Starting phenix.real_space_refine
on Thu Mar  6 10:32:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nrx_12552/03_2025/7nrx_12552.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nrx_12552/03_2025/7nrx_12552.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nrx_12552/03_2025/7nrx_12552.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nrx_12552/03_2025/7nrx_12552.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nrx_12552/03_2025/7nrx_12552.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nrx_12552/03_2025/7nrx_12552.cif"
  }
  resolution = 3.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.006
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      10      5.16       5
     C    3670      2.51       5
     N    1080      2.21       5
     O    1110      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5870
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
    Chain: "C"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
  Restraints were copied for chains:
    B, D, F, H, E, G, I, J
  Time building chain proxies: 3.45, per 1000 atoms: 0.59
  Number of scatterers: 5870
  At special positions: 0
  Unit cell: (132.25, 92, 44.85, 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      10     16.00
     O    1110      8.00
     N    1080      7.00
     C    3670      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.43
  Conformation dependent library (CDL) restraints added in 768.2 milliseconds
  

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1340

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 15 sheets defined
      0.0% alpha, 27.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 306 through 310
      removed outlier: 6.516A  pdb=" N   GLN A 307 " --> pdb=" O   ILE F 308 " (cutoff:3.500A)
      removed outlier: 7.679A  pdb=" N   TYR F 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.379A  pdb=" N   VAL A 309 " --> pdb=" O   TYR F 310 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   GLN F 307 " --> pdb=" O   ILE H 308 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   TYR H 310 " --> pdb=" O   GLN F 307 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   VAL F 309 " --> pdb=" O   TYR H 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314
      removed outlier: 6.668A  pdb=" N   VAL A 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   VAL F 313 " --> pdb=" O   ASP H 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 322
      removed outlier: 6.472A  pdb=" N   LYS A 317 " --> pdb=" O   VAL F 318 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   SER F 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   THR A 319 " --> pdb=" O   SER F 320 " (cutoff:3.500A)
      removed outlier: 7.972A  pdb=" N   CYS F 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   LYS A 321 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
      removed outlier: 6.482A  pdb=" N   LYS F 317 " --> pdb=" O   VAL H 318 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   SER H 320 " --> pdb=" O   LYS F 317 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   THR F 319 " --> pdb=" O   SER H 320 " (cutoff:3.500A)
      removed outlier: 7.971A  pdb=" N   CYS H 322 " --> pdb=" O   THR F 319 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   LYS F 321 " --> pdb=" O   CYS H 322 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 337 through 340
      removed outlier: 6.176A  pdb=" N   VAL B 337 " --> pdb=" O   GLU D 338 " (cutoff:3.500A)
      removed outlier: 7.688A  pdb=" N   LYS D 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   VAL B 339 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   VAL A 337 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 7.713A  pdb=" N   LYS B 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   VAL A 339 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 359 through 362
      removed outlier: 6.472A  pdb=" N   ASN B 359 " --> pdb=" O   ILE D 360 " (cutoff:3.500A)
      removed outlier: 7.650A  pdb=" N   HIS D 362 " --> pdb=" O   ASN B 359 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   THR B 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   ASN A 359 " --> pdb=" O   ILE B 360 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   HIS B 362 " --> pdb=" O   ASN A 359 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   THR A 361 " --> pdb=" O   HIS B 362 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 371 through 373
      removed outlier: 6.223A  pdb=" N   ILE A 371 " --> pdb=" O   GLU F 372 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   ILE F 371 " --> pdb=" O   GLU H 372 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 376 through 378
      removed outlier: 6.539A  pdb=" N   LEU B 376 " --> pdb=" O   THR D 377 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   LEU A 376 " --> pdb=" O   THR B 377 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 306 through 310
      removed outlier: 6.219A  pdb=" N   VAL C 306 " --> pdb=" O   GLN E 307 " (cutoff:3.500A)
      removed outlier: 7.641A  pdb=" N   VAL E 309 " --> pdb=" O   VAL C 306 " (cutoff:3.500A)
      removed outlier: 6.352A  pdb=" N   ILE C 308 " --> pdb=" O   VAL E 309 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   VAL I 306 " --> pdb=" O   GLN C 307 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   VAL C 309 " --> pdb=" O   VAL I 306 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ILE I 308 " --> pdb=" O   VAL C 309 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 313 through 314
      removed outlier: 6.646A  pdb=" N   VAL I 313 " --> pdb=" O   ASP G 314 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   VAL G 313 " --> pdb=" O   ASP J 314 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 317 through 322
      removed outlier: 6.496A  pdb=" N   LYS I 317 " --> pdb=" O   VAL G 318 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   SER G 320 " --> pdb=" O   LYS I 317 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   THR I 319 " --> pdb=" O   SER G 320 " (cutoff:3.500A)
      removed outlier: 7.838A  pdb=" N   CYS G 322 " --> pdb=" O   THR I 319 " (cutoff:3.500A)
      removed outlier: 6.091A  pdb=" N   LYS I 321 " --> pdb=" O   CYS G 322 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   LYS G 317 " --> pdb=" O   VAL J 318 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   SER J 320 " --> pdb=" O   LYS G 317 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   THR G 319 " --> pdb=" O   SER J 320 " (cutoff:3.500A)
      removed outlier: 7.853A  pdb=" N   CYS J 322 " --> pdb=" O   THR G 319 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   LYS G 321 " --> pdb=" O   CYS J 322 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 328 through 330
      removed outlier: 6.275A  pdb=" N   ILE C 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   ILE I 328 " --> pdb=" O   HIS C 329 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 336 through 339
      removed outlier: 6.553A  pdb=" N   VAL C 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   VAL I 337 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 353 through 354
      removed outlier: 6.763A  pdb=" N   LYS I 353 " --> pdb=" O   ILE G 354 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   LYS G 353 " --> pdb=" O   ILE J 354 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 359 through 362
      removed outlier: 6.760A  pdb=" N   ILE I 360 " --> pdb=" O   THR G 361 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ILE G 360 " --> pdb=" O   THR J 361 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 369 through 371
      removed outlier: 6.289A  pdb=" N   LYS C 370 " --> pdb=" O   ILE E 371 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   LYS I 370 " --> pdb=" O   ILE C 371 " (cutoff:3.500A)

