Starting phenix.real_space_refine
on Wed Jan 15 21:42:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ria_19185/01_2025/8ria_19185.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ria_19185/01_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_19185/01_2025/8ria_19185.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ria_19185/01_2025/8ria_19185.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ria_19185/01_2025/8ria_19185.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ria_19185/01_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-5571/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: 5.26, 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: 2.42
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.89
  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: 2.49

  Time building geometry restraints manager: 2.76 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:             0.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     22.640
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.830
-------------------------------------------------------------------------------
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  : 1.004 
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: 0.1823
  time to fit residues: 52.0686
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  : 1.025 
-------------------------------------------------------------------------------
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 = 51)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.084406 restraints weight = 25080.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.087169 restraints weight = 16083.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.089075 restraints weight = 11702.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
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  : 1.062 
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: 0.9129 (tptm)
REVERT: A   91 ASN cc_start: 0.9246 (m-40) cc_final: 0.8998 (m-40)
REVERT: A  101 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8546 (mt-10)
REVERT: A  131 THR cc_start: 0.9356 (p) cc_final: 0.9073 (p)
REVERT: A  231 MET cc_start: 0.8919 (mpp) cc_final: 0.8711 (mpp)
REVERT: A  317 MET cc_start: 0.8931 (mmt) cc_final: 0.8537 (mmm)
REVERT: A  414 ARG cc_start: 0.9186 (tpp80) cc_final: 0.8795 (ttm-80)
REVERT: A  427 MET cc_start: 0.8206 (mpp) cc_final: 0.7635 (mpp)
REVERT: A  567 HIS cc_start: 0.7158 (t-90) cc_final: 0.6762 (p90)
REVERT: B  208 GLN cc_start: 0.9368 (tm-30) cc_final: 0.9140 (tm-30)
REVERT: B  225 GLU cc_start: 0.8835 (tp30) cc_final: 0.8141 (tp30)
REVERT: B  413 TRP cc_start: 0.8280 (t60) cc_final: 0.8047 (t60)
REVERT: B  500 LEU cc_start: 0.9239 (tp) cc_final: 0.9023 (tp)
REVERT: B  501 MET cc_start: 0.9347 (ppp) cc_final: 0.9059 (ppp)
  outliers start: 4
  outliers final: 1
  residues processed: 205
  average time/residue: 0.1886
  time to fit residues: 56.4520
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  : 0.979 
-------------------------------------------------------------------------------
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:    0.6980
   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:    1.1386

-------------------------------------------------------------------------------
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 = 0.3992 r_free = 0.3992 target = 0.126375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.085412 restraints weight = 25848.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.088307 restraints weight = 16470.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.090415 restraints weight = 11924.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8920  Z= 0.221
  Angle     :  0.760  11.701  12072  Z= 0.397
  Chirality :  0.046   0.244   1462
  Planarity :  0.006   0.074   1514
  Dihedral  :  5.749  34.073   1222
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 17.75
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  8.35 %
    Favored  : 91.30 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  6.24 %
    Favored  : 93.56 %
  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:  0.91 (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   0.011   0.001   HIS B 560 
 PHE   0.022   0.002   PHE B 304 
 TYR   0.017   0.002   TYR B 408 
 ARG   0.007   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  : 0.968 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9192 (tttt) cc_final: 0.8823 (ttmt)
REVERT: A   91 ASN cc_start: 0.9162 (m-40) cc_final: 0.8913 (m-40)
REVERT: A  101 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8373 (tt0)
