Starting phenix.real_space_refine
on Mon Feb 10 21:48:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ot6_17171/02_2025/8ot6_17171.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ot6_17171/02_2025/8ot6_17171.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ot6_17171/02_2025/8ot6_17171.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ot6_17171/02_2025/8ot6_17171.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ot6_17171/02_2025/8ot6_17171.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ot6_17171/02_2025/8ot6_17171.cif"
  }
  resolution = 2.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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       5      5.16       5
     C    1800      2.51       5
     N     530      2.21       5
     O     535      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 2870
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 574
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 3, 'TRANS': 71}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 2.55, per 1000 atoms: 0.89
  Number of scatterers: 2870
  At special positions: 0
  Unit cell: (139.256, 119.48, 32.96, 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       5     16.00
     O     535      8.00
     N     530      7.00
     C    1800      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: 0.79
  Conformation dependent library (CDL) restraints added in 359.4 milliseconds
  

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  660

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 16 sheets defined
      0.0% alpha, 56.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 310
      removed outlier: 6.392A  pdb=" N   GLN A 307 " --> pdb=" O   ILE B 308 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   TYR B 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   VAL A 309 " --> pdb=" O   TYR B 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314
      removed outlier: 6.764A  pdb=" N   VAL A 313 " --> pdb=" O   ASP B 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 322
      removed outlier: 6.445A  pdb=" N   LYS A 317 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 8.172A  pdb=" N   SER B 320 " --> pdb=" O   LYS A 317 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   THR A 319 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
      removed outlier: 8.458A  pdb=" N   CYS B 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   LYS A 321 " --> pdb=" O   CYS B 322 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 325 through 330
      removed outlier: 6.800A  pdb=" N   GLY B 326 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ASN A 327 " --> pdb=" O   GLY B 326 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   GLY A 326 " --> pdb=" O   ASN E 327 " (cutoff:3.500A)
      removed outlier: 8.602A  pdb=" N   HIS E 329 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   ILE A 328 " --> pdb=" O   HIS E 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 346
      removed outlier: 8.995A  pdb=" N   VAL A 337 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 10.116A  pdb=" N   LYS B 340 " --> pdb=" O   VAL A 337 " (cutoff:3.500A)
      removed outlier: 8.912A  pdb=" N   VAL A 339 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
      removed outlier: 10.083A  pdb=" N   GLU B 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 9.214A  pdb=" N   SER A 341 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
      removed outlier: 9.316A  pdb=" N   LEU B 344 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   LYS A 343 " --> pdb=" O   LEU B 344 " (cutoff:3.500A)
      removed outlier: 8.093A  pdb=" N   PHE B 346 " --> pdb=" O   LYS A 343 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   ASP A 345 " --> pdb=" O   PHE B 346 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   GLU A 338 " --> pdb=" O   VAL E 337 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   VAL E 339 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   LYS A 340 " --> pdb=" O   VAL E 339 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   SER E 341 " --> pdb=" O   LYS A 340 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   GLU A 342 " --> pdb=" O   SER E 341 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   LYS E 343 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 357
      removed outlier: 6.411A  pdb=" N   GLN A 351 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   ILE B 354 " --> pdb=" O   GLN A 351 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   LYS A 353 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 7.371A  pdb=" N   SER B 356 " --> pdb=" O   LYS A 353 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   GLY A 355 " --> pdb=" O   SER B 356 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 360 through 362
      removed outlier: 6.323A  pdb=" N   THR A 361 " --> pdb=" O   HIS E 362 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 369 through 378
      removed outlier: 6.618A  pdb=" N   LYS A 369 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
      removed outlier: 8.147A  pdb=" N   GLU B 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   ILE A 371 " --> pdb=" O   GLU B 372 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   HIS B 374 " --> pdb=" O   ILE A 371 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   THR A 373 " --> pdb=" O   HIS B 374 " (cutoff:3.500A)
      removed outlier: 7.946A  pdb=" N   LEU B 376 " --> pdb=" O   THR A 373 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   LYS A 375 " --> pdb=" O   LEU B 376 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   PHE B 378 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   THR A 377 " --> pdb=" O   PHE B 378 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 306 through 310
    Processing sheet with id=AB1, first strand: chain 'C' and resid 313 through 314
    Processing sheet with id=AB2, first strand: chain 'C' and resid 317 through 322
    Processing sheet with id=AB3, first strand: chain 'C' and resid 325 through 330
      removed outlier: 6.141A  pdb=" N   GLY C 326 " --> pdb=" O   ASN D 327 " (cutoff:3.500A)
      removed outlier: 8.601A  pdb=" N   HIS D 329 " --> pdb=" O   GLY C 326 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   ILE C 328 " --> pdb=" O   HIS D 329 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'C' and resid 337 through 346
      removed outlier: 6.918A  pdb=" N   GLU C 338 " --> pdb=" O   VAL D 337 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   VAL D 339 " --> pdb=" O   GLU C 338 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   LYS C 340 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   SER D 341 " --> pdb=" O   LYS C 340 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   GLU C 342 " --> pdb=" O   SER D 341 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   LYS D 343 " --> pdb=" O   GLU C 342 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 350 through 357
    Processing sheet with id=AB6, first strand: chain 'C' and resid 360 through 362
      removed outlier: 6.323A  pdb=" N   THR C 361 " --> pdb=" O   HIS D 362 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'C' and resid 369 through 378