    84 hydrogen bonds defined for protein.
    249 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.47

  Time building geometry restraints manager: 1.68 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1836
        1.33 -     1.45: 820
        1.45 -     1.57: 3294
        1.57 -     1.69: 0
        1.69 -     1.81: 10
  Bond restraints: 5960
  Sorted by residual:
  bond pdb=" CG1 ILE J 354 "
       pdb=" CD1 ILE J 354 "
    ideal  model  delta    sigma   weight residual
    1.513  1.377  0.136 3.90e-02 6.57e+02 1.22e+01
  bond pdb=" CG1 ILE G 354 "
       pdb=" CD1 ILE G 354 "
    ideal  model  delta    sigma   weight residual
    1.513  1.377  0.136 3.90e-02 6.57e+02 1.21e+01
  bond pdb=" CG1 ILE C 354 "
       pdb=" CD1 ILE C 354 "
    ideal  model  delta    sigma   weight residual
    1.513  1.378  0.135 3.90e-02 6.57e+02 1.20e+01
  bond pdb=" CG1 ILE I 354 "
       pdb=" CD1 ILE I 354 "
    ideal  model  delta    sigma   weight residual
    1.513  1.378  0.135 3.90e-02 6.57e+02 1.20e+01
  bond pdb=" CG1 ILE E 354 "
       pdb=" CD1 ILE E 354 "
    ideal  model  delta    sigma   weight residual
    1.513  1.378  0.135 3.90e-02 6.57e+02 1.20e+01
  ... (remaining 5955 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 7175
        1.90 -     3.81: 694
        3.81 -     5.71: 71
        5.71 -     7.61: 20
        7.61 -     9.52: 10
  Bond angle restraints: 7970
  Sorted by residual:
  angle pdb=" CA  LYS B 311 "
        pdb=" CB  LYS B 311 "
        pdb=" CG  LYS B 311 "
      ideal   model   delta    sigma   weight residual
     114.10  123.62   -9.52 2.00e+00 2.50e-01 2.26e+01
  angle pdb=" CA  LYS H 311 "
        pdb=" CB  LYS H 311 "
        pdb=" CG  LYS H 311 "
      ideal   model   delta    sigma   weight residual
     114.10  123.61   -9.51 2.00e+00 2.50e-01 2.26e+01
  angle pdb=" CA  LYS D 311 "
        pdb=" CB  LYS D 311 "
        pdb=" CG  LYS D 311 "
      ideal   model   delta    sigma   weight residual
     114.10  123.58   -9.48 2.00e+00 2.50e-01 2.25e+01
  angle pdb=" CA  LYS F 311 "
        pdb=" CB  LYS F 311 "
        pdb=" CG  LYS F 311 "
      ideal   model   delta    sigma   weight residual
     114.10  123.57   -9.47 2.00e+00 2.50e-01 2.24e+01
  angle pdb=" CA  LYS A 311 "
        pdb=" CB  LYS A 311 "
        pdb=" CG  LYS A 311 "
      ideal   model   delta    sigma   weight residual
     114.10  123.51   -9.41 2.00e+00 2.50e-01 2.21e+01
  ... (remaining 7965 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.37: 3186
       14.37 -    28.74: 329
       28.74 -    43.12: 100
       43.12 -    57.49: 10
       57.49 -    71.86: 5
  Dihedral angle restraints: 3630
    sinusoidal: 1520
      harmonic: 2110
  Sorted by residual:
  dihedral pdb=" CA  LYS F 347 "
           pdb=" C   LYS F 347 "
           pdb=" N   ASP F 348 "
           pdb=" CA  ASP F 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.66  -26.34     0      5.00e+00 4.00e-02 2.78e+01
  dihedral pdb=" CA  LYS D 347 "
           pdb=" C   LYS D 347 "
           pdb=" N   ASP D 348 "
           pdb=" CA  ASP D 348 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.68  -26.32     0      5.00e+00 4.00e-02 2.77e+01
  dihedral pdb=" CA  LYS H 347 "
           pdb=" C   LYS H 347 "
           pdb=" N   ASP H 348 "
           pdb=" CA  ASP H 348 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.70  -26.30     0      5.00e+00 4.00e-02 2.77e+01
  ... (remaining 3627 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.144: 845
       0.144 -    0.289: 35
       0.289 -    0.433: 5
       0.433 -    0.577: 0
       0.577 -    0.722: 5
  Chirality restraints: 890
  Sorted by residual:
  chirality pdb=" CB  VAL H 306 "
            pdb=" CA  VAL H 306 "
            pdb=" CG1 VAL H 306 "
            pdb=" CG2 VAL H 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.91   -0.72 2.00e-01 2.50e+01 1.30e+01
  chirality pdb=" CB  VAL A 306 "
            pdb=" CA  VAL A 306 "
            pdb=" CG1 VAL A 306 "
            pdb=" CG2 VAL A 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.91   -0.72 2.00e-01 2.50e+01 1.29e+01
  chirality pdb=" CB  VAL B 306 "
            pdb=" CA  VAL B 306 "
            pdb=" CG1 VAL B 306 "
            pdb=" CG2 VAL B 306 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -1.91   -0.72 2.00e-01 2.50e+01 1.29e+01
  ... (remaining 887 not shown)

