Starting phenix.real_space_refine
on Tue Mar  3 14:10:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nrx_12552/03_2026/7nrx_12552.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nrx_12552/03_2026/7nrx_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nrx_12552/03_2026/7nrx_12552.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nrx_12552/03_2026/7nrx_12552.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nrx_12552/03_2026/7nrx_12552.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nrx_12552/03_2026/7nrx_12552.map"
  }
  resolution = 3.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.81, per 1000 atoms: 0.14
  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: 0.34
  Conformation dependent library (CDL) restraints added in 273.4 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: 0.25
  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: 0.84

  Time building geometry restraints manager: 0.49 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: 0.00
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:             1.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.470
  Find NCS groups from input model:        0.110
  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:1.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.670
-------------------------------------------------------------------------------
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= 0.485
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.002   0.000   ARG G 349 
 TYR   0.046   0.008   TYR B 310 
 PHE   0.010   0.004   PHE A 346 
 HIS   0.005   0.001   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00984 ( 5960)
  covalent geometry    : angle       1.20140 ( 7970)
  hydrogen bonds       : bond        0.12299 (   84)
  hydrogen bonds       : angle       7.65011 (  249)

*********************** 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  : 0.241 
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: 0.7550 (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: 0.7605 (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: 0.7521 (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: 0.8315 (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: 0.7593 (mttp)
REVERT: H  379 ARG cc_start: 0.7011 (mtm-85) cc_final: 0.6519 (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: 0.1195
  time to fit residues: 36.4564
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  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    3.3588

-------------------------------------------------------------------------------
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 = 0.3767 r_free = 0.3767 target = 0.105783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.082366 restraints weight = 9518.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.084860 restraints weight = 4303.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.086376 restraints weight = 2591.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.087385 restraints weight = 1892.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.087925 restraints weight = 1555.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5960  Z= 0.196
  Angle     :  0.641   4.856   7970  Z= 0.330
  Chirality :  0.050   0.136    890
  Planarity :  0.006   0.057   1020
  Dihedral  :  5.508  20.189    790
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 13.43 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.004   0.001   ARG A 379 
 TYR   0.009   0.002   TYR F 310 
 PHE   0.010   0.001   PHE F 378 
 HIS   0.003   0.001   HIS I 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 5960)
  covalent geometry    : angle       0.64109 ( 7970)
  hydrogen bonds       : bond        0.02059 (   84)
  hydrogen bonds       : angle       4.78648 (  249)

*********************** 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
  199 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 189
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: A  342 GLU cc_start: 0.7806 (mp0) cc_final: 0.7487 (mp0)
REVERT: B  380 GLU cc_start: 0.5672 (tm-30) cc_final: 0.4810 (tm-30)
REVERT: C  349 ARG cc_start: 0.6575 (mtt180) cc_final: 0.5884 (ttm-80)
REVERT: C  351 GLN cc_start: 0.7763 (mt0) cc_final: 0.7512 (mp10)
REVERT: D  311 LYS cc_start: 0.8401 (tptm) cc_final: 0.8093 (tppt)
REVERT: D  317 LYS cc_start: 0.7550 (mttt) cc_final: 0.7101 (mtpt)
REVERT: D  331 LYS cc_start: 0.8822 (mttt) cc_final: 0.7837 (mmtt)
REVERT: E  349 ARG cc_start: 0.6904 (mtt180) cc_final: 0.5633 (mmt-90)
REVERT: G  368 ASN cc_start: 0.9675 (m-40) cc_final: 0.8893 (m-40)
REVERT: G  369 LYS cc_start: 0.7408 (mttt) cc_final: 0.7151 (mtmt)
REVERT: G  375 LYS cc_start: 0.8366 (ttmt) cc_final: 0.7803 (mtpp)
REVERT: G  380 GLU cc_start: 0.7421 (tp30) cc_final: 0.7208 (tp30)
REVERT: H  379 ARG cc_start: 0.7209 (mtm-85) cc_final: 0.6588 (pmt-80)
REVERT: J  320 SER cc_start: 0.9281 (t) cc_final: 0.8584 (m)
REVERT: J  322 CYS cc_start: 0.8412 (t) cc_final: 0.8131 (t)
REVERT: J  354 ILE cc_start: 0.8608 (mm) cc_final: 0.8316 (mp)
REVERT: J  368 ASN cc_start: 0.8733 (m-40) cc_final: 0.8486 (m-40)
REVERT: J  375 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8256 (ttmm)
  outliers start: 10
  outliers final: 10
  residues processed: 193
  average time/residue: 0.0906
  time to fit residues: 22.1220
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  : 0.184 
-------------------------------------------------------------------------------
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 23 optimal weight:    6.9990
   chunk 17 optimal weight:    9.9990
   chunk 64 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 40 optimal weight:    6.9990
   chunk 12 optimal weight:   20.0000
   chunk 21 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    3.9988