    63 hydrogen bonds defined for protein.
    189 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: 0.64

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 628
        1.34 -     1.45: 634
        1.45 -     1.57: 1648
        1.57 -     1.69: 0
        1.69 -     1.81: 5
  Bond restraints: 2915
  Sorted by residual:
  bond pdb=" C   LYS B 331 "
       pdb=" N   PRO B 332 "
    ideal  model  delta    sigma   weight residual
    1.331  1.355 -0.024 1.28e-02 6.10e+03 3.38e+00
  bond pdb=" CA  SER D 352 "
       pdb=" CB  SER D 352 "
    ideal  model  delta    sigma   weight residual
    1.533  1.498  0.035 1.90e-02 2.77e+03 3.37e+00
  bond pdb=" CA  SER A 352 "
       pdb=" CB  SER A 352 "
    ideal  model  delta    sigma   weight residual
    1.533  1.499  0.034 1.90e-02 2.77e+03 3.23e+00
  bond pdb=" CA  SER E 352 "
       pdb=" CB  SER E 352 "
    ideal  model  delta    sigma   weight residual
    1.533  1.499  0.034 1.90e-02 2.77e+03 3.23e+00
  bond pdb=" CA  SER C 352 "
       pdb=" CB  SER C 352 "
    ideal  model  delta    sigma   weight residual
    1.533  1.499  0.034 1.90e-02 2.77e+03 3.23e+00
  ... (remaining 2910 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 2697
        1.04 -     2.07: 931
        2.07 -     3.11: 184
        3.11 -     4.14: 63
        4.14 -     5.18: 25
  Bond angle restraints: 3900
  Sorted by residual:
  angle pdb=" N   GLY D 326 "
        pdb=" CA  GLY D 326 "
        pdb=" C   GLY D 326 "
      ideal   model   delta    sigma   weight residual
     110.69  115.87   -5.18 1.33e+00 5.65e-01 1.52e+01
  angle pdb=" N   GLY A 326 "
        pdb=" CA  GLY A 326 "
        pdb=" C   GLY A 326 "
      ideal   model   delta    sigma   weight residual
     110.69  115.86   -5.17 1.33e+00 5.65e-01 1.51e+01
  angle pdb=" N   GLY E 326 "
        pdb=" CA  GLY E 326 "
        pdb=" C   GLY E 326 "
      ideal   model   delta    sigma   weight residual
     110.69  115.86   -5.17 1.33e+00 5.65e-01 1.51e+01
  angle pdb=" N   GLY C 326 "
        pdb=" CA  GLY C 326 "
        pdb=" C   GLY C 326 "
      ideal   model   delta    sigma   weight residual
     110.69  115.85   -5.16 1.33e+00 5.65e-01 1.51e+01
  angle pdb=" N   GLY B 326 "
        pdb=" CA  GLY B 326 "
        pdb=" C   GLY B 326 "
      ideal   model   delta    sigma   weight residual
     110.69  115.85   -5.16 1.33e+00 5.65e-01 1.51e+01
  ... (remaining 3895 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.54: 1684
       15.54 -    31.08: 61
       31.08 -    46.61: 25
       46.61 -    62.15: 5
       62.15 -    77.69: 5
  Dihedral angle restraints: 1780
    sinusoidal: 745
      harmonic: 1035
  Sorted by residual:
  dihedral pdb=" CA  ILE C 360 "
           pdb=" C   ILE C 360 "
           pdb=" N   THR C 361 "
           pdb=" CA  THR C 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.23   18.77     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  ILE D 360 "
           pdb=" C   ILE D 360 "
           pdb=" N   THR D 361 "
           pdb=" CA  THR D 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.26   18.74     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  ILE A 360 "
           pdb=" C   ILE A 360 "
           pdb=" N   THR A 361 "
           pdb=" CA  THR A 361 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.26   18.74     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 1777 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 121
       0.038 -    0.077: 175
       0.077 -    0.115: 124
       0.115 -    0.153: 5
       0.153 -    0.192: 15
  Chirality restraints: 440
  Sorted by residual:
  chirality pdb=" CB  ILE D 328 "
            pdb=" CA  ILE D 328 "
            pdb=" CG1 ILE D 328 "
            pdb=" CG2 ILE D 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.20e-01
  chirality pdb=" CB  ILE E 328 "
            pdb=" CA  ILE E 328 "
            pdb=" CG1 ILE E 328 "
            pdb=" CG2 ILE E 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.15e-01
  chirality pdb=" CB  ILE A 328 "
            pdb=" CA  ILE A 328 "
            pdb=" CG1 ILE A 328 "
            pdb=" CG2 ILE A 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.10e-01
  ... (remaining 437 not shown)