REVERT: A  414 ARG cc_start: 0.9119 (tpp80) cc_final: 0.8502 (ttm110)
REVERT: A  427 MET cc_start: 0.8212 (mpp) cc_final: 0.7628 (mpp)
REVERT: A  567 HIS cc_start: 0.7101 (t-90) cc_final: 0.6698 (p90)
REVERT: B  208 GLN cc_start: 0.9485 (tm-30) cc_final: 0.9091 (tm-30)
REVERT: B  217 LYS cc_start: 0.9348 (tptt) cc_final: 0.8787 (tptt)
REVERT: B  225 GLU cc_start: 0.8801 (tp30) cc_final: 0.8080 (tp30)
REVERT: B  413 TRP cc_start: 0.8266 (t60) cc_final: 0.7983 (t60)
REVERT: B  454 MET cc_start: 0.8624 (mmp) cc_final: 0.8409 (mmm)
REVERT: B  485 GLN cc_start: 0.9026 (pp30) cc_final: 0.8710 (pp30)
  outliers start: 2
  outliers final: 0
  residues processed: 198
  average time/residue: 0.1848
  time to fit residues: 52.6351
Evaluate side-chains
  157 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.918 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 93 optimal weight:   40.0000
   chunk 56 optimal weight:    6.9990
   chunk 107 optimal weight:    7.9990
   chunk 80 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0980
   chunk 68 optimal weight:    0.8980
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 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 = 0.4012 r_free = 0.4012 target = 0.127616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.086654 restraints weight = 25161.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.089506 restraints weight = 16154.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.091625 restraints weight = 11730.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8920  Z= 0.216
  Angle     :  0.753  11.689  12072  Z= 0.391
  Chirality :  0.045   0.232   1462
  Planarity :  0.006   0.073   1514
  Dihedral  :  5.626  34.046   1222
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 17.75
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  8.08 %
    Favored  : 91.56 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  4.47 %
    Favored  : 95.22 %
  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: -0.49 (0.25), residues: 1138
  helix:  0.95 (0.19), residues: 757
  sheet:  0.05 (0.67), residues: 63
  loop : -3.67 (0.29), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 104 
 HIS   0.004   0.001   HIS A 535 
 PHE   0.062   0.002   PHE A 384 
 TYR   0.018   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
  206 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 203
  time to evaluate  : 1.023 
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: 0.9090 (tttt) cc_final: 0.8699 (ttmm)
REVERT: A   91 ASN cc_start: 0.9166 (m-40) cc_final: 0.8931 (m-40)
REVERT: A  101 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8504 (tt0)
REVERT: A  106 LYS cc_start: 0.9518 (tptm) cc_final: 0.9296 (tptm)
REVERT: A  427 MET cc_start: 0.8178 (mpp) cc_final: 0.7574 (mpp)
REVERT: A  501 MET cc_start: 0.9229 (tmm) cc_final: 0.8972 (tmm)
REVERT: A  567 HIS cc_start: 0.7148 (t-90) cc_final: 0.6667 (p-80)
REVERT: B  225 GLU cc_start: 0.8799 (tp30) cc_final: 0.8106 (tp30)
REVERT: B  292 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8396 (tm-30)
REVERT: B  454 MET cc_start: 0.8645 (mmp) cc_final: 0.8429 (mmm)
REVERT: B  485 GLN cc_start: 0.8981 (pp30) cc_final: 0.8743 (pp30)
  outliers start: 3
  outliers final: 0
  residues processed: 205
  average time/residue: 0.1801
  time to fit residues: 52.8361
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  : 0.962 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 107 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0170
   chunk 76 optimal weight:    9.9990
   chunk 91 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 94 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.6818

-------------------------------------------------------------------------------
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 = 0.4016 r_free = 0.4016 target = 0.127930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.087692 restraints weight = 25341.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.090660 restraints weight = 16098.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.092828 restraints weight = 11563.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.2716

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= 0.207
  Angle     :  0.748  12.017  12072  Z= 0.388
  Chirality :  0.046   0.230   1462
  Planarity :  0.006   0.072   1514
  Dihedral  :  5.533  33.665   1222
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 15.85
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.73 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  4.47 %
    Favored  : 95.11 %
