REVERT: A  131 THR cc_start: 0.9357 (p) cc_final: 0.9104 (p)
REVERT: A  317 MET cc_start: 0.8927 (mmt) cc_final: 0.8407 (mmm)
REVERT: A  427 MET cc_start: 0.8212 (mpp) cc_final: 0.7612 (mpp)
REVERT: A  501 MET cc_start: 0.9222 (tmm) cc_final: 0.8942 (tmm)
REVERT: A  567 HIS cc_start: 0.7028 (t-90) cc_final: 0.6558 (p-80)
REVERT: B  217 LYS cc_start: 0.9390 (tptt) cc_final: 0.9175 (tptt)
REVERT: B  292 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8447 (tm-30)
REVERT: B  295 MET cc_start: 0.7028 (ttt) cc_final: 0.6793 (ttt)
REVERT: B  413 TRP cc_start: 0.8291 (t60) cc_final: 0.8090 (t60)
REVERT: B  454 MET cc_start: 0.8651 (mmp) cc_final: 0.8426 (mmm)
REVERT: B  485 GLN cc_start: 0.8991 (pp30) cc_final: 0.8680 (pp30)
  outliers start: 2
  outliers final: 0
  residues processed: 195
  average time/residue: 0.1805
  time to fit residues: 50.5885
Evaluate side-chains
  150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 107 optimal weight:   40.0000
   chunk 96 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 76 optimal weight:    7.9990
   chunk 91 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   chunk 94 optimal weight:    6.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 272 GLN
A 338 HIS
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 ASN
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 561 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.126291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.085958 restraints weight = 25405.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.088926 restraints weight = 16091.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.091013 restraints weight = 11542.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8920  Z= 0.218
  Angle     :  0.761  11.995  12072  Z= 0.394
  Chirality :  0.046   0.238   1462
  Planarity :  0.006   0.072   1514
  Dihedral  :  5.613  35.228   1222
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 17.41
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  8.08 %
    Favored  : 91.56 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  4.26 %
    Favored  : 95.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -0.50 (0.25), residues: 1138
  helix:  0.98 (0.19), residues: 752
  sheet: -0.04 (0.67), residues: 63
  loop : -3.69 (0.29), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 104 
 HIS   0.002   0.001   HIS B 141 
 PHE   0.037   0.002   PHE B  74 
 TYR   0.028   0.002   TYR A 408 
 ARG   0.009   0.000   ARG B 345 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 201
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9056 (tttt) cc_final: 0.8650 (ttmm)
REVERT: A   91 ASN cc_start: 0.9222 (m-40) cc_final: 0.8990 (m-40)
REVERT: A  131 THR cc_start: 0.9286 (p) cc_final: 0.8920 (p)
REVERT: A  225 GLU cc_start: 0.8717 (tp30) cc_final: 0.7677 (tp30)
REVERT: A  294 ILE cc_start: 0.9019 (tt) cc_final: 0.8750 (tp)
REVERT: A  317 MET cc_start: 0.8856 (mmt) cc_final: 0.8360 (mmm)
REVERT: A  365 GLU cc_start: 0.9031 (tp30) cc_final: 0.8754 (tp30)
REVERT: A  384 PHE cc_start: 0.8399 (m-10) cc_final: 0.8164 (m-80)
REVERT: A  414 ARG cc_start: 0.9199 (tpp80) cc_final: 0.8527 (ttp-110)
REVERT: A  427 MET cc_start: 0.8206 (mpp) cc_final: 0.7521 (mpp)
REVERT: A  456 TYR cc_start: 0.6658 (t80) cc_final: 0.6382 (t80)
REVERT: A  567 HIS cc_start: 0.7046 (t-90) cc_final: 0.6575 (p-80)
REVERT: B  217 LYS cc_start: 0.9290 (tptt) cc_final: 0.8615 (tptt)
REVERT: B  225 GLU cc_start: 0.8753 (tp30) cc_final: 0.8110 (tp30)
REVERT: B  292 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8384 (tm-30)
REVERT: B  295 MET cc_start: 0.6916 (ttt) cc_final: 0.6673 (ttt)
REVERT: B  410 LEU cc_start: 0.9454 (tp) cc_final: 0.9238 (tp)
REVERT: B  413 TRP cc_start: 0.8415 (t60) cc_final: 0.8020 (t60)
REVERT: B  454 MET cc_start: 0.8639 (mmp) cc_final: 0.8401 (mmm)
  outliers start: 4
  outliers final: 1
  residues processed: 204
  average time/residue: 0.1748