  Planarity restraints: 495
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 363 "    0.010 2.00e-02 2.50e+03   1.99e-02 3.94e+00
        pdb=" C   VAL D 363 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   VAL D 363 "    0.013 2.00e-02 2.50e+03
        pdb=" N   PRO D 364 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 363 "   -0.010 2.00e-02 2.50e+03   1.97e-02 3.88e+00
        pdb=" C   VAL A 363 "    0.034 2.00e-02 2.50e+03
        pdb=" O   VAL A 363 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   PRO A 364 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 363 "    0.010 2.00e-02 2.50e+03   1.97e-02 3.86e+00
        pdb=" C   VAL C 363 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   VAL C 363 "    0.013 2.00e-02 2.50e+03
        pdb=" N   PRO C 364 "    0.011 2.00e-02 2.50e+03
  ... (remaining 492 not shown)

  Histogram of nonbonded interaction distances:
        2.63 -     3.08: 1689
        3.08 -     3.54: 2595
        3.54 -     3.99: 4320
        3.99 -     4.45: 4408
        4.45 -     4.90: 8692
  Nonbonded interactions: 21704
  Sorted by model distance:
  nonbonded pdb=" N   ASP D 348 "
            pdb=" O   ASP D 348 "
     model   vdw
     2.631 2.496
  nonbonded pdb=" N   ASP A 348 "
            pdb=" O   ASP A 348 "
     model   vdw
     2.631 2.496
  nonbonded pdb=" N   ASP E 348 "
            pdb=" O   ASP E 348 "
     model   vdw
     2.631 2.496
  nonbonded pdb=" N   ASP C 348 "
            pdb=" O   ASP C 348 "
     model   vdw
     2.631 2.496
  nonbonded pdb=" N   ASP B 348 "
            pdb=" O   ASP B 348 "
     model   vdw
     2.632 2.496
  ... (remaining 21699 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

