Starting phenix.real_space_refine
on Fri Aug 22 13:01:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ot6_17171/08_2025/8ot6_17171.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ot6_17171/08_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_17171/08_2025/8ot6_17171.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ot6_17171/08_2025/8ot6_17171.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ot6_17171/08_2025/8ot6_17171.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ot6_17171/08_2025/8ot6_17171.cif"
  }
  resolution = 2.0
  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=   0.000 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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:
    B, C, D, E
  Time building chain proxies: 0.51, per 1000 atoms: 0.18
  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: 0.21
  Conformation dependent library (CDL) restraints added in 75.7 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.11
  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: 0.25

  Time building geometry restraints manager: 0.29 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             4.040
  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:          0.070
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.680
  Find NCS groups from input model:        0.020
  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:5.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.520
-------------------------------------------------------------------------------
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= 0.493
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.005   0.001   ARG E 349 
 TYR   0.008   0.004   TYR C 310 
 PHE   0.007   0.003   PHE C 346 
 HIS   0.007   0.003   HIS C 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00733 ( 2915)
  covalent geometry    : angle       1.16538 ( 3900)
  hydrogen bonds       : bond        0.10971 (   63)
  hydrogen bonds       : angle       7.23846 (  189)

*********************** 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  : 0.129 
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: 0.7310
  time to fit residues: 113.6858
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  : 0.131 
-------------------------------------------------------------------------------
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 24 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    8.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 30 optimal weight:    8.9990
   chunk 22 optimal weight:    8.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    4.3588

-------------------------------------------------------------------------------
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 = 0.3921 r_free = 0.3921 target = 0.125087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.108263 restraints weight = 3128.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.3647 rms_B_bonded: 1.26
r_work: 0.3548 rms_B_bonded: 1.45 restraints_weight: 0.5000
r_work: 0.3468 rms_B_bonded: 2.44 restraints_weight: 0.2500
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9054
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   2915  Z= 0.258
  Angle     :  0.691   5.323   3900  Z= 0.349
  Chirality :  0.052   0.157    440
  Planarity :  0.004   0.021    495
  Dihedral  :  5.512  26.453    387
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.73 %
    Favored  : 85.15 %
  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 aren not related in a simple way.
  whole: -2.17 (0.35), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 379 
 TYR   0.010   0.003   TYR E 310 
 PHE   0.006   0.002   PHE E 346 
 HIS   0.003   0.001   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00602 ( 2915)
  covalent geometry    : angle       0.69114 ( 3900)
  hydrogen bonds       : bond        0.03535 (   63)
  hydrogen bonds       : angle       6.20868 (  189)

*********************** 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
  91 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A  338 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7505 (tp30)
REVERT: D  379 ARG cc_start: 0.5953 (OUTLIER) cc_final: 0.5504 (mmt-90)
REVERT: E  349 ARG cc_start: 0.8700 (mtt180) cc_final: 0.7720 (mmm160)
  outliers start: 7
  outliers final: 0
  residues processed: 87
  average time/residue: 0.6664
  time to fit residues: 59.1569
Evaluate side-chains
  84 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 82
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
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 9 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 32 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9980
   chunk 8 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 30 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 25 optimal weight:    0.1980
   overall best weight:    3.4386

-------------------------------------------------------------------------------
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 = 0.3938 r_free = 0.3938 target = 0.125675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.109621 restraints weight = 3142.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 1.23
r_work: 0.3568 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.3489 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9041
moved from start:          0.2904

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= 0.211
  Angle     :  0.628   5.173   3900  Z= 0.315
  Chirality :  0.050   0.145    440
  Planarity :  0.003   0.027    495
  Dihedral  :  5.220  15.070    385
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.45 %
    Favored  : 82.12 %
  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 aren not related in a simple way.
  whole: -1.97 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.49 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 379 
 TYR   0.012   0.003   TYR E 310 
 PHE   0.006   0.002   PHE E 346 
 HIS   0.002   0.001   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 2915)
  covalent geometry    : angle       0.62832 ( 3900)
  hydrogen bonds       : bond        0.03085 (   63)
  hydrogen bonds       : angle       5.87342 (  189)