  time to fit residues: 51.7584
Evaluate side-chains
  157 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 156
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 44 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 3 optimal weight:    0.6980
   chunk 51 optimal weight:   20.0000
   chunk 105 optimal weight:    6.9990
   chunk 29 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 338 HIS
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 561 HIS
B  91 ASN
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 467 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.127536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.087469 restraints weight = 25279.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.090558 restraints weight = 15907.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.092735 restraints weight = 11336.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8920  Z= 0.210
  Angle     :  0.757  12.183  12072  Z= 0.390
  Chirality :  0.046   0.220   1462
  Planarity :  0.006   0.074   1514
  Dihedral  :  5.566  34.852   1222
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 16.24
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  8.00 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.91 %
    Favored  : 96.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.25), residues: 1138
  helix:  1.06 (0.19), residues: 754
  sheet: -0.02 (0.66), residues: 63
  loop : -3.70 (0.29), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 164 
 HIS   0.004   0.001   HIS B 141 
 PHE   0.035   0.002   PHE B  74 
 TYR   0.021   0.002   TYR A 268 
 ARG   0.011   0.000   ARG B 345 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 194
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9045 (tttt) cc_final: 0.8688 (tptt)
REVERT: A   91 ASN cc_start: 0.9045 (m-40) cc_final: 0.8829 (m-40)
REVERT: A  101 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8498 (mt-10)
REVERT: A  197 ASP cc_start: 0.8957 (t70) cc_final: 0.8484 (m-30)
REVERT: A  231 MET cc_start: 0.8985 (mpp) cc_final: 0.8722 (mpp)
REVERT: A  365 GLU cc_start: 0.9070 (tp30) cc_final: 0.8812 (tp30)
REVERT: A  384 PHE cc_start: 0.8539 (m-10) cc_final: 0.8242 (m-80)
REVERT: A  414 ARG cc_start: 0.9288 (tpp80) cc_final: 0.8642 (ttp-110)
REVERT: A  427 MET cc_start: 0.8255 (mpp) cc_final: 0.7444 (mpp)
REVERT: A  456 TYR cc_start: 0.6629 (t80) cc_final: 0.6390 (t80)
REVERT: A  567 HIS cc_start: 0.7053 (t-90) cc_final: 0.6587 (p-80)
REVERT: B  217 LYS cc_start: 0.9323 (tptt) cc_final: 0.8741 (tptt)
REVERT: B  225 GLU cc_start: 0.8792 (tp30) cc_final: 0.8118 (tp30)
REVERT: B  295 MET cc_start: 0.6797 (ttt) cc_final: 0.6557 (ttt)
REVERT: B  410 LEU cc_start: 0.9465 (tp) cc_final: 0.9207 (tp)
REVERT: B  413 TRP cc_start: 0.8485 (t60) cc_final: 0.8078 (t60)
REVERT: B  454 MET cc_start: 0.8626 (mmp) cc_final: 0.8389 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 195
  average time/residue: 0.1783
  time to fit residues: 49.9328
Evaluate side-chains
  154 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 35 optimal weight:   20.0000
   chunk 20 optimal weight:    1.9990
   chunk 101 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9990
   chunk 36 optimal weight:    9.9990
   chunk 83 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   chunk 55 optimal weight:    8.9990
   chunk 67 optimal weight:    0.1980
   chunk 13 optimal weight:    2.9990
   overall best weight:    2.6388

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

Flipped N/Q/H residues before XYZ refinement:
A 272 GLN
A 338 HIS
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 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 = 0.3963 r_free = 0.3963 target = 0.124196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.083634 restraints weight = 25958.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.086460 restraints weight = 16579.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.088437 restraints weight = 12006.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.2996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   8920  Z= 0.278