  Planarity restraints: 1020
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 363 "    0.064 5.00e-02 4.00e+02   9.65e-02 1.49e+01
        pdb=" N   PRO D 364 "   -0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO D 364 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO D 364 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 363 "    0.064 5.00e-02 4.00e+02   9.63e-02 1.48e+01
        pdb=" N   PRO B 364 "   -0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO B 364 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO B 364 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL H 363 "    0.064 5.00e-02 4.00e+02   9.62e-02 1.48e+01
        pdb=" N   PRO H 364 "   -0.166 5.00e-02 4.00e+02
        pdb=" CA  PRO H 364 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO H 364 "    0.052 5.00e-02 4.00e+02
  ... (remaining 1017 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 1897
        2.87 -     3.37: 4466
        3.37 -     3.88: 9908
        3.88 -     4.39: 10017
        4.39 -     4.90: 21866
  Nonbonded interactions: 48154
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU G 372 "
            pdb=" OD2 ASP J 314 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" OE2 GLU I 372 "
            pdb=" OD2 ASP G 314 "
     model   vdw
     2.372 3.040
  nonbonded pdb=" OD2 ASP C 314 "
            pdb=" OE2 GLU E 372 "
     model   vdw
     2.376 3.040
  nonbonded pdb=" OD2 ASP I 314 "
            pdb=" OE2 GLU C 372 "
     model   vdw
     2.377 3.040
  nonbonded pdb=" NZ  LYS A 353 "
            pdb=" OD2 ASP A 358 "
     model   vdw
     2.418 3.120
  ... (remaining 48149 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.840
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.850
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.010
  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:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
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      :  0.010   0.136   5960  Z= 0.671
  Angle     :  1.201   9.516   7970  Z= 0.703
  Chirality :  0.092   0.722    890
  Planarity :  0.011   0.097   1020
  Dihedral  : 12.756  71.859   2290
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.60 (0.24), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.73 (0.18), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B 330 
 PHE   0.010   0.004   PHE A 346 
 TYR   0.046   0.008   TYR B 310 
 ARG   0.002   0.000   ARG G 349 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 0.753 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.8221 (mmmm) cc_final: 0.7824 (mmmm)
REVERT: B  353 LYS cc_start: 0.9030 (ttmt) cc_final: 0.7549 (mttt)
REVERT: C  349 ARG cc_start: 0.7320 (mtt180) cc_final: 0.6261 (ttm-80)
REVERT: D  331 LYS cc_start: 0.8878 (mttt) cc_final: 0.8044 (mmtt)
REVERT: D  353 LYS cc_start: 0.9030 (ttmt) cc_final: 0.7607 (mttp)
REVERT: E  311 LYS cc_start: 0.8841 (mttt) cc_final: 0.8107 (mmmt)
REVERT: E  349 ARG cc_start: 0.7475 (mtt180) cc_final: 0.6298 (mmt-90)
REVERT: E  350 VAL cc_start: 0.9052 (m) cc_final: 0.8797 (t)
REVERT: E  353 LYS cc_start: 0.8666 (ttmt) cc_final: 0.6971 (mttp)
REVERT: E  369 LYS cc_start: 0.8180 (mttt) cc_final: 0.7568 (mmmt)
REVERT: E  375 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8174 (mtpt)
REVERT: F  353 LYS cc_start: 0.8931 (ttmt) cc_final: 0.7524 (mttt)
REVERT: G  320 SER cc_start: 0.9176 (t) cc_final: 0.8700 (m)
REVERT: G  327 ASN cc_start: 0.8562 (m-40) cc_final: 0.8314 (m110)
REVERT: G  353 LYS cc_start: 0.8422 (ttmt) cc_final: 0.6875 (mttp)
REVERT: G  369 LYS cc_start: 0.8304 (mttt) cc_final: 0.7882 (mtmt)
REVERT: G  375 LYS cc_start: 0.8522 (ttmt) cc_final: 0.8155 (mtpp)
REVERT: G  377 THR cc_start: 0.9122 (m) cc_final: 0.8706 (m)
REVERT: H  331 LYS cc_start: 0.8824 (mttt) cc_final: 0.8609 (mttp)
REVERT: H  347 LYS cc_start: 0.8478 (mmmm) cc_final: 0.6930 (pptt)
REVERT: H  353 LYS cc_start: 0.9184 (ttmt) cc_final: 0.7600 (mttp)
REVERT: H  379 ARG cc_start: 0.7011 (mtm-85) cc_final: 0.6521 (pmt-80)
REVERT: J  320 SER cc_start: 0.9069 (t) cc_final: 0.8857 (m)
REVERT: J  343 LYS cc_start: 0.7997 (tptt) cc_final: 0.7553 (pptt)
REVERT: J  375 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8253 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 255
  average time/residue: 0.2948
  time to fit residues: 89.6345
Evaluate side-chains
  192 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    8.9990
   chunk 53 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   chunk 18 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 21 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    3.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.105537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.082205 restraints weight = 9444.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.084682 restraints weight = 4265.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.086238 restraints weight = 2575.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   5960  Z= 0.310
  Angle     :  0.645   4.873   7970  Z= 0.332
  Chirality :  0.050   0.135    890
  Planarity :  0.006   0.056   1020
  Dihedral  :  5.512  20.110    790
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 13.58 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.62 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.75 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I 330 
 PHE   0.010   0.001   PHE F 378 
 TYR   0.009   0.001   TYR F 310 
 ARG   0.003   0.000   ARG I 379 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 188
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
REVERT: A  342 GLU cc_start: 0.7810 (mp0) cc_final: 0.7499 (mp0)
REVERT: B  380 GLU cc_start: 0.5727 (tm-30) cc_final: 0.4849 (tm-30)
REVERT: C  349 ARG cc_start: 0.6569 (mtt180) cc_final: 0.5874 (ttm-80)
REVERT: C  351 GLN cc_start: 0.7745 (mt0) cc_final: 0.7455 (mp10)
REVERT: D  311 LYS cc_start: 0.8410 (tptm) cc_final: 0.8095 (tppt)
REVERT: D  317 LYS cc_start: 0.7549 (mttt) cc_final: 0.7101 (mtpt)
REVERT: D  331 LYS cc_start: 0.8817 (mttt) cc_final: 0.7835 (mmtt)
REVERT: E  349 ARG cc_start: 0.6903 (mtt180) cc_final: 0.5634 (mmt-90)
REVERT: G  368 ASN cc_start: 0.9678 (m-40) cc_final: 0.8903 (m-40)
REVERT: G  369 LYS cc_start: 0.7423 (mttt) cc_final: 0.7136 (mtmt)
REVERT: G  375 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7772 (mtpp)
REVERT: H  379 ARG cc_start: 0.7274 (mtm-85) cc_final: 0.6577 (pmt-80)
REVERT: J  320 SER cc_start: 0.9290 (t) cc_final: 0.8590 (m)
REVERT: J  322 CYS cc_start: 0.8444 (t) cc_final: 0.8139 (t)
REVERT: J  354 ILE cc_start: 0.8601 (mm) cc_final: 0.8298 (mp)
REVERT: J  368 ASN cc_start: 0.8708 (m-40) cc_final: 0.8457 (m-40)
REVERT: J  375 LYS cc_start: 0.8558 (ttmt) cc_final: 0.8228 (ttmm)
  outliers start: 10
  outliers final: 10
  residues processed: 193
  average time/residue: 0.2207
  time to fit residues: 53.7192
Evaluate side-chains
  184 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 174
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  316 SER
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain H residue  324 SER
Chi-restraints excluded: chain H residue  352 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 30 optimal weight:    8.9990
   chunk 56 optimal weight:    2.9990
   chunk 28 optimal weight:    9.9990
   chunk 24 optimal weight:   20.0000
   chunk 47 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 46 optimal weight:    9.9990
   chunk 32 optimal weight:    0.0670
   chunk 39 optimal weight:    9.9990
   chunk 17 optimal weight:    9.9990
   chunk 66 optimal weight:   30.0000
   overall best weight:    6.4126