-------------------------------------------------------------------------------
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 = 0.3727 r_free = 0.3727 target = 0.103936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.081183 restraints weight = 9591.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.083655 restraints weight = 4291.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.085158 restraints weight = 2573.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.086167 restraints weight = 1866.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.086737 restraints weight = 1522.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   5960  Z= 0.223
  Angle     :  0.638   5.884   7970  Z= 0.326
  Chirality :  0.050   0.138    890
  Planarity :  0.005   0.050   1020
  Dihedral  :  5.306  21.072    790
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.67 %
    Favored  : 81.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.58 (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
 ARG   0.003   0.000   ARG A 379 
 TYR   0.023   0.002   TYR F 310 
 PHE   0.010   0.002   PHE B 378 
 HIS   0.003   0.001   HIS I 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 5960)
  covalent geometry    : angle       0.63761 ( 7970)
  hydrogen bonds       : bond        0.01716 (   84)
  hydrogen bonds       : angle       4.19963 (  249)

*********************** 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
  194 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 177
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: A  342 GLU cc_start: 0.7870 (mp0) cc_final: 0.7499 (mp0)
REVERT: I  327 ASN cc_start: 0.8636 (m110) cc_final: 0.8392 (m110)
REVERT: I  353 LYS cc_start: 0.7957 (ttmt) cc_final: 0.6571 (mttp)
REVERT: C  349 ARG cc_start: 0.6619 (mtt180) cc_final: 0.5894 (ttm-80)
REVERT: D  311 LYS cc_start: 0.8575 (tptm) cc_final: 0.8369 (mmtt)
REVERT: D  317 LYS cc_start: 0.7576 (mttt) cc_final: 0.7152 (mtpt)
REVERT: D  325 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8493 (tt)
REVERT: D  331 LYS cc_start: 0.8866 (mttt) cc_final: 0.7835 (mmtt)
REVERT: D  336 GLN cc_start: 0.8831 (mp10) cc_final: 0.8575 (mp10)
REVERT: F  311 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8312 (mtpt)
REVERT: G  320 SER cc_start: 0.9386 (t) cc_final: 0.8485 (m)
REVERT: G  375 LYS cc_start: 0.8377 (ttmt) cc_final: 0.7766 (mtpp)
REVERT: H  379 ARG cc_start: 0.7219 (mtm-85) cc_final: 0.6592 (pmt-80)
REVERT: J  322 CYS cc_start: 0.8538 (t) cc_final: 0.8238 (t)
REVERT: J  375 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8288 (ttmm)
  outliers start: 17
  outliers final: 15
  residues processed: 189
  average time/residue: 0.0822
  time to fit residues: 19.9747
Evaluate side-chains
  180 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 164
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
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  306 VAL
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain D residue  325 LEU
Chi-restraints excluded: chain E residue  352 SER
Chi-restraints excluded: chain E residue  356 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  324 SER
Chi-restraints excluded: chain H residue  352 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 12 optimal weight:   20.0000
   chunk 49 optimal weight:    0.8980
   chunk 38 optimal weight:    9.9990
   chunk 7 optimal weight:    0.8980
   chunk 34 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 48 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 41 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    2.3584