  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: -0.37 (0.25), residues: 1138
  helix:  1.10 (0.19), residues: 752
  sheet:  0.07 (0.67), residues: 63
  loop : -3.71 (0.29), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 413 
 HIS   0.002   0.001   HIS A 416 
 PHE   0.038   0.002   PHE B  74 
 TYR   0.025   0.002   TYR B 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
  203 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 199
  time to evaluate  : 1.042 
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: 0.9066 (tttt) cc_final: 0.8701 (tptt)
REVERT: A   91 ASN cc_start: 0.9072 (m-40) cc_final: 0.8793 (m-40)
REVERT: A  101 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8442 (tt0)
REVERT: A  131 THR cc_start: 0.9262 (p) cc_final: 0.8965 (p)
REVERT: A  197 ASP cc_start: 0.8940 (t70) cc_final: 0.8435 (m-30)
REVERT: A  225 GLU cc_start: 0.8684 (tp30) cc_final: 0.7665 (tp30)
REVERT: A  317 MET cc_start: 0.8921 (mmt) cc_final: 0.8512 (mmm)
REVERT: A  365 GLU cc_start: 0.9026 (tp30) cc_final: 0.8737 (tp30)
REVERT: A  384 PHE cc_start: 0.8410 (m-10) cc_final: 0.8149 (m-80)
REVERT: A  414 ARG cc_start: 0.9184 (tpp80) cc_final: 0.8983 (ttp-110)
REVERT: A  427 MET cc_start: 0.8192 (mpp) cc_final: 0.7590 (mpp)
REVERT: A  456 TYR cc_start: 0.6599 (t80) cc_final: 0.6399 (t80)
REVERT: A  567 HIS cc_start: 0.7264 (t-90) cc_final: 0.6806 (p-80)
REVERT: B  225 GLU cc_start: 0.8783 (tp30) cc_final: 0.8040 (tp30)
REVERT: B  410 LEU cc_start: 0.9431 (tp) cc_final: 0.9174 (tp)
REVERT: B  413 TRP cc_start: 0.8420 (t60) cc_final: 0.8095 (t60)
REVERT: B  454 MET cc_start: 0.8633 (mmp) cc_final: 0.8405 (mmm)
  outliers start: 4
  outliers final: 1
  residues processed: 203
  average time/residue: 0.1764
  time to fit residues: 51.4847
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  : 1.055 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 51 optimal weight:    8.9990
   chunk 105 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 ** 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 = 0.4016 r_free = 0.4016 target = 0.127752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.087163 restraints weight = 25638.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.090101 restraints weight = 16435.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.092196 restraints weight = 11893.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   8920  Z= 0.220
  Angle     :  0.753  12.167  12072  Z= 0.390
  Chirality :  0.046   0.225   1462
  Planarity :  0.005   0.069   1514
  Dihedral  :  5.520  35.509   1222
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 16.35
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.91 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.49 %
    Favored  : 97.40 %
  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: -0.45 (0.25), residues: 1138
  helix:  1.05 (0.19), residues: 754
  sheet:  0.03 (0.66), residues: 63
  loop : -3.81 (0.27), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 413 
 HIS   0.005   0.001   HIS B 141 
 PHE   0.034   0.002   PHE B  74 
 TYR   0.019   0.002   TYR B 289 
 ARG   0.012   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
  194 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 193
  time to evaluate  : 0.959 
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: 0.9166 (tttt) cc_final: 0.8774 (tptt)
REVERT: A   91 ASN cc_start: 0.9068 (m-40) cc_final: 0.8851 (m-40)
REVERT: A  197 ASP cc_start: 0.8948 (t70) cc_final: 0.8469 (m-30)
REVERT: A  225 GLU cc_start: 0.8748 (tp30) cc_final: 0.7679 (tp30)
REVERT: A  231 MET cc_start: 0.8942 (mpp) cc_final: 0.8716 (mpp)
REVERT: A  365 GLU cc_start: 0.9073 (tp30) cc_final: 0.8812 (tp30)
REVERT: A  384 PHE cc_start: 0.8524 (m-10) cc_final: 0.8224 (m-80)
REVERT: A  427 MET cc_start: 0.8266 (mpp) cc_final: 0.7492 (mpp)
REVERT: A  456 TYR cc_start: 0.6617 (t80) cc_final: 0.6401 (t80)
REVERT: A  501 MET cc_start: 0.9118 (tmm) cc_final: 0.8909 (tmm)
REVERT: A  567 HIS cc_start: 0.7071 (t-90) cc_final: 0.6601 (p-80)
REVERT: B  225 GLU cc_start: 0.8845 (tp30) cc_final: 0.8124 (tp30)
REVERT: B  410 LEU cc_start: 0.9453 (tp) cc_final: 0.9171 (tp)
REVERT: B  413 TRP cc_start: 0.8480 (t60) cc_final: 0.8116 (t60)
REVERT: B  454 MET cc_start: 0.8506 (mmp) cc_final: 0.8285 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 194
  average time/residue: 0.1881
  time to fit residues: 52.2779
Evaluate side-chains
  157 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 35 optimal weight:   20.0000
   chunk 20 optimal weight:    5.9990
   chunk 101 optimal weight:    8.9990