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 individual isotropic
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:             3.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.090
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.000
  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:11.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8984
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      :  0.007   0.037   2915  Z= 0.499
  Angle     :  1.165   5.180   3900  Z= 0.754
  Chirality :  0.071   0.192    440
  Planarity :  0.008   0.041    495
  Dihedral  : 11.962  77.688   1120
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 0.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  0.00 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.003   HIS C 329 
 PHE   0.007   0.003   PHE C 346 
 TYR   0.008   0.004   TYR C 310 
 ARG   0.005   0.001   ARG E 349 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 148
  time to evaluate  : 0.275 
Fit side-chains
REVERT: B  347 LYS cc_start: 0.8879 (mttm) cc_final: 0.8288 (pmtt)
REVERT: B  379 ARG cc_start: 0.7889 (mtt180) cc_final: 0.7674 (ptt-90)
REVERT: C  311 LYS cc_start: 0.8575 (mtmt) cc_final: 0.8369 (mtmt)
REVERT: C  347 LYS cc_start: 0.8959 (mttm) cc_final: 0.8354 (pmtt)
REVERT: C  379 ARG cc_start: 0.7844 (mtt180) cc_final: 0.7614 (ptt-90)
REVERT: D  311 LYS cc_start: 0.8424 (mtmt) cc_final: 0.7870 (mptp)
REVERT: D  349 ARG cc_start: 0.8872 (mtt180) cc_final: 0.7801 (mmm160)
REVERT: E  311 LYS cc_start: 0.8519 (mtmt) cc_final: 0.8020 (mptp)
REVERT: E  349 ARG cc_start: 0.8863 (mtt180) cc_final: 0.7952 (mmm160)
  outliers start: 5
  outliers final: 1
  residues processed: 153
  average time/residue: 1.5930
  time to fit residues: 247.6106
Evaluate side-chains
  87 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  325 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 26 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 17 optimal weight:    7.9990
   chunk 27 optimal weight:    0.7980
   chunk 10 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 20 optimal weight:    0.0030
   chunk 31 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   overall best weight:    2.0794

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
B 351 GLN
D 307 GLN
D 351 GLN
E 351 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.128230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.111607 restraints weight = 3073.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 1.25
r_work: 0.3594 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.3517 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9023
moved from start:          0.2485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2915  Z= 0.223
  Angle     :  0.608   5.659   3900  Z= 0.298
  Chirality :  0.049   0.141    440
  Planarity :  0.003   0.022    495
  Dihedral  :  5.249  29.263    387
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.03 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.67 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 329 
 PHE   0.004   0.001   PHE A 346 
 TYR   0.009   0.002   TYR E 310 
 ARG   0.002   0.000   ARG D 379 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A  338 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7409 (tp30)
REVERT: C  351 GLN cc_start: 0.8877 (mt0) cc_final: 0.8667 (mt0)
REVERT: D  379 ARG cc_start: 0.5819 (OUTLIER) cc_final: 0.5420 (tpt170)
REVERT: E  349 ARG cc_start: 0.8704 (mtt180) cc_final: 0.7771 (mmp-170)
  outliers start: 7
  outliers final: 0
  residues processed: 88
  average time/residue: 1.3674
  time to fit residues: 122.8569
Evaluate side-chains
  85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain D residue  379 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 34 optimal weight:    7.9990
   chunk 22 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    0.0370
   chunk 7 optimal weight:   10.0000
   chunk 32 optimal weight:    9.9990
   chunk 30 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 8 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    3.1262