-------------------------------------------------------------------------------
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 = 0.3788 r_free = 0.3788 target = 0.108637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.085744 restraints weight = 9196.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.088429 restraints weight = 3917.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.090167 restraints weight = 2294.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.091222 restraints weight = 1627.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.091773 restraints weight = 1323.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5960  Z= 0.149
  Angle     :  0.594   5.221   7970  Z= 0.302
  Chirality :  0.049   0.124    890
  Planarity :  0.004   0.046   1020
  Dihedral  :  4.886  18.586    790
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 19.40 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.56 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.71 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 379 
 TYR   0.022   0.002   TYR F 310 
 PHE   0.009   0.001   PHE G 346 
 HIS   0.003   0.001   HIS F 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 5960)
  covalent geometry    : angle       0.59359 ( 7970)
  hydrogen bonds       : bond        0.01300 (   84)
  hydrogen bonds       : angle       3.96464 (  249)

*********************** 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
  186 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 171
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.7849 (mmmm) cc_final: 0.7448 (mmmm)
REVERT: I  327 ASN cc_start: 0.8582 (m110) cc_final: 0.8326 (m-40)
REVERT: I  360 ILE cc_start: 0.9106 (mt) cc_final: 0.8764 (mp)
REVERT: B  338 GLU cc_start: 0.7905 (mp0) cc_final: 0.7692 (mp0)
REVERT: B  347 LYS cc_start: 0.8012 (mmmm) cc_final: 0.7412 (mmmm)
REVERT: C  349 ARG cc_start: 0.6645 (mtt180) cc_final: 0.6011 (ttm-80)
REVERT: C  360 ILE cc_start: 0.8864 (mt) cc_final: 0.8537 (mp)
REVERT: D  317 LYS cc_start: 0.7449 (mttt) cc_final: 0.7036 (mtpt)
REVERT: D  331 LYS cc_start: 0.8820 (mttt) cc_final: 0.7782 (mmtt)
REVERT: D  336 GLN cc_start: 0.8879 (mp10) cc_final: 0.8618 (mp10)
REVERT: E  348 ASP cc_start: 0.7992 (t0) cc_final: 0.7641 (t0)
REVERT: F  311 LYS cc_start: 0.8773 (mtpt) cc_final: 0.8317 (mtpt)
REVERT: G  320 SER cc_start: 0.9373 (t) cc_final: 0.8475 (m)
REVERT: G  345 ASP cc_start: 0.8096 (t70) cc_final: 0.7885 (t70)
REVERT: G  375 LYS cc_start: 0.8450 (ttmt) cc_final: 0.7866 (mtpp)
REVERT: H  379 ARG cc_start: 0.7112 (mtm-85) cc_final: 0.6664 (ptt-90)
REVERT: J  322 CYS cc_start: 0.8561 (t) cc_final: 0.8200 (t)
  outliers start: 15
  outliers final: 14
  residues processed: 179
  average time/residue: 0.0793
  time to fit residues: 18.5329
Evaluate side-chains
  178 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 164
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
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  324 SER
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  324 SER
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  325 LEU
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 10 optimal weight:   40.0000
   chunk 61 optimal weight:    9.9990
   chunk 6 optimal weight:    0.9990
   chunk 42 optimal weight:   10.0000
   chunk 9 optimal weight:    7.9990
   chunk 62 optimal weight:    8.9990
   chunk 11 optimal weight:   20.0000
   chunk 51 optimal weight:    5.9990
   chunk 13 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 12 optimal weight:    7.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
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 = 0.3713 r_free = 0.3713 target = 0.102031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.079641 restraints weight = 9934.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.082080 restraints weight = 4444.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.083612 restraints weight = 2641.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.084549 restraints weight = 1906.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.085151 restraints weight = 1558.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.3473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.043   5960  Z= 0.305
  Angle     :  0.697   6.796   7970  Z= 0.360
  Chirality :  0.052   0.152    890
  Planarity :  0.005   0.049   1020
  Dihedral  :  5.364  20.704    790
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.85 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.57 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.71 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG I 379 
 TYR   0.025   0.003   TYR F 310 
 PHE   0.013   0.002   PHE B 378 
 HIS   0.003   0.001   HIS I 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00683 ( 5960)
  covalent geometry    : angle       0.69717 ( 7970)
  hydrogen bonds       : bond        0.01608 (   84)
  hydrogen bonds       : angle       3.91944 (  249)