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

Flipped N/Q/H residues before XYZ refinement:
G 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.101658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.079291 restraints weight = 9785.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.081730 restraints weight = 4369.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.083252 restraints weight = 2607.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044   5960  Z= 0.499
  Angle     :  0.715   5.392   7970  Z= 0.371
  Chirality :  0.052   0.154    890
  Planarity :  0.005   0.052   1020
  Dihedral  :  5.696  21.949    790
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 16.42 %
    Favored  : 80.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.63 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.76 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D 329 
 PHE   0.014   0.002   PHE B 378 
 TYR   0.025   0.003   TYR F 310 
 ARG   0.003   0.000   ARG A 379 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 178
  time to evaluate  : 1.208 
Fit side-chains
   revert: symmetry clash
REVERT: A  328 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.9048 (mm)
REVERT: A  342 GLU cc_start: 0.7907 (mp0) cc_final: 0.7369 (mp0)
REVERT: I  327 ASN cc_start: 0.8616 (m110) cc_final: 0.8390 (m110)
REVERT: I  353 LYS cc_start: 0.7941 (ttmt) cc_final: 0.6600 (mttp)
REVERT: C  349 ARG cc_start: 0.6563 (mtt180) cc_final: 0.5804 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7666 (mttt) cc_final: 0.7324 (mtpt)
REVERT: D  331 LYS cc_start: 0.8850 (mttt) cc_final: 0.7791 (mmtt)
REVERT: D  336 GLN cc_start: 0.8864 (mp10) cc_final: 0.8642 (mp10)
REVERT: F  311 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8467 (mtpt)
REVERT: G  368 ASN cc_start: 0.9552 (m-40) cc_final: 0.9279 (m110)
REVERT: G  379 ARG cc_start: 0.8156 (mmm-85) cc_final: 0.7952 (mmm-85)
REVERT: H  379 ARG cc_start: 0.7300 (mtm-85) cc_final: 0.6811 (ptt-90)
REVERT: J  322 CYS cc_start: 0.8639 (t) cc_final: 0.8247 (t)
  outliers start: 21
  outliers final: 16
  residues processed: 194
  average time/residue: 0.2445
  time to fit residues: 60.3350
Evaluate side-chains
  179 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 162
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  322 CYS
Chi-restraints excluded: chain H residue  324 SER
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain J residue  316 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 56 optimal weight:    0.0010
   chunk 2 optimal weight:    9.9990
   chunk 22 optimal weight:    6.9990
   chunk 23 optimal weight:    0.7980
   chunk 28 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 12 optimal weight:   20.0000
   chunk 11 optimal weight:   20.0000
   chunk 38 optimal weight:   10.0000
   chunk 47 optimal weight:    1.9990
   overall best weight:    2.5592

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

Flipped N/Q/H residues before XYZ refinement:
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.107769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.084755 restraints weight = 9343.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.087461 restraints weight = 3996.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.089146 restraints weight = 2322.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.3353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5960  Z= 0.241
  Angle     :  0.611   5.323   7970  Z= 0.311
  Chirality :  0.050   0.128    890
  Planarity :  0.004   0.047   1020
  Dihedral  :  5.063  19.697    790
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.70 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.61 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.74 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I 330 
 PHE   0.011   0.001   PHE I 346 
 TYR   0.022   0.002   TYR F 310 
 ARG   0.003   0.000   ARG I 379 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 167
  time to evaluate  : 0.751 
Fit side-chains
REVERT: I  327 ASN cc_start: 0.8595 (m110) cc_final: 0.8357 (m110)
REVERT: B  325 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8459 (tt)
REVERT: C  349 ARG cc_start: 0.6545 (mtt180) cc_final: 0.5924 (ttm-80)
REVERT: D  336 GLN cc_start: 0.8841 (mp10) cc_final: 0.8580 (mp10)
REVERT: F  311 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8345 (mtpt)
REVERT: F  338 GLU cc_start: 0.7904 (mp0) cc_final: 0.7644 (mp0)
REVERT: F  342 GLU cc_start: 0.8360 (mp0) cc_final: 0.8049 (mp0)
REVERT: G  345 ASP cc_start: 0.8127 (t70) cc_final: 0.7872 (t70)
REVERT: G  379 ARG cc_start: 0.8076 (mmm-85) cc_final: 0.7850 (mmm-85)
REVERT: H  379 ARG cc_start: 0.7166 (mtm-85) cc_final: 0.6750 (ptt-90)
REVERT: J  322 CYS cc_start: 0.8566 (t) cc_final: 0.8200 (t)
  outliers start: 17
  outliers final: 14
  residues processed: 178
  average time/residue: 0.1691
  time to fit residues: 39.6629
Evaluate side-chains
  174 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 159
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain B residue  325 LEU
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain H residue  322 CYS
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain J residue  316 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 34 optimal weight:    8.9990
   chunk 25 optimal weight:   20.0000
   chunk 59 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 40 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   chunk 4 optimal weight:    7.9990
   chunk 3 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    7.5990