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
D 307 GLN
E 351 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.125844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.109824 restraints weight = 3077.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3673 rms_B_bonded: 1.22
r_work: 0.3573 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.3495 rms_B_bonded: 2.43 restraints_weight: 0.2500
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9035
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   2915  Z= 0.302
  Angle     :  0.612   5.149   3900  Z= 0.306
  Chirality :  0.050   0.145    440
  Planarity :  0.003   0.020    495
  Dihedral  :  5.117  15.298    385
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.45 %
    Favored  : 82.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.04 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.55 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 329 
 PHE   0.006   0.002   PHE E 346 
 TYR   0.010   0.002   TYR E 310 
 ARG   0.002   0.001   ARG D 379 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8472 (mtt180)
REVERT: B  338 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7486 (tp30)
REVERT: D  379 ARG cc_start: 0.6056 (OUTLIER) cc_final: 0.5512 (mmt-90)
REVERT: E  349 ARG cc_start: 0.8659 (mtt180) cc_final: 0.7409 (tpt90)
  outliers start: 7
  outliers final: 0
  residues processed: 85
  average time/residue: 1.4845
  time to fit residues: 129.0153
Evaluate side-chains
  86 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain D residue  379 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 13 optimal weight:    0.0570
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0870
   chunk 30 optimal weight:    0.0040
   chunk 17 optimal weight:    9.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    1.0090

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
B 351 GLN
D 307 GLN
D 351 GLN
E 351 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.127893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.112637 restraints weight = 3274.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 1.21
r_work: 0.3639 rms_B_bonded: 1.45 restraints_weight: 0.5000
r_work: 0.3565 rms_B_bonded: 2.44 restraints_weight: 0.2500
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8992
moved from start:          0.3120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   2915  Z= 0.130
  Angle     :  0.516   5.356   3900  Z= 0.248
  Chirality :  0.048   0.126    440
  Planarity :  0.003   0.018    495
  Dihedral  :  4.642  13.185    385
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 1.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.97 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.37), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.45 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B 374 
 PHE   0.005   0.001   PHE D 346 
 TYR   0.010   0.002   TYR A 310 
 ARG   0.001   0.000   ARG C 379 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.382 
Fit side-chains
REVERT: B  338 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7287 (tp30)
REVERT: D  379 ARG cc_start: 0.5910 (OUTLIER) cc_final: 0.5372 (mmt-90)
REVERT: E  349 ARG cc_start: 0.8663 (mtt180) cc_final: 0.7563 (mmp-170)
  outliers start: 5
  outliers final: 0
  residues processed: 86
  average time/residue: 1.4407
  time to fit residues: 126.4200
Evaluate side-chains
  85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain D residue  379 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 7 optimal weight:    6.9990
   chunk 14 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 24 optimal weight:    9.9990
   chunk 8 optimal weight:   10.0000
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
B 351 GLN
C 307 GLN
D 307 GLN
E 351 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.125157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.109061 restraints weight = 3124.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 1.23
r_work: 0.3559 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.3482 rms_B_bonded: 2.40 restraints_weight: 0.2500
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9041
moved from start:          0.3030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   2915  Z= 0.355
  Angle     :  0.613   5.322   3900  Z= 0.308
  Chirality :  0.050   0.146    440
  Planarity :  0.003   0.028    495
  Dihedral  :  5.124  14.789    385
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.36 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.45 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 329 
 PHE   0.007   0.002   PHE A 346 
 TYR   0.010   0.003   TYR E 310 
 ARG   0.003   0.001   ARG D 379 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8458 (mtt180)
REVERT: B  338 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7547 (tp30)
REVERT: D  379 ARG cc_start: 0.5730 (OUTLIER) cc_final: 0.5127 (mmt-90)
REVERT: E  349 ARG cc_start: 0.8662 (mtt180) cc_final: 0.7403 (tpt90)
  outliers start: 7
  outliers final: 1
  residues processed: 86
  average time/residue: 1.4595
  time to fit residues: 127.9599
Evaluate side-chains
  87 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain D residue  379 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0980
   chunk 3 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 31 optimal weight:    7.9990
   chunk 8 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    3.6188