*********************** 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
  196 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 176
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8426 (tt)
REVERT: A  342 GLU cc_start: 0.7700 (mp0) cc_final: 0.7382 (mp0)
REVERT: I  327 ASN cc_start: 0.8619 (m110) cc_final: 0.8377 (m110)
REVERT: C  349 ARG cc_start: 0.6820 (mtt180) cc_final: 0.5904 (ttm-80)
REVERT: C  360 ILE cc_start: 0.8985 (mt) cc_final: 0.8600 (mp)
REVERT: D  317 LYS cc_start: 0.7565 (mttt) cc_final: 0.7177 (mtpt)
REVERT: D  331 LYS cc_start: 0.8852 (mttt) cc_final: 0.7750 (mmtt)
REVERT: D  336 GLN cc_start: 0.8866 (mp10) cc_final: 0.8578 (mp10)
REVERT: D  353 LYS cc_start: 0.8987 (ttmt) cc_final: 0.7437 (mttp)
REVERT: E  379 ARG cc_start: 0.4476 (mmp-170) cc_final: 0.4193 (mmp-170)
REVERT: F  311 LYS cc_start: 0.8825 (mtpt) cc_final: 0.8415 (mtpt)
REVERT: F  342 GLU cc_start: 0.7984 (mp0) cc_final: 0.7430 (mp0)
REVERT: G  320 SER cc_start: 0.9408 (t) cc_final: 0.8464 (m)
REVERT: G  375 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8223 (ttmm)
REVERT: H  379 ARG cc_start: 0.7333 (mtm-85) cc_final: 0.6922 (ptt-90)
REVERT: J  322 CYS cc_start: 0.8702 (t) cc_final: 0.8233 (t)
  outliers start: 20
  outliers final: 16
  residues processed: 191
  average time/residue: 0.0847
  time to fit residues: 20.8147
Evaluate side-chains
  188 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 171
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 66 optimal weight:   20.0000
   chunk 16 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 36 optimal weight:    9.9990
   chunk 47 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.9184

-------------------------------------------------------------------------------
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 = 0.3799 r_free = 0.3799 target = 0.108710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.085986 restraints weight = 9148.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.088619 restraints weight = 3931.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.090372 restraints weight = 2309.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.091442 restraints weight = 1632.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.092182 restraints weight = 1313.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.3643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5960  Z= 0.139
  Angle     :  0.610   6.394   7970  Z= 0.311
  Chirality :  0.049   0.125    890
  Planarity :  0.004   0.047   1020
  Dihedral  :  4.882  18.854    790
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 22.39 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.53 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.68 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I 379 
 TYR   0.019   0.002   TYR F 310 
 PHE   0.007   0.001   PHE G 378 
 HIS   0.004   0.001   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 5960)
  covalent geometry    : angle       0.61017 ( 7970)
  hydrogen bonds       : bond        0.01201 (   84)
  hydrogen bonds       : angle       3.88147 (  249)