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

Flipped N/Q/H residues before XYZ refinement:
D 329 HIS
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.100434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.078461 restraints weight = 9844.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.080816 restraints weight = 4396.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.082260 restraints weight = 2647.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.3636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.051   5960  Z= 0.576
  Angle     :  0.752   6.742   7970  Z= 0.392
  Chirality :  0.054   0.162    890
  Planarity :  0.005   0.052   1020
  Dihedral  :  5.658  21.441    790
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 20.45 %
    Favored  : 76.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.71 (0.24), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.82 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G 374 
 PHE   0.016   0.002   PHE B 378 
 TYR   0.026   0.003   TYR F 310 
 ARG   0.003   0.001   ARG E 379 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 0.682 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8458 (tt)
REVERT: A  328 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8996 (mm)
REVERT: I  327 ASN cc_start: 0.8627 (m110) cc_final: 0.8415 (m110)
REVERT: C  349 ARG cc_start: 0.6856 (mtt180) cc_final: 0.5818 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7794 (mttt) cc_final: 0.7251 (mttt)
REVERT: D  331 LYS cc_start: 0.8876 (mttt) cc_final: 0.7775 (mmtt)
REVERT: D  336 GLN cc_start: 0.8882 (mp10) cc_final: 0.8641 (mp10)
REVERT: D  353 LYS cc_start: 0.9072 (ttmt) cc_final: 0.8718 (ttpp)
REVERT: E  349 ARG cc_start: 0.6844 (mtt180) cc_final: 0.5298 (mmp80)
REVERT: F  311 LYS cc_start: 0.8892 (mtpt) cc_final: 0.8600 (mtpt)
REVERT: H  379 ARG cc_start: 0.7343 (mtm-85) cc_final: 0.6948 (ptt-90)
REVERT: J  322 CYS cc_start: 0.8759 (t) cc_final: 0.8275 (t)
  outliers start: 21
  outliers final: 17
  residues processed: 183
  average time/residue: 0.1918
  time to fit residues: 44.6994
Evaluate side-chains
  182 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 163
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain G residue  375 LYS
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  322 CYS
Chi-restraints excluded: chain H residue  324 SER
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain J residue  316 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 2 optimal weight:    8.9990
   chunk 46 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9990
   chunk 51 optimal weight:   10.0000
   chunk 52 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   chunk 1 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   chunk 21 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0870
   overall best weight:    2.5564