   chunk 61 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 83 optimal weight:    0.7980
   chunk 50 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.126409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.086441 restraints weight = 25780.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.089314 restraints weight = 16511.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.091410 restraints weight = 11925.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.3097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8920  Z= 0.233
  Angle     :  0.765  12.618  12072  Z= 0.396
  Chirality :  0.045   0.228   1462
  Planarity :  0.006   0.071   1514
  Dihedral  :  5.500  36.483   1222
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 16.57
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.82 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  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:  1.06 (0.19), residues: 755
  sheet: -0.00 (0.65), residues: 63
  loop : -3.80 (0.28), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 104 
 HIS   0.003   0.001   HIS B 141 
 PHE   0.032   0.002   PHE B  74 
 TYR   0.027   0.002   TYR A 268 
 ARG   0.014   0.000   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  : 1.002 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9164 (tttt) cc_final: 0.8791 (tptt)
REVERT: A   91 ASN cc_start: 0.9074 (m-40) cc_final: 0.8839 (m-40)
REVERT: A  131 THR cc_start: 0.9324 (p) cc_final: 0.9026 (p)
REVERT: A  197 ASP cc_start: 0.8962 (t70) cc_final: 0.8489 (m-30)
REVERT: A  225 GLU cc_start: 0.8734 (tp30) cc_final: 0.7682 (tp30)
REVERT: A  317 MET cc_start: 0.8864 (mmt) cc_final: 0.8463 (mmm)
REVERT: A  365 GLU cc_start: 0.9070 (tp30) cc_final: 0.8826 (tp30)
REVERT: A  384 PHE cc_start: 0.8529 (m-10) cc_final: 0.8272 (m-80)
REVERT: A  427 MET cc_start: 0.8232 (mpp) cc_final: 0.7452 (mpp)
REVERT: A  456 TYR cc_start: 0.6620 (t80) cc_final: 0.6387 (t80)
REVERT: A  567 HIS cc_start: 0.7090 (t-90) cc_final: 0.6571 (p-80)
REVERT: B  217 LYS cc_start: 0.9448 (tptt) cc_final: 0.8990 (tptt)
REVERT: B  292 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8399 (tm-30)
REVERT: B  410 LEU cc_start: 0.9469 (tp) cc_final: 0.9189 (tp)
REVERT: B  413 TRP cc_start: 0.8407 (t60) cc_final: 0.8085 (t60)
REVERT: B  454 MET cc_start: 0.8465 (mmp) cc_final: 0.8236 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 187
  average time/residue: 0.1711
  time to fit residues: 46.3587
Evaluate side-chains
  152 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 55 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 30 optimal weight:    6.9990
   chunk 0 optimal weight:    8.9990
   chunk 47 optimal weight:    9.9990
   chunk 50 optimal weight:    6.9990
   chunk 92 optimal weight:    5.9990
   chunk 94 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    1.3182

-------------------------------------------------------------------------------
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
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 = 0.4015 r_free = 0.4015 target = 0.127650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.087376 restraints weight = 26058.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.090372 restraints weight = 16621.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.092491 restraints weight = 11945.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.3298

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= 0.219
  Angle     :  0.766  12.834  12072  Z= 0.394
  Chirality :  0.046   0.230   1462
  Planarity :  0.006   0.075   1514
  Dihedral  :  5.461  36.267   1222
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 16.13
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.64 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  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: -0.37 (0.25), residues: 1138
  helix:  1.12 (0.19), residues: 756
  sheet: -0.46 (0.64), residues: 68
  loop : -3.76 (0.28), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 104 
 HIS   0.004   0.001   HIS B 561 
 PHE   0.030   0.002   PHE B  74 
 TYR   0.015   0.001   TYR A 268 
 ARG   0.015   0.001   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
  190 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9074 (tttt) cc_final: 0.8711 (tptt)
REVERT: A   59 MET cc_start: 0.7323 (mpp) cc_final: 0.7079 (mpp)
REVERT: A   91 ASN cc_start: 0.9009 (m-40) cc_final: 0.8790 (m-40)
REVERT: A  101 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8624 (mt-10)
REVERT: A  197 ASP cc_start: 0.8985 (t70) cc_final: 0.8508 (m-30)
REVERT: A  231 MET cc_start: 0.8969 (mpp) cc_final: 0.8760 (mpp)