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
C 307 GLN
D 307 GLN
E 351 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.125178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.109142 restraints weight = 3151.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 1.23
r_work: 0.3562 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.3484 rms_B_bonded: 2.41 restraints_weight: 0.2500
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9041
moved from start:          0.3037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   2915  Z= 0.339
  Angle     :  0.607   4.938   3900  Z= 0.308
  Chirality :  0.050   0.144    440
  Planarity :  0.003   0.033    495
  Dihedral  :  5.164  14.687    385
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.67 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.88 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.42 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E 329 
 PHE   0.008   0.002   PHE A 346 
 TYR   0.011   0.003   TYR E 310 
 ARG   0.003   0.001   ARG D 379 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.344 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8460 (mtt180)
REVERT: B  338 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7622 (tp30)
REVERT: D  379 ARG cc_start: 0.5729 (OUTLIER) cc_final: 0.4469 (mpt90)
REVERT: E  349 ARG cc_start: 0.8671 (mtt180) cc_final: 0.7397 (tpt90)
  outliers start: 5
  outliers final: 1
  residues processed: 85
  average time/residue: 1.4595
  time to fit residues: 126.5084
Evaluate side-chains
  87 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain D residue  379 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 34 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
B 307 GLN
C 307 GLN
D 307 GLN
E 351 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.128865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.113311 restraints weight = 3189.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 1.22
r_work: 0.3624 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.3549 rms_B_bonded: 2.41 restraints_weight: 0.2500
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9004
moved from start:          0.3198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   2915  Z= 0.144
  Angle     :  0.518   5.343   3900  Z= 0.254
  Chirality :  0.048   0.128    440
  Planarity :  0.003   0.019    495
  Dihedral  :  4.722  13.542    385
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 1.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 17.27 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.37), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.36 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS D 374 
 PHE   0.005   0.001   PHE A 346 
 TYR   0.011   0.003   TYR E 310 
 ARG   0.002   0.000   ARG B 379 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8474 (mtt180)
REVERT: D  379 ARG cc_start: 0.5586 (OUTLIER) cc_final: 0.4454 (mmp-170)
REVERT: E  349 ARG cc_start: 0.8641 (mtt180) cc_final: 0.7551 (mmp-170)
  outliers start: 4
  outliers final: 0
  residues processed: 84
  average time/residue: 1.4713
  time to fit residues: 126.0292
Evaluate side-chains
  85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain D residue  379 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 32 optimal weight:    9.9990
   chunk 2 optimal weight:    8.9990
   chunk 30 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   chunk 28 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9980
   chunk 24 optimal weight:    7.9990
   overall best weight:    2.2784