  Angle     :  0.790  12.735  12072  Z= 0.411
  Chirality :  0.046   0.247   1462
  Planarity :  0.006   0.071   1514
  Dihedral  :  5.609  39.042   1222
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 18.86
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  8.61 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -0.62 (0.25), residues: 1138
  helix:  0.88 (0.19), residues: 759
  sheet: -0.07 (0.65), residues: 63
  loop : -3.81 (0.28), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 104 
 HIS   0.005   0.001   HIS B 141 
 PHE   0.030   0.002   PHE B  74 
 TYR   0.016   0.002   TYR B 408 
 ARG   0.015   0.001   ARG B 345 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9208 (tttt) cc_final: 0.8802 (tptt)
REVERT: A   91 ASN cc_start: 0.9255 (m-40) cc_final: 0.9023 (m-40)
REVERT: A  231 MET cc_start: 0.8990 (mpp) cc_final: 0.8790 (mpp)
REVERT: A  317 MET cc_start: 0.8640 (mmt) cc_final: 0.8374 (mmm)
REVERT: A  365 GLU cc_start: 0.9109 (tp30) cc_final: 0.8840 (tp30)
REVERT: A  384 PHE cc_start: 0.8539 (m-10) cc_final: 0.8314 (m-80)
REVERT: A  414 ARG cc_start: 0.9235 (tpp80) cc_final: 0.8591 (ttp-110)
REVERT: A  427 MET cc_start: 0.8259 (mpp) cc_final: 0.7331 (mpp)
REVERT: A  456 TYR cc_start: 0.6720 (t80) cc_final: 0.6365 (t80)
REVERT: A  567 HIS cc_start: 0.6872 (t-90) cc_final: 0.6360 (p-80)
REVERT: B  217 LYS cc_start: 0.9370 (tptt) cc_final: 0.8789 (tptt)
REVERT: B  225 GLU cc_start: 0.8888 (tp30) cc_final: 0.8162 (tp30)
REVERT: B  292 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8398 (tm-30)
REVERT: B  410 LEU cc_start: 0.9505 (tp) cc_final: 0.9277 (tp)
REVERT: B  413 TRP cc_start: 0.8461 (t60) cc_final: 0.8098 (t60)
REVERT: B  454 MET cc_start: 0.8452 (mmp) cc_final: 0.8224 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.1796
  time to fit residues: 48.5404
Evaluate side-chains
  153 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 60 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 50 optimal weight:    5.9990
   chunk 92 optimal weight:    5.9990
   chunk 94 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 483 GLN
B  91 ASN
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 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 = 0.4001 r_free = 0.4001 target = 0.126556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.085828 restraints weight = 25939.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.088809 restraints weight = 16579.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.090910 restraints weight = 11922.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.3239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8920  Z= 0.222
  Angle     :  0.780  12.994  12072  Z= 0.403
  Chirality :  0.046   0.220   1462
  Planarity :  0.006   0.076   1514
  Dihedral  :  5.574  37.211   1222
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 17.13
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.38 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -0.56 (0.25), residues: 1138
  helix:  0.93 (0.19), residues: 758
  sheet: -0.51 (0.64), residues: 68
  loop : -3.72 (0.29), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 104 
 HIS   0.004   0.001   HIS B 561 
 PHE   0.039   0.002   PHE A 286 
 TYR   0.013   0.001   TYR A 268 
 ARG   0.015   0.000   ARG B 345 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9201 (tttt) cc_final: 0.8852 (ttmt)
REVERT: A   91 ASN cc_start: 0.9192 (m-40) cc_final: 0.8979 (m-40)
REVERT: A  197 ASP cc_start: 0.9070 (t0) cc_final: 0.8649 (m-30)
REVERT: A  231 MET cc_start: 0.8969 (mpp) cc_final: 0.8741 (mpp)
REVERT: A  365 GLU cc_start: 0.9110 (tp30) cc_final: 0.8845 (tp30)
REVERT: A  384 PHE cc_start: 0.8808 (m-10) cc_final: 0.8519 (m-80)
REVERT: A  427 MET cc_start: 0.8227 (mpp) cc_final: 0.7622 (mpp)