REVERT: A  317 MET cc_start: 0.8800 (mmt) cc_final: 0.8340 (mmm)
REVERT: A  365 GLU cc_start: 0.9111 (tp30) cc_final: 0.8841 (tp30)
REVERT: A  384 PHE cc_start: 0.8601 (m-10) cc_final: 0.8270 (m-80)
REVERT: A  427 MET cc_start: 0.8205 (mpp) cc_final: 0.7550 (mpp)
REVERT: A  456 TYR cc_start: 0.6611 (t80) cc_final: 0.6366 (t80)
REVERT: A  489 ILE cc_start: 0.8924 (pt) cc_final: 0.8720 (pt)
REVERT: A  501 MET cc_start: 0.9213 (tmm) cc_final: 0.8946 (tmm)
REVERT: A  567 HIS cc_start: 0.6988 (t-90) cc_final: 0.6457 (p90)
REVERT: B  212 GLU cc_start: 0.9017 (mp0) cc_final: 0.8787 (mt-10)
REVERT: B  217 LYS cc_start: 0.9432 (tptt) cc_final: 0.8925 (tptt)
REVERT: B  225 GLU cc_start: 0.8779 (tp30) cc_final: 0.8120 (tp30)
REVERT: B  292 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8361 (tm-30)
REVERT: B  410 LEU cc_start: 0.9486 (tp) cc_final: 0.9197 (tp)
REVERT: B  454 MET cc_start: 0.8462 (mmp) cc_final: 0.8227 (mmm)
REVERT: B  485 GLN cc_start: 0.9051 (pp30) cc_final: 0.8813 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1771
  time to fit residues: 48.8223
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  : 1.013 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 70 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 34 optimal weight:    9.9990
   chunk 66 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 48 optimal weight:    8.9990
   chunk 67 optimal weight:    0.9990
   chunk 104 optimal weight:    0.9990
   chunk 18 optimal weight:    6.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.9386

-------------------------------------------------------------------------------
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 ** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.128113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.087965 restraints weight = 25836.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.090941 restraints weight = 16463.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.093112 restraints weight = 11831.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.3475

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= 0.211
  Angle     :  0.770  13.055  12072  Z= 0.391
  Chirality :  0.046   0.209   1462
  Planarity :  0.005   0.064   1514
  Dihedral  :  5.432  35.445   1222
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.47 %
    Favored  : 92.18 %
  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: -0.34 (0.25), residues: 1138
  helix:  1.14 (0.19), residues: 756
  sheet: -0.36 (0.65), residues: 68
  loop : -3.76 (0.28), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 413 
 HIS   0.003   0.001   HIS B 561 
 PHE   0.020   0.002   PHE B  57 
 TYR   0.028   0.001   TYR B 408 
 ARG   0.013   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
  193 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.074 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9076 (tttt) cc_final: 0.8722 (tptt)
REVERT: A   59 MET cc_start: 0.7329 (mpp) cc_final: 0.7127 (mpp)
REVERT: A   91 ASN cc_start: 0.8982 (m-40) cc_final: 0.8766 (m-40)
REVERT: A  101 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8552 (mt-10)
REVERT: A  131 THR cc_start: 0.9309 (p) cc_final: 0.9000 (p)
REVERT: A  197 ASP cc_start: 0.8967 (t70) cc_final: 0.8513 (m-30)
REVERT: A  231 MET cc_start: 0.8932 (mpp) cc_final: 0.8728 (mpp)
REVERT: A  317 MET cc_start: 0.8797 (mmt) cc_final: 0.8330 (mmm)
REVERT: A  365 GLU cc_start: 0.9108 (tp30) cc_final: 0.8834 (tp30)
REVERT: A  384 PHE cc_start: 0.8571 (m-10) cc_final: 0.8256 (m-80)
REVERT: A  414 ARG cc_start: 0.8896 (ptp-110) cc_final: 0.8137 (ptp90)
REVERT: A  427 MET cc_start: 0.8135 (mpp) cc_final: 0.7647 (mpp)
REVERT: A  456 TYR cc_start: 0.6698 (t80) cc_final: 0.6435 (t80)
REVERT: A  501 MET cc_start: 0.9110 (tmm) cc_final: 0.8909 (tmm)
REVERT: A  567 HIS cc_start: 0.6864 (t-90) cc_final: 0.6406 (p90)
REVERT: B  212 GLU cc_start: 0.8998 (mp0) cc_final: 0.8707 (mt-10)
REVERT: B  217 LYS cc_start: 0.9436 (tptt) cc_final: 0.9147 (tptt)
REVERT: B  225 GLU cc_start: 0.8725 (tp30) cc_final: 0.8076 (tp30)
REVERT: B  259 MET cc_start: 0.8560 (tpp) cc_final: 0.8079 (mmt)
REVERT: B  292 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8292 (tm-30)
REVERT: B  410 LEU cc_start: 0.9487 (tp) cc_final: 0.9190 (tp)
REVERT: B  413 TRP cc_start: 0.8382 (t60) cc_final: 0.8023 (t60)
REVERT: B  454 MET cc_start: 0.8449 (mmp) cc_final: 0.8208 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.1809
  time to fit residues: 50.4885
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  : 0.963 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 69 optimal weight:    0.7980