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

Flipped N/Q/H residues before XYZ refinement:
B 307 GLN
B 351 GLN
C 307 GLN
D 307 GLN
E 351 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.126676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.110795 restraints weight = 3177.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 1.22
r_work: 0.3591 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.3514 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9024
moved from start:          0.3140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2915  Z= 0.227
  Angle     :  0.561   5.685   3900  Z= 0.278
  Chirality :  0.049   0.136    440
  Planarity :  0.003   0.022    495
  Dihedral  :  4.938  14.312    385
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 1.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 17.58 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.79 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.36 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 329 
 PHE   0.006   0.002   PHE A 346 
 TYR   0.011   0.002   TYR E 310 
 ARG   0.002   0.000   ARG D 379 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8471 (mtt180)
REVERT: D  379 ARG cc_start: 0.5540 (OUTLIER) cc_final: 0.3926 (mmt-90)
REVERT: E  349 ARG cc_start: 0.8642 (mtt180) cc_final: 0.7401 (tpt90)
  outliers start: 4
  outliers final: 1
  residues processed: 85
  average time/residue: 1.4566
  time to fit residues: 126.3336
Evaluate side-chains
  86 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain D residue  379 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 18 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 16 optimal weight:   10.0000
   chunk 26 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 351 GLN
B 307 GLN
B 351 GLN
C 307 GLN
D 307 GLN
E 351 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.125768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.109782 restraints weight = 3141.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 1.22
r_work: 0.3572 rms_B_bonded: 1.42 restraints_weight: 0.5000
r_work: 0.3494 rms_B_bonded: 2.40 restraints_weight: 0.2500
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9032
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2915  Z= 0.286
  Angle     :  0.594   6.701   3900  Z= 0.298
  Chirality :  0.050   0.141    440
  Planarity :  0.003   0.031    495
  Dihedral  :  5.067  14.496    385
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 1.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 17.88 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.36 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 329 
 PHE   0.007   0.002   PHE A 346 
 TYR   0.011   0.002   TYR E 310 
 ARG   0.003   0.001   ARG D 379 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8460 (mtt180)
REVERT: D  379 ARG cc_start: 0.5601 (OUTLIER) cc_final: 0.4219 (mmp80)
REVERT: E  349 ARG cc_start: 0.8652 (mtt180) cc_final: 0.7404 (tpt90)
  outliers start: 4
  outliers final: 1
  residues processed: 85
  average time/residue: 1.4763
  time to fit residues: 128.0212
Evaluate side-chains
  86 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain D residue  379 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 11 optimal weight:    0.0980
   chunk 8 optimal weight:    9.9990
   chunk 2 optimal weight:    7.9990
   chunk 23 optimal weight:   10.0000
   chunk 10 optimal weight:    8.9990
   chunk 0 optimal weight:    9.9990
   chunk 18 optimal weight:    0.9980
   chunk 7 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 29 optimal weight:   10.0000
   overall best weight:    3.6186

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
B 307 GLN
B 351 GLN
C 307 GLN
D 307 GLN
E 351 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.125168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.109140 restraints weight = 3175.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 1.22
r_work: 0.3561 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.3485 rms_B_bonded: 2.40 restraints_weight: 0.2500
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9038
moved from start:          0.3096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   2915  Z= 0.335
  Angle     :  0.621   7.437   3900  Z= 0.313
  Chirality :  0.050   0.144    440
  Planarity :  0.004   0.038    495
  Dihedral  :  5.151  14.796    385
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 18.18 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.80 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.36 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 329 
 PHE   0.008   0.002   PHE A 346 
 TYR   0.011   0.002   TYR E 310 
 ARG   0.003   0.001   ARG D 379 

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

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

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  730 Ramachandran restraints generated.
    365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.345 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8461 (mtt180)
REVERT: D  379 ARG cc_start: 0.5554 (OUTLIER) cc_final: 0.4782 (tpm170)
REVERT: E  349 ARG cc_start: 0.8665 (mtt180) cc_final: 0.7394 (tpt90)
  outliers start: 3
  outliers final: 1
  residues processed: 84
  average time/residue: 1.4488
  time to fit residues: 124.1400
Evaluate side-chains
  86 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain D residue  340 LYS
Chi-restraints excluded: chain D residue  379 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0010
   chunk 18 optimal weight:    0.9990
   chunk 3 optimal weight:    9.9990
   chunk 31 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   chunk 10 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 14 optimal weight:    8.9990
   overall best weight:    2.9994

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 351 GLN
B 307 GLN
B 351 GLN
C 307 GLN
D 307 GLN
E 351 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.125608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.109700 restraints weight = 3092.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 1.21
r_work: 0.3573 rms_B_bonded: 1.42 restraints_weight: 0.5000
r_work: 0.3495 rms_B_bonded: 2.40 restraints_weight: 0.2500
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9032
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   2915  Z= 0.287
  Angle     :  0.601   7.249   3900  Z= 0.301
  Chirality :  0.050   0.140    440
  Planarity :  0.003   0.032    495
  Dihedral  :  5.122  14.749    385
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 17.88 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.34 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E 329 
 PHE   0.007   0.002   PHE A 346 
 TYR   0.011   0.002   TYR E 310 
 ARG   0.003   0.001   ARG D 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4461.92 seconds
wall clock time: 79 minutes 17.43 seconds (4757.43 seconds total)