*********************** 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
  91 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8457 (mtt180)
REVERT: D  379 ARG cc_start: 0.5814 (OUTLIER) cc_final: 0.5266 (mmt-90)
REVERT: E  349 ARG cc_start: 0.8663 (mtt180) cc_final: 0.7400 (tpt90)
  outliers start: 8
  outliers final: 0
  residues processed: 86
  average time/residue: 0.5917
  time to fit residues: 51.8696
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  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
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 16 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    7.9990
   chunk 33 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 4 optimal weight:    8.9990
   chunk 21 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   overall best weight:    5.9988

-------------------------------------------------------------------------------
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 = 0.3904 r_free = 0.3904 target = 0.123222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.107038 restraints weight = 3135.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 1.23
r_work: 0.3529 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.3449 rms_B_bonded: 2.41 restraints_weight: 0.2500
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9062
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.062   2915  Z= 0.338
  Angle     :  0.705   5.376   3900  Z= 0.362
  Chirality :  0.053   0.161    440
  Planarity :  0.005   0.053    495
  Dihedral  :  5.473  15.460    385
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 13.64 %
    Favored  : 83.94 %
  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 aren not related in a simple way.
  whole: -1.85 (0.35), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.40 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 379 
 TYR   0.013   0.003   TYR E 310 
 PHE   0.009   0.003   PHE E 378 
 HIS   0.003   0.001   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00784 ( 2915)
  covalent geometry    : angle       0.70484 ( 3900)
  hydrogen bonds       : bond        0.03712 (   63)
  hydrogen bonds       : angle       6.26545 (  189)

*********************** 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: 8
    poor density    : 81
  time to evaluate  : 0.092 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8452 (mtt180)
REVERT: B  338 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7635 (tp30)
REVERT: D  379 ARG cc_start: 0.5786 (OUTLIER) cc_final: 0.4471 (mpt90)
REVERT: E  349 ARG cc_start: 0.8676 (mtt180) cc_final: 0.7357 (tpt90)
  outliers start: 8
  outliers final: 1
  residues processed: 85
  average time/residue: 0.6145
  time to fit residues: 53.1794
Evaluate side-chains
  85 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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
D 351 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 = 0.3926 r_free = 0.3926 target = 0.125035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.109114 restraints weight = 3114.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.3661 rms_B_bonded: 1.22
r_work: 0.3561 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.3483 rms_B_bonded: 2.41 restraints_weight: 0.2500
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9042
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   0.039   2915  Z= 0.209
  Angle     :  0.613   5.212   3900  Z= 0.308
  Chirality :  0.050   0.145    440
  Planarity :  0.003   0.029    495
  Dihedral  :  5.254  14.926    385
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 2.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 14.55 %
    Favored  : 83.33 %
  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 aren not related in a simple way.
  whole: -1.76 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.33 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 379 
 TYR   0.013   0.003   TYR E 310 
 PHE   0.007   0.002   PHE A 346 
 HIS   0.002   0.001   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 2915)
  covalent geometry    : angle       0.61312 ( 3900)
  hydrogen bonds       : bond        0.02964 (   63)
  hydrogen bonds       : angle       5.81604 (  189)

*********************** 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  : 0.074 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8462 (mtt180)
REVERT: D  379 ARG cc_start: 0.5586 (OUTLIER) cc_final: 0.3942 (mpt90)
REVERT: E  349 ARG cc_start: 0.8662 (mtt180) cc_final: 0.7357 (tpt90)
  outliers start: 7
  outliers final: 1
  residues processed: 86
  average time/residue: 0.5559
  time to fit residues: 48.7623
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  : 0.086 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 15 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
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
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 = 0.3949 r_free = 0.3949 target = 0.127007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.111239 restraints weight = 3133.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 1.21
r_work: 0.3594 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.3516 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9026
moved from start:          0.3106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2915  Z= 0.136
  Angle     :  0.563   5.602   3900  Z= 0.277
  Chirality :  0.049   0.135    440
  Planarity :  0.003   0.021    495
  Dihedral  :  5.008  14.184    385
  Min Nonbonded Distance : 2.635