   chunk 86 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 74 optimal weight:    0.0770
   chunk 100 optimal weight:    0.0170
   chunk 26 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 102 optimal weight:    0.0980
   overall best weight:    0.5978

-------------------------------------------------------------------------------
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  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 = 0.4038 r_free = 0.4038 target = 0.129643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.089314 restraints weight = 25591.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.092395 restraints weight = 16329.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.094559 restraints weight = 11736.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.3676

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= 0.204
  Angle     :  0.770  13.194  12072  Z= 0.390
  Chirality :  0.046   0.198   1462
  Planarity :  0.006   0.073   1514
  Dihedral  :  5.417  34.500   1222
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.21 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  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: -0.24 (0.25), residues: 1138
  helix:  1.21 (0.19), residues: 758
  sheet: -0.30 (0.66), residues: 68
  loop : -3.72 (0.29), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 413 
 HIS   0.004   0.001   HIS B 561 
 PHE   0.020   0.002   PHE A 460 
 TYR   0.026   0.001   TYR B 408 
 ARG   0.018   0.000   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
  192 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9040 (tttt) cc_final: 0.8640 (tptt)
REVERT: A   59 MET cc_start: 0.7334 (mpp) cc_final: 0.7097 (mpp)
REVERT: A   91 ASN cc_start: 0.9142 (m-40) cc_final: 0.8859 (m-40)
REVERT: A  101 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8548 (mt-10)
REVERT: A  197 ASP cc_start: 0.8956 (t70) cc_final: 0.8492 (m-30)
REVERT: A  317 MET cc_start: 0.8709 (mmt) cc_final: 0.8307 (mmm)
REVERT: A  365 GLU cc_start: 0.9083 (tp30) cc_final: 0.8841 (tp30)
REVERT: A  384 PHE cc_start: 0.8601 (m-10) cc_final: 0.8195 (m-80)
REVERT: A  414 ARG cc_start: 0.8961 (ptp-110) cc_final: 0.7969 (ptp90)
REVERT: A  427 MET cc_start: 0.8118 (mpp) cc_final: 0.7672 (mpp)
REVERT: A  456 TYR cc_start: 0.6665 (t80) cc_final: 0.6435 (t80)
REVERT: B  152 VAL cc_start: 0.9280 (t) cc_final: 0.9079 (p)
REVERT: B  212 GLU cc_start: 0.8973 (mp0) cc_final: 0.8729 (mt-10)
REVERT: B  217 LYS cc_start: 0.9447 (tptt) cc_final: 0.8948 (tptt)
REVERT: B  225 GLU cc_start: 0.8708 (tp30) cc_final: 0.8056 (tp30)
REVERT: B  259 MET cc_start: 0.8585 (tpp) cc_final: 0.8218 (mmt)
REVERT: B  292 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8278 (tm-30)
REVERT: B  410 LEU cc_start: 0.9485 (tp) cc_final: 0.9186 (tp)
REVERT: B  413 TRP cc_start: 0.8335 (t60) cc_final: 0.8110 (t60)
REVERT: B  454 MET cc_start: 0.8435 (mmp) cc_final: 0.8140 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.1845
  time to fit residues: 50.5943
Evaluate side-chains
  160 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 62 optimal weight:    0.3980
   chunk 48 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 94 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 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 = 0.4044 r_free = 0.4044 target = 0.130211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.089572 restraints weight = 25580.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.092625 restraints weight = 16380.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.094735 restraints weight = 11803.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.3841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8920  Z= 0.207
  Angle     :  0.763  13.002  12072  Z= 0.385
  Chirality :  0.045   0.190   1462
  Planarity :  0.006   0.072   1514
  Dihedral  :  5.353  34.639   1222
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 15.07
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.56 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  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: -0.20 (0.25), residues: 1138
  helix:  1.22 (0.19), residues: 757
  sheet: -0.22 (0.67), residues: 68
  loop : -3.67 (0.29), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 413 
 HIS   0.003   0.001   HIS B 561 
 PHE   0.018   0.002   PHE B  57 
 TYR   0.026   0.001   TYR B 408 
 ARG   0.018   0.000   ARG B 345 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2623.78 seconds
wall clock time: 48 minutes 1.26 seconds (2881.26 seconds total)