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

Flipped N/Q/H residues before XYZ refinement:
** E 368 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 = 0.3767 r_free = 0.3767 target = 0.105288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.083003 restraints weight = 9509.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.085484 restraints weight = 4208.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.087041 restraints weight = 2516.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5960  Z= 0.246
  Angle     :  0.618   5.202   7970  Z= 0.319
  Chirality :  0.050   0.134    890
  Planarity :  0.004   0.049   1020
  Dihedral  :  5.097  20.498    790
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 23.28 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.64 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B 330 
 PHE   0.008   0.001   PHE I 346 
 TYR   0.022   0.003   TYR F 310 
 ARG   0.003   0.000   ARG I 379 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 168
  time to evaluate  : 0.722 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8269 (tt)
REVERT: I  327 ASN cc_start: 0.8577 (m110) cc_final: 0.8311 (m110)
REVERT: C  349 ARG cc_start: 0.6705 (mtt180) cc_final: 0.5745 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7492 (mttt) cc_final: 0.6960 (mttt)
REVERT: D  331 LYS cc_start: 0.8836 (mttt) cc_final: 0.7700 (mmpt)
REVERT: D  336 GLN cc_start: 0.8846 (mp10) cc_final: 0.8566 (mp10)
REVERT: D  353 LYS cc_start: 0.8930 (ttmt) cc_final: 0.7390 (mttp)
REVERT: E  349 ARG cc_start: 0.7014 (mtt180) cc_final: 0.5654 (mmt-90)
REVERT: F  311 LYS cc_start: 0.8841 (mtpt) cc_final: 0.8406 (mtpt)
REVERT: H  379 ARG cc_start: 0.7379 (mtm-85) cc_final: 0.6898 (ptt-90)
REVERT: J  322 CYS cc_start: 0.8619 (t) cc_final: 0.8193 (t)
REVERT: J  375 LYS cc_start: 0.8739 (ttmt) cc_final: 0.8388 (ttmm)
  outliers start: 17
  outliers final: 14
  residues processed: 179
  average time/residue: 0.1920
  time to fit residues: 43.6063
Evaluate side-chains
  179 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 164
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain G residue  375 LYS
Chi-restraints excluded: chain H residue  322 CYS
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain J residue  316 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 20 optimal weight:    2.9990
   chunk 46 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 58 optimal weight:    9.9990
   chunk 53 optimal weight:    9.9990
   chunk 9 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 60 optimal weight:    1.9990
   chunk 16 optimal weight:    9.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.102391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.080259 restraints weight = 9799.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.082695 restraints weight = 4411.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.084197 restraints weight = 2639.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.3755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   5960  Z= 0.405
  Angle     :  0.668   5.274   7970  Z= 0.349
  Chirality :  0.051   0.163    890
  Planarity :  0.004   0.050   1020
  Dihedral  :  5.240  20.060    790
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 23.13 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.63 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.76 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I 330 
 PHE   0.012   0.002   PHE G 346 
 TYR   0.024   0.003   TYR F 310 
 ARG   0.003   0.001   ARG G 379 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 159
  time to evaluate  : 0.745 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8349 (tt)
REVERT: A  328 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8981 (mm)
REVERT: I  327 ASN cc_start: 0.8624 (m110) cc_final: 0.8391 (m110)
REVERT: C  349 ARG cc_start: 0.6822 (mtt180) cc_final: 0.5795 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7618 (mttt) cc_final: 0.7296 (mtpt)
REVERT: D  331 LYS cc_start: 0.8894 (mttt) cc_final: 0.7803 (mmtt)
REVERT: D  336 GLN cc_start: 0.8877 (mp10) cc_final: 0.8612 (mp10)
REVERT: D  353 LYS cc_start: 0.9047 (ttmt) cc_final: 0.7497 (mttp)
REVERT: F  311 LYS cc_start: 0.8871 (mtpt) cc_final: 0.8463 (mtpt)
REVERT: G  320 SER cc_start: 0.9427 (t) cc_final: 0.8480 (m)
REVERT: H  379 ARG cc_start: 0.7394 (mtm-85) cc_final: 0.6932 (ptt-90)
REVERT: J  322 CYS cc_start: 0.8740 (t) cc_final: 0.8264 (t)
  outliers start: 18
  outliers final: 16
  residues processed: 172
  average time/residue: 0.1932
  time to fit residues: 42.5610
Evaluate side-chains
  176 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain G residue  375 LYS
Chi-restraints excluded: chain H residue  322 CYS
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain J residue  315 LEU
Chi-restraints excluded: chain J residue  316 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 47 optimal weight:   10.0000
   chunk 35 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 68 optimal weight:    9.9990
   chunk 53 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 69 optimal weight:    7.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** E 368 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 = 0.3740 r_free = 0.3740 target = 0.103271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.081085 restraints weight = 9571.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.083452 restraints weight = 4295.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.084933 restraints weight = 2587.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.3811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   5960  Z= 0.387