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 15.45 %
    Favored  : 82.73 %
  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 aren not related in a simple way.
  whole: -1.69 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.28 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 379 
 TYR   0.013   0.003   TYR E 310 
 PHE   0.006   0.001   PHE A 346 
 HIS   0.002   0.001   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 2915)
  covalent geometry    : angle       0.56296 ( 3900)
  hydrogen bonds       : bond        0.02388 (   63)
  hydrogen bonds       : angle       5.39675 (  189)

*********************** 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
  90 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8478 (mtt180)
REVERT: B  338 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7641 (tp30)
REVERT: D  379 ARG cc_start: 0.5531 (OUTLIER) cc_final: 0.3858 (mpt90)
REVERT: E  349 ARG cc_start: 0.8656 (mtt180) cc_final: 0.7383 (tpt90)
  outliers start: 6
  outliers final: 1
  residues processed: 87
  average time/residue: 0.5852
  time to fit residues: 51.8762
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  : 0.073 
-------------------------------------------------------------------------------
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 10 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 8 optimal weight:   10.0000
   chunk 25 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 3 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   overall best weight:    3.0988

-------------------------------------------------------------------------------
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 = 0.3931 r_free = 0.3931 target = 0.125445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.109488 restraints weight = 3123.328|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 1.22
r_work: 0.3565 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.3488 rms_B_bonded: 2.40 restraints_weight: 0.2500
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9036
moved from start:          0.3103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   2915  Z= 0.193
  Angle     :  0.607   6.606   3900  Z= 0.303
  Chirality :  0.050   0.144    440
  Planarity :  0.003   0.030    495
  Dihedral  :  5.175  14.646    385
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 2.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 14.85 %
    Favored  : 83.03 %
  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 aren not related in a simple way.
  whole: -1.72 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.30 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D 379 
 TYR   0.013   0.003   TYR E 310 
 PHE   0.007   0.002   PHE A 346 
 HIS   0.002   0.001   HIS D 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 2915)
  covalent geometry    : angle       0.60682 ( 3900)
  hydrogen bonds       : bond        0.02773 (   63)
  hydrogen bonds       : angle       5.55349 (  189)

*********************** 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
  90 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A  349 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8466 (mtt180)
REVERT: B  338 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7674 (tp30)
REVERT: B  379 ARG cc_start: 0.5970 (OUTLIER) cc_final: 0.4673 (ttp-170)
REVERT: D  379 ARG cc_start: 0.5597 (OUTLIER) cc_final: 0.3867 (mpt90)
REVERT: E  349 ARG cc_start: 0.8663 (mtt180) cc_final: 0.7366 (tpt90)
  outliers start: 7
  outliers final: 1
  residues processed: 86
  average time/residue: 0.5584
  time to fit residues: 48.8588
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  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  349 ARG
Chi-restraints excluded: chain B residue  338 GLU
Chi-restraints excluded: chain B residue  379 ARG
Chi-restraints excluded: chain D residue  340 LYS
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 34 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 13 optimal weight:    8.9990
   chunk 3 optimal weight:    8.9990
   chunk 1 optimal weight:    0.0060
   chunk 18 optimal weight:    0.7980
   chunk 7 optimal weight:   10.0000
   chunk 20 optimal weight:    0.3980
   chunk 22 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.8198