REVERT: A  456 TYR cc_start: 0.6674 (t80) cc_final: 0.6379 (t80)
REVERT: A  489 ILE cc_start: 0.8995 (pt) cc_final: 0.8774 (pt)
REVERT: A  501 MET cc_start: 0.9225 (tmm) cc_final: 0.8974 (tmm)
REVERT: A  567 HIS cc_start: 0.6904 (t-90) cc_final: 0.6404 (p-80)
REVERT: B  212 GLU cc_start: 0.9216 (mp0) cc_final: 0.8908 (mt-10)
REVERT: B  225 GLU cc_start: 0.8784 (tp30) cc_final: 0.8106 (tp30)
REVERT: B  292 GLN cc_start: 0.8922 (tm-30) cc_final: 0.8401 (tm-30)
REVERT: B  410 LEU cc_start: 0.9509 (tp) cc_final: 0.9259 (tp)
REVERT: B  413 TRP cc_start: 0.8260 (t60) cc_final: 0.8054 (t60)
REVERT: B  454 MET cc_start: 0.8476 (mmp) cc_final: 0.8195 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.1829
  time to fit residues: 49.3815
Evaluate side-chains
  156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 70 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   chunk 34 optimal weight:    6.9990
   chunk 66 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 67 optimal weight:    5.9990
   chunk 104 optimal weight:    0.6980
   chunk 18 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 483 GLN
B  91 ASN
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 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 = 0.3976 r_free = 0.3976 target = 0.124932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.085604 restraints weight = 25563.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.088407 restraints weight = 16305.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.090602 restraints weight = 11828.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8920  Z= 0.232
  Angle     :  0.788  12.884  12072  Z= 0.405
  Chirality :  0.046   0.225   1462
  Planarity :  0.006   0.067   1514
  Dihedral  :  5.544  37.945   1222
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 16.96
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.73 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -0.58 (0.25), residues: 1138
  helix:  0.93 (0.19), residues: 757
  sheet: -0.50 (0.65), residues: 68
  loop : -3.75 (0.29), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 104 
 HIS   0.004   0.001   HIS B 141 
 PHE   0.025   0.002   PHE A 286 
 TYR   0.029   0.001   TYR B 408 
 ARG   0.011   0.000   ARG B 345 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9112 (tttt) cc_final: 0.8731 (ttmt)
REVERT: A  131 THR cc_start: 0.9357 (p) cc_final: 0.9053 (p)
REVERT: A  162 MET cc_start: 0.8809 (tpp) cc_final: 0.8603 (tpp)
REVERT: A  197 ASP cc_start: 0.9090 (t0) cc_final: 0.8673 (m-30)
REVERT: A  317 MET cc_start: 0.8851 (mmt) cc_final: 0.8440 (mmm)
REVERT: A  365 GLU cc_start: 0.9083 (tp30) cc_final: 0.8820 (tp30)
REVERT: A  384 PHE cc_start: 0.8809 (m-10) cc_final: 0.8523 (m-80)
REVERT: A  414 ARG cc_start: 0.9164 (tpp80) cc_final: 0.8879 (ttp-110)
REVERT: A  427 MET cc_start: 0.8215 (mpp) cc_final: 0.7664 (mpp)
REVERT: A  456 TYR cc_start: 0.6762 (t80) cc_final: 0.6442 (t80)
REVERT: A  501 MET cc_start: 0.9218 (tmm) cc_final: 0.9006 (tmm)
REVERT: A  567 HIS cc_start: 0.6890 (t-90) cc_final: 0.6408 (p90)
REVERT: B  212 GLU cc_start: 0.9210 (mp0) cc_final: 0.8938 (mt-10)
REVERT: B  225 GLU cc_start: 0.8825 (tp30) cc_final: 0.8098 (tp30)
REVERT: B  292 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8339 (tm-30)
REVERT: B  410 LEU cc_start: 0.9520 (tp) cc_final: 0.9279 (tp)
REVERT: B  413 TRP cc_start: 0.8449 (t60) cc_final: 0.8073 (t60)
REVERT: B  454 MET cc_start: 0.8461 (mmp) cc_final: 0.8189 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.1740
  time to fit residues: 45.2235
Evaluate side-chains
  155 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 52 optimal weight:    7.9990
   chunk 74 optimal weight:    0.0770
   chunk 100 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 77 optimal weight:    0.0020
   chunk 102 optimal weight:    0.9980
   overall best weight:    0.5546

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