*********************** 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
  190 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 176
  time to evaluate  : 0.239 
Fit side-chains
REVERT: I  327 ASN cc_start: 0.8573 (m110) cc_final: 0.8329 (m110)
REVERT: C  349 ARG cc_start: 0.6784 (mtt180) cc_final: 0.5721 (ttm-80)
REVERT: C  360 ILE cc_start: 0.8913 (mt) cc_final: 0.8571 (mp)
REVERT: D  317 LYS cc_start: 0.7519 (mttt) cc_final: 0.6975 (mtpt)
REVERT: D  331 LYS cc_start: 0.8885 (mttt) cc_final: 0.7847 (mmtt)
REVERT: D  336 GLN cc_start: 0.8820 (mp10) cc_final: 0.8519 (mp10)
REVERT: D  340 LYS cc_start: 0.8570 (mptt) cc_final: 0.8355 (mmtm)
REVERT: D  353 LYS cc_start: 0.8907 (ttmt) cc_final: 0.7430 (mttp)
REVERT: E  348 ASP cc_start: 0.8151 (t0) cc_final: 0.7757 (t0)
REVERT: E  379 ARG cc_start: 0.4383 (mmp-170) cc_final: 0.4116 (mmp-170)
REVERT: F  311 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8341 (mtpt)
REVERT: F  328 ILE cc_start: 0.9416 (mm) cc_final: 0.9151 (mt)
REVERT: F  342 GLU cc_start: 0.8227 (mp0) cc_final: 0.7464 (mp0)
REVERT: G  320 SER cc_start: 0.9383 (t) cc_final: 0.8464 (m)
REVERT: G  345 ASP cc_start: 0.8067 (t70) cc_final: 0.7795 (t70)
REVERT: H  347 LYS cc_start: 0.8263 (mmmm) cc_final: 0.6716 (pttp)
REVERT: H  379 ARG cc_start: 0.7285 (mtm-85) cc_final: 0.6910 (ptt-90)
REVERT: J  322 CYS cc_start: 0.8610 (t) cc_final: 0.8227 (t)
  outliers start: 14
  outliers final: 13
  residues processed: 183
  average time/residue: 0.0836
  time to fit residues: 19.6934
Evaluate side-chains
  186 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 173
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
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  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  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 20 optimal weight:    0.8980
   chunk 17 optimal weight:    9.9990
   chunk 33 optimal weight:    0.0470
   chunk 23 optimal weight:    2.9990
   chunk 47 optimal weight:    7.9990
   chunk 68 optimal weight:    0.7980
   chunk 24 optimal weight:    7.9990
   chunk 36 optimal weight:    6.9990
   chunk 58 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 40 optimal weight:    0.4980
   overall best weight:    1.0480

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

Flipped N/Q/H residues before XYZ refinement:
D 329 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.112962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.090100 restraints weight = 9037.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.092947 restraints weight = 3824.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.094730 restraints weight = 2201.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.095800 restraints weight = 1554.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.096446 restraints weight = 1259.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.3808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5960  Z= 0.108
  Angle     :  0.586   6.271   7970  Z= 0.299
  Chirality :  0.049   0.151    890
  Planarity :  0.004   0.044   1020
  Dihedral  :  4.565  17.377    790
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.13 %
    Favored  : 93.87 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 23.13 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.47 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.63 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G 379 
 TYR   0.014   0.002   TYR B 310 
 PHE   0.007   0.001   PHE G 378 
 HIS   0.004   0.001   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 5960)
  covalent geometry    : angle       0.58647 ( 7970)
  hydrogen bonds       : bond        0.01108 (   84)
  hydrogen bonds       : angle       3.82730 (  249)

*********************** 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
  189 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 181
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8095 (ttmm)
REVERT: I  360 ILE cc_start: 0.9064 (mt) cc_final: 0.8756 (mp)
REVERT: B  338 GLU cc_start: 0.7929 (mp0) cc_final: 0.7601 (mp0)
REVERT: C  349 ARG cc_start: 0.6889 (mtt180) cc_final: 0.5936 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7422 (mttt) cc_final: 0.6892 (mtmt)
REVERT: D  331 LYS cc_start: 0.8848 (mttt) cc_final: 0.7846 (mmpt)
REVERT: D  336 GLN cc_start: 0.8717 (mp10) cc_final: 0.8382 (mp10)
REVERT: D  343 LYS cc_start: 0.8340 (ttmm) cc_final: 0.7099 (tppt)
REVERT: D  353 LYS cc_start: 0.8792 (ttmt) cc_final: 0.7283 (mttp)
REVERT: D  356 SER cc_start: 0.8818 (t) cc_final: 0.8527 (p)
REVERT: E  379 ARG cc_start: 0.4539 (mmp-170) cc_final: 0.4286 (mmp-170)
REVERT: F  311 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8265 (mtpp)
REVERT: F  328 ILE cc_start: 0.9411 (mm) cc_final: 0.9151 (mt)
REVERT: G  320 SER cc_start: 0.9371 (t) cc_final: 0.8436 (m)
REVERT: H  347 LYS cc_start: 0.7976 (mmmm) cc_final: 0.6533 (pttp)
REVERT: H  379 ARG cc_start: 0.7171 (mtm-85) cc_final: 0.6772 (ptt-90)
REVERT: J  310 TYR cc_start: 0.8816 (t80) cc_final: 0.8156 (t80)
REVERT: J  322 CYS cc_start: 0.8614 (t) cc_final: 0.8305 (t)
  outliers start: 8
  outliers final: 8
  residues processed: 187
  average time/residue: 0.0804
  time to fit residues: 19.3223
Evaluate side-chains
  178 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 170
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain H residue  306 VAL
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 13 optimal weight:   10.0000
   chunk 38 optimal weight:   30.0000
   chunk 34 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 30 optimal weight:    8.9990
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    9.9990
   chunk 53 optimal weight:    6.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    3.5788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.107194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.084580 restraints weight = 9247.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.087215 restraints weight = 4004.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.088841 restraints weight = 2363.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.090006 restraints weight = 1695.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.090577 restraints weight = 1358.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.3771