  Angle     :  0.674   7.882   7970  Z= 0.349
  Chirality :  0.051   0.163    890
  Planarity :  0.004   0.050   1020
  Dihedral  :  5.267  20.695    790
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 22.99 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.61 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.75 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I 330 
 PHE   0.015   0.002   PHE G 346 
 TYR   0.023   0.003   TYR F 310 
 ARG   0.003   0.001   ARG E 379 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 157
  time to evaluate  : 0.598 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8372 (tt)
REVERT: A  328 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8940 (mm)
REVERT: I  327 ASN cc_start: 0.8565 (m110) cc_final: 0.8331 (m110)
REVERT: C  349 ARG cc_start: 0.6772 (mtt180) cc_final: 0.5770 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7518 (mttt) cc_final: 0.7147 (mtpt)
REVERT: D  327 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8296 (t0)
REVERT: D  331 LYS cc_start: 0.8924 (mttt) cc_final: 0.7829 (mmtt)
REVERT: D  336 GLN cc_start: 0.8867 (mp10) cc_final: 0.8589 (mp10)
REVERT: D  353 LYS cc_start: 0.9014 (ttmt) cc_final: 0.8628 (ttpp)
REVERT: H  379 ARG cc_start: 0.7405 (mtm-85) cc_final: 0.7013 (ptt-90)
REVERT: J  322 CYS cc_start: 0.8690 (t) cc_final: 0.8220 (t)
REVERT: J  375 LYS cc_start: 0.8750 (ttmt) cc_final: 0.8449 (ttmm)
  outliers start: 21
  outliers final: 18
  residues processed: 172
  average time/residue: 0.1889
  time to fit residues: 41.3107
Evaluate side-chains
  176 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 155
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  327 ASN
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain G residue  375 LYS
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  322 CYS
Chi-restraints excluded: chain H residue  324 SER
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain J residue  315 LEU
Chi-restraints excluded: chain J residue  316 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 57 optimal weight:   10.0000
   chunk 64 optimal weight:    9.9990
   chunk 55 optimal weight:    5.9990
   chunk 7 optimal weight:    8.9990
   chunk 20 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 40 optimal weight:   10.0000
   chunk 43 optimal weight:    6.9990
   chunk 60 optimal weight:    6.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.106783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.084332 restraints weight = 9331.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.086889 restraints weight = 4015.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.088511 restraints weight = 2369.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.3893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   5960  Z= 0.312
  Angle     :  0.654   7.235   7970  Z= 0.339
  Chirality :  0.051   0.175    890
  Planarity :  0.004   0.049   1020
  Dihedral  :  5.066  19.420    790
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 23.73 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.57 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.72 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS I 330 
 PHE   0.016   0.002   PHE G 346 
 TYR   0.023   0.003   TYR F 310 
 ARG   0.006   0.001   ARG G 379 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.676 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8309 (tt)
REVERT: I  327 ASN cc_start: 0.8625 (m110) cc_final: 0.8383 (m110)
REVERT: C  349 ARG cc_start: 0.6775 (mtt180) cc_final: 0.5797 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7508 (mttt) cc_final: 0.7077 (mtpt)
REVERT: D  331 LYS cc_start: 0.8896 (mttt) cc_final: 0.7830 (mmtt)
REVERT: D  336 GLN cc_start: 0.8870 (mp10) cc_final: 0.8579 (mp10)
REVERT: D  340 LYS cc_start: 0.8620 (mptt) cc_final: 0.8260 (mmtp)
REVERT: D  343 LYS cc_start: 0.8254 (ttmm) cc_final: 0.6914 (tppt)
REVERT: D  353 LYS cc_start: 0.9007 (ttmt) cc_final: 0.7529 (mttp)
REVERT: F  311 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8614 (mtpt)
REVERT: G  320 SER cc_start: 0.9404 (t) cc_final: 0.8508 (m)
REVERT: H  379 ARG cc_start: 0.7486 (mtm-85) cc_final: 0.7026 (ptt-90)
REVERT: J  322 CYS cc_start: 0.8715 (t) cc_final: 0.8297 (t)
REVERT: J  375 LYS cc_start: 0.8733 (ttmt) cc_final: 0.8436 (ttmm)
  outliers start: 18
  outliers final: 17
  residues processed: 171
  average time/residue: 0.1847
  time to fit residues: 40.2745
Evaluate side-chains
  176 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain G residue  375 LYS
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  322 CYS
Chi-restraints excluded: chain H residue  324 SER
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain J residue  316 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 25 optimal weight:   20.0000
   chunk 18 optimal weight:    3.9990
   chunk 44 optimal weight:    8.9990
   chunk 41 optimal weight:    0.3980
   chunk 50 optimal weight:    9.9990
   chunk 24 optimal weight:   20.0000
   chunk 60 optimal weight:    9.9990
   chunk 10 optimal weight:   20.0000
   chunk 58 optimal weight:    3.9990
   chunk 3 optimal weight:   10.0000
   overall best weight:    4.2788