Flipped N/Q/H residues before XYZ refinement:
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.128636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.087891 restraints weight = 25766.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.090932 restraints weight = 16518.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.093055 restraints weight = 11924.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.3625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8920  Z= 0.206
  Angle     :  0.786  12.964  12072  Z= 0.399
  Chirality :  0.047   0.231   1462
  Planarity :  0.006   0.087   1514
  Dihedral  :  5.509  35.269   1222
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.56 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -0.43 (0.25), residues: 1138
  helix:  1.03 (0.19), residues: 759
  sheet: -0.41 (0.66), residues: 68
  loop : -3.70 (0.29), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 104 
 HIS   0.003   0.001   HIS B 561 
 PHE   0.027   0.002   PHE A 286 
 TYR   0.028   0.001   TYR B 408 
 ARG   0.019   0.001   ARG B 345 

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.053 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9106 (tttt) cc_final: 0.8708 (tppt)
REVERT: A   59 MET cc_start: 0.7306 (mpp) cc_final: 0.7067 (mpp)
REVERT: A   91 ASN cc_start: 0.9343 (m-40) cc_final: 0.9049 (m-40)
REVERT: A  101 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8501 (mt-10)
REVERT: A  175 PRO cc_start: 0.8632 (Cg_exo) cc_final: 0.8366 (Cg_endo)
REVERT: A  197 ASP cc_start: 0.9053 (t0) cc_final: 0.8591 (m-30)
REVERT: A  317 MET cc_start: 0.8774 (mmt) cc_final: 0.8419 (mmm)
REVERT: A  365 GLU cc_start: 0.9091 (tp30) cc_final: 0.8825 (tp30)
REVERT: A  384 PHE cc_start: 0.8827 (m-10) cc_final: 0.8532 (m-80)
REVERT: A  414 ARG cc_start: 0.9276 (tpp80) cc_final: 0.8792 (ttp-110)
REVERT: A  427 MET cc_start: 0.8079 (mpp) cc_final: 0.7691 (mpp)
REVERT: A  456 TYR cc_start: 0.6724 (t80) cc_final: 0.6423 (t80)
REVERT: B  212 GLU cc_start: 0.9085 (mp0) cc_final: 0.8813 (mt-10)
REVERT: B  225 GLU cc_start: 0.8713 (tp30) cc_final: 0.8001 (tp30)
REVERT: B  292 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8253 (tm-30)
REVERT: B  410 LEU cc_start: 0.9506 (tp) cc_final: 0.9249 (tp)
REVERT: B  413 TRP cc_start: 0.8375 (t60) cc_final: 0.8026 (t60)
REVERT: B  454 MET cc_start: 0.8446 (mmp) cc_final: 0.8162 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.1760
  time to fit residues: 49.1337
Evaluate side-chains
  161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 37 optimal weight:    5.9990
   chunk 58 optimal weight:    7.9990
   chunk 62 optimal weight:    5.9990
   chunk 48 optimal weight:    9.9990
   chunk 50 optimal weight:    6.9990
   chunk 94 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.127835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.086771 restraints weight = 25819.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.089644 restraints weight = 16701.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.091761 restraints weight = 12172.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8920  Z= 0.216
  Angle     :  0.782  12.869  12072  Z= 0.397
  Chirality :  0.046   0.206   1462
  Planarity :  0.006   0.080   1514
  Dihedral  :  5.417  36.900   1222
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 15.90
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.56 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -0.40 (0.25), residues: 1138
  helix:  1.05 (0.19), residues: 759
  sheet: -0.36 (0.66), residues: 68
  loop : -3.70 (0.30), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 104 
 HIS   0.003   0.001   HIS B 561 
 PHE   0.035   0.002   PHE A 160 
 TYR   0.025   0.001   TYR B 408 
 ARG   0.017   0.000   ARG B 345 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2631.65 seconds
wall clock time: 46 minutes 35.48 seconds (2795.48 seconds total)