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= 0.203
  Angle     :  0.650   6.890   7970  Z= 0.332
  Chirality :  0.050   0.139    890
  Planarity :  0.004   0.046   1020
  Dihedral  :  4.832  17.996    790
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 22.69 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.47 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.64 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G 379 
 TYR   0.021   0.002   TYR F 310 
 PHE   0.010   0.002   PHE G 346 
 HIS   0.003   0.001   HIS I 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 5960)
  covalent geometry    : angle       0.65006 ( 7970)
  hydrogen bonds       : bond        0.01260 (   84)
  hydrogen bonds       : angle       3.76717 (  249)

*********************** 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
  187 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 172
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8238 (tt)
REVERT: A  347 LYS cc_start: 0.7721 (mmmm) cc_final: 0.7481 (mmmm)
REVERT: I  327 ASN cc_start: 0.8570 (m110) cc_final: 0.8319 (m-40)
REVERT: B  338 GLU cc_start: 0.8024 (mp0) cc_final: 0.7709 (mp0)
REVERT: B  347 LYS cc_start: 0.7898 (mmmm) cc_final: 0.7493 (mmmm)
REVERT: C  349 ARG cc_start: 0.6949 (mtt180) cc_final: 0.5881 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7483 (mttt) cc_final: 0.6907 (mtmt)
REVERT: D  331 LYS cc_start: 0.8886 (mttt) cc_final: 0.7825 (mmtt)
REVERT: D  336 GLN cc_start: 0.8812 (mp10) cc_final: 0.8501 (mp10)
REVERT: D  353 LYS cc_start: 0.8921 (ttmt) cc_final: 0.7403 (mttp)
REVERT: E  348 ASP cc_start: 0.8176 (t0) cc_final: 0.7755 (t0)
REVERT: F  311 LYS cc_start: 0.8809 (mtpt) cc_final: 0.8294 (mtpp)
REVERT: G  320 SER cc_start: 0.9391 (t) cc_final: 0.8447 (m)
REVERT: H  347 LYS cc_start: 0.8231 (mmmm) cc_final: 0.6740 (pttp)
REVERT: H  379 ARG cc_start: 0.7256 (mtm-85) cc_final: 0.6866 (ptt-90)
REVERT: J  322 CYS cc_start: 0.8683 (t) cc_final: 0.8316 (t)
REVERT: J  354 ILE cc_start: 0.8656 (mm) cc_final: 0.8441 (mp)
  outliers start: 15
  outliers final: 13
  residues processed: 181
  average time/residue: 0.0802
  time to fit residues: 18.6814
Evaluate side-chains
  184 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 170
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 SER
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain I residue  325 LEU
Chi-restraints excluded: chain I residue  350 VAL
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain F residue  306 VAL
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain G residue  325 LEU
Chi-restraints excluded: chain H residue  306 VAL
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 5 optimal weight:    9.9990
   chunk 39 optimal weight:   20.0000
   chunk 9 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 59 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 53 optimal weight:    6.9990
   chunk 63 optimal weight:   10.0000
   overall best weight:    5.5990