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

Flipped N/Q/H residues before XYZ refinement:
** E 368 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 = 0.3764 r_free = 0.3764 target = 0.106559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.084071 restraints weight = 9512.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.086506 restraints weight = 4252.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.088090 restraints weight = 2554.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.3920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5960  Z= 0.359
  Angle     :  0.679   6.853   7970  Z= 0.353
  Chirality :  0.051   0.174    890
  Planarity :  0.004   0.049   1020
  Dihedral  :  5.176  19.984    790
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 24.18 %
    Favored  : 72.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.59 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.73 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS I 330 
 PHE   0.016   0.002   PHE G 346 
 TYR   0.012   0.002   TYR B 310 
 ARG   0.006   0.001   ARG G 379 

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

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

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1500 Ramachandran restraints generated.
    750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 153
  time to evaluate  : 0.694 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8344 (tt)
REVERT: A  328 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8981 (mm)
REVERT: I  327 ASN cc_start: 0.8628 (m110) cc_final: 0.8370 (m110)
REVERT: C  349 ARG cc_start: 0.6828 (mtt180) cc_final: 0.5828 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7536 (mttt) cc_final: 0.7114 (mtpt)
REVERT: D  331 LYS cc_start: 0.8918 (mttt) cc_final: 0.7869 (mmtt)
REVERT: D  336 GLN cc_start: 0.8871 (mp10) cc_final: 0.8587 (mp10)
REVERT: D  340 LYS cc_start: 0.8494 (mptt) cc_final: 0.8206 (mmtp)
REVERT: D  343 LYS cc_start: 0.8254 (ttmm) cc_final: 0.6936 (tppt)
REVERT: D  353 LYS cc_start: 0.9019 (ttmt) cc_final: 0.7538 (mttp)
REVERT: G  320 SER cc_start: 0.9428 (t) cc_final: 0.8544 (m)
REVERT: H  379 ARG cc_start: 0.7401 (mtm-85) cc_final: 0.7086 (ptt-90)
REVERT: J  354 ILE cc_start: 0.8711 (mm) cc_final: 0.8493 (mp)
REVERT: J  375 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8431 (ttmm)
  outliers start: 19
  outliers final: 17
  residues processed: 167
  average time/residue: 0.1849
  time to fit residues: 39.6302
Evaluate side-chains
  172 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 153
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  306 VAL
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  306 VAL
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain G residue  375 LYS
Chi-restraints excluded: chain H residue  306 VAL
Chi-restraints excluded: chain H residue  322 CYS
Chi-restraints excluded: chain H residue  324 SER
Chi-restraints excluded: chain H residue  352 SER
Chi-restraints excluded: chain J residue  316 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 61 optimal weight:    0.0970
   chunk 4 optimal weight:    0.8980
   chunk 12 optimal weight:   20.0000
   chunk 30 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9990
   chunk 55 optimal weight:    7.9990
   chunk 68 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 24 optimal weight:   20.0000
   chunk 36 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    1.7782

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

Flipped N/Q/H residues before XYZ refinement:
** E 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.110379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.087427 restraints weight = 9151.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.090103 restraints weight = 3987.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.091856 restraints weight = 2353.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.4008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5960  Z= 0.207
  Angle     :  0.611   6.717   7970  Z= 0.316
  Chirality :  0.050   0.128    890
  Planarity :  0.004   0.048   1020
  Dihedral  :  4.805  18.468    790
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 24.78 %
    Favored  : 73.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.51 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.67 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H 330 
 PHE   0.016   0.001   PHE G 346 
 TYR   0.023   0.003   TYR F 310 
 ARG   0.005   0.000   ARG G 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2030.84 seconds
wall clock time: 37 minutes 24.63 seconds (2244.63 seconds total)