-------------------------------------------------------------------------------
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 = 0.3729 r_free = 0.3729 target = 0.102476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.080402 restraints weight = 9942.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.082838 restraints weight = 4420.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.084390 restraints weight = 2642.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.085342 restraints weight = 1902.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.085852 restraints weight = 1544.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.3825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048   5960  Z= 0.296
  Angle     :  0.719   7.080   7970  Z= 0.371
  Chirality :  0.052   0.154    890
  Planarity :  0.004   0.047   1020
  Dihedral  :  5.243  20.660    790
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.33 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 22.69 %
    Favored  : 74.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.54 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G 379 
 TYR   0.011   0.002   TYR D 310 
 PHE   0.013   0.002   PHE I 346 
 HIS   0.003   0.001   HIS I 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00662 ( 5960)
  covalent geometry    : angle       0.71853 ( 7970)
  hydrogen bonds       : bond        0.01472 (   84)
  hydrogen bonds       : angle       3.81891 (  249)

*********************** 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
  188 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 168
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A  325 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8288 (tt)
REVERT: A  342 GLU cc_start: 0.7590 (mp0) cc_final: 0.7089 (mp0)
REVERT: I  327 ASN cc_start: 0.8599 (m110) cc_final: 0.8371 (m110)
REVERT: C  349 ARG cc_start: 0.6949 (mtt180) cc_final: 0.5909 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7539 (mttt) cc_final: 0.7101 (mtpt)
REVERT: D  327 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8294 (t0)
REVERT: D  331 LYS cc_start: 0.8920 (mttt) cc_final: 0.7842 (mmtt)
REVERT: D  336 GLN cc_start: 0.8872 (mp10) cc_final: 0.8583 (mp10)
REVERT: D  353 LYS cc_start: 0.9038 (ttmt) cc_final: 0.7496 (mttp)
REVERT: E  348 ASP cc_start: 0.8379 (t0) cc_final: 0.8132 (t70)
REVERT: E  349 ARG cc_start: 0.7203 (mtt180) cc_final: 0.6068 (mmt-90)
REVERT: F  311 LYS cc_start: 0.8926 (mtpt) cc_final: 0.8353 (mtpp)
REVERT: H  379 ARG cc_start: 0.7316 (mtm-85) cc_final: 0.7057 (ptt-90)
REVERT: J  322 CYS cc_start: 0.8708 (t) cc_final: 0.8280 (t)
REVERT: J  354 ILE cc_start: 0.8742 (mm) cc_final: 0.8505 (mp)
  outliers start: 20
  outliers final: 17
  residues processed: 181
  average time/residue: 0.0839
  time to fit residues: 19.4867
Evaluate side-chains
  187 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 168
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
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 I residue  350 VAL
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain C residue  352 SER
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  316 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 12 optimal weight:   20.0000
   chunk 40 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 44 optimal weight:    6.9990
   chunk 0 optimal weight:    8.9990
   chunk 68 optimal weight:    7.9990
   chunk 59 optimal weight:    0.2980
   chunk 63 optimal weight:    3.9990
   overall best weight:    2.2586

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.110016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.087513 restraints weight = 9395.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.090065 restraints weight = 4142.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.091672 restraints weight = 2454.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.092746 restraints weight = 1762.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.093395 restraints weight = 1423.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.3912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5960  Z= 0.155
  Angle     :  0.644   6.865   7970  Z= 0.333
  Chirality :  0.050   0.151    890
  Planarity :  0.004   0.047   1020
  Dihedral  :  4.893  20.405    790
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 23.88 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.49 (0.25), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.65 (0.19), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G 379 
 TYR   0.022   0.002   TYR F 310 
 PHE   0.012   0.002   PHE J 346 
 HIS   0.004   0.001   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 5960)
  covalent geometry    : angle       0.64427 ( 7970)
  hydrogen bonds       : bond        0.01187 (   84)
  hydrogen bonds       : angle       3.75984 (  249)

********************** 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
  193 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 178
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.7909 (mmmm) cc_final: 0.7606 (mmmm)
REVERT: I  327 ASN cc_start: 0.8606 (m110) cc_final: 0.8368 (m110)
REVERT: B  338 GLU cc_start: 0.8014 (mp0) cc_final: 0.7695 (mp0)
REVERT: B  347 LYS cc_start: 0.8068 (mmmm) cc_final: 0.7488 (mmmm)
REVERT: C  349 ARG cc_start: 0.6945 (mtt180) cc_final: 0.5976 (ttm-80)
REVERT: D  317 LYS cc_start: 0.7497 (mttt) cc_final: 0.6987 (mtpt)
REVERT: D  327 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8338 (t0)
REVERT: D  331 LYS cc_start: 0.8896 (mttt) cc_final: 0.7919 (mmtt)
REVERT: D  336 GLN cc_start: 0.8839 (mp10) cc_final: 0.8559 (mp10)
REVERT: D  343 LYS cc_start: 0.8453 (ttmm) cc_final: 0.7225 (tppt)
REVERT: D  353 LYS cc_start: 0.8914 (ttmt) cc_final: 0.7464 (mttp)
REVERT: E  348 ASP cc_start: 0.8139 (t0) cc_final: 0.7687 (t0)
REVERT: E  376 LEU cc_start: 0.9496 (tt) cc_final: 0.9269 (tt)
REVERT: F  311 LYS cc_start: 0.8866 (mtpt) cc_final: 0.8338 (mtpp)
REVERT: F  328 ILE cc_start: 0.9460 (mm) cc_final: 0.9182 (mt)
REVERT: F  338 GLU cc_start: 0.7802 (mp0) cc_final: 0.7540 (mp0)
REVERT: G  320 SER cc_start: 0.9409 (t) cc_final: 0.8469 (m)
REVERT: H  347 LYS cc_start: 0.8252 (mmmm) cc_final: 0.6713 (pttp)
REVERT: H  379 ARG cc_start: 0.7240 (mtm-85) cc_final: 0.6912 (ptt-90)
REVERT: J  310 TYR cc_start: 0.8902 (t80) cc_final: 0.8108 (t80)
REVERT: J  322 CYS cc_start: 0.8630 (t) cc_final: 0.8293 (t)
REVERT: J  354 ILE cc_start: 0.8816 (mm) cc_final: 0.8577 (mp)
REVERT: J  375 LYS cc_start: 0.8715 (ttmt) cc_final: 0.8376 (ttmm)
REVERT: J  380 GLU cc_start: 0.7608 (tm-30) cc_final: 0.6657 (tp30)
  outliers start: 15
  outliers final: 14
  residues processed: 184
  average time/residue: 0.0848
  time to fit residues: 20.0338
Evaluate side-chains
  193 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 178
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
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  350 VAL
Chi-restraints excluded: chain B residue  306 VAL
Chi-restraints excluded: chain B residue  324 SER
Chi-restraints excluded: chain C residue  352 SER
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  324 SER
Chi-restraints excluded: chain F residue  352 SER
Chi-restraints excluded: chain H residue  306 VAL
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 8 optimal weight:   10.0000
   chunk 63 optimal weight:    9.9990
   chunk 33 optimal weight:    8.9990
   chunk 37 optimal weight:    9.9990
   chunk 32 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0040
   chunk 58 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.1194

-------------------------------------------------------------------------------
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 = 0.3880 r_free = 0.3880 target = 0.113374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.090092 restraints weight = 8940.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.092908 restraints weight = 3851.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.094699 restraints weight = 2258.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.095845 restraints weight = 1608.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.096393 restraints weight = 1289.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.4025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5960  Z= 0.118
  Angle     :  0.626   6.204   7970  Z= 0.322
  Chirality :  0.049   0.140    890
  Planarity :  0.004   0.046   1020
  Dihedral  :  4.542  17.174    790
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 24.48 %
    Favored  : 73.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.42 (0.26), residues: 750
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.60 (0.20), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G 379 
 TYR   0.015   0.002   TYR B 310 
 PHE   0.012   0.001   PHE J 346 
 HIS   0.004   0.001   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 5960)
  covalent geometry    : angle       0.62571 ( 7970)
  hydrogen bonds       : bond        0.01130 (   84)
  hydrogen bonds       : angle       3.71751 (  249)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1025.47 seconds
wall clock time: 18 minutes 37.15 seconds (1117.15 seconds total)