-------------------------------------------------------------------------------
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 = 0.3991 r_free = 0.3991 target = 0.130342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.114965 restraints weight = 3189.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 1.22
r_work: 0.3645 rms_B_bonded: 1.44 restraints_weight: 0.5000
r_work: 0.3570 rms_B_bonded: 2.44 restraints_weight: 0.2500
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8992
moved from start:          0.3298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.012   2915  Z= 0.082
  Angle     :  0.527   7.342   3900  Z= 0.251
  Chirality :  0.049   0.126    440
  Planarity :  0.003   0.020    495
  Dihedral  :  4.658  13.375    385
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 1.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 15.15 %
    Favored  : 83.64 %
  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 aren not related in a simple way.
  whole: -1.64 (0.37), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.24 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 379 
 TYR   0.013   0.003   TYR E 310 
 PHE   0.005   0.001   PHE A 346 
 HIS   0.001   0.000   HIS B 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00177 ( 2915)
  covalent geometry    : angle       0.52669 ( 3900)
  hydrogen bonds       : bond        0.01784 (   63)
  hydrogen bonds       : angle       4.98296 (  189)

*********************** 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  : 0.142 
Fit side-chains
REVERT: D  379 ARG cc_start: 0.5544 (OUTLIER) cc_final: 0.4497 (mmp80)
REVERT: E  349 ARG cc_start: 0.8633 (mtt180) cc_final: 0.7524 (mmp-170)
  outliers start: 4
  outliers final: 1
  residues processed: 86
  average time/residue: 0.6200
  time to fit residues: 54.2833
Evaluate side-chains
  83 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 81
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 32 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   chunk 10 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   overall best weight:    4.3786

-------------------------------------------------------------------------------
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 = 0.3920 r_free = 0.3920 target = 0.124598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.108511 restraints weight = 3190.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 1.23
r_work: 0.3551 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9046
moved from start:          0.3128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   2915  Z= 0.255
  Angle     :  0.636   6.617   3900  Z= 0.321
  Chirality :  0.051   0.151    440
  Planarity :  0.004   0.045    495
  Dihedral  :  5.236  14.705    385
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 15.76 %
    Favored  : 83.03 %
  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 aren not related in a simple way.
  whole: -1.69 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.28 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 379 
 TYR   0.011   0.003   TYR E 310 
 PHE   0.009   0.002   PHE A 346 
 HIS   0.002   0.001   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00590 ( 2915)
  covalent geometry    : angle       0.63608 ( 3900)
  hydrogen bonds       : bond        0.03053 (   63)
  hydrogen bonds       : angle       5.61337 (  189)

*********************** 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  : 0.084 
Fit side-chains
REVERT: B  338 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7689 (tp30)
REVERT: D  379 ARG cc_start: 0.5688 (OUTLIER) cc_final: 0.4059 (mmp-170)
REVERT: E  349 ARG cc_start: 0.8672 (mtt180) cc_final: 0.7354 (tpt90)
  outliers start: 4
  outliers final: 2
  residues processed: 85
  average time/residue: 0.6092
  time to fit residues: 52.7641
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  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  325 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 19 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 14 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 32 optimal weight:    8.9990
   chunk 1 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    5.3588

-------------------------------------------------------------------------------
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 = 0.3912 r_free = 0.3912 target = 0.123772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.107645 restraints weight = 3135.165|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 1.23
r_work: 0.3539 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.3460 rms_B_bonded: 2.40 restraints_weight: 0.2500
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9053
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   2915  Z= 0.306
  Angle     :  0.683   6.445   3900  Z= 0.351
  Chirality :  0.053   0.164    440
  Planarity :  0.005   0.064    495
  Dihedral  :  5.424  15.406    385
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 15.76 %
    Favored  : 83.03 %
  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 aren not related in a simple way.
  whole: -1.73 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.31 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 379 
 TYR   0.011   0.003   TYR E 310 
 PHE   0.009   0.003   PHE A 346 
 HIS   0.003   0.001   HIS E 329 

Details of bonding type rmsd
  covalent geometry    : bond        0.00708 ( 2915)
  covalent geometry    : angle       0.68345 ( 3900)
  hydrogen bonds       : bond        0.03392 (   63)
  hydrogen bonds       : angle       5.87362 (  189)

********************** 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
  87 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.086 
Fit side-chains
REVERT: B  338 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7696 (tp30)
REVERT: D  379 ARG cc_start: 0.5796 (OUTLIER) cc_final: 0.4302 (mmp80)
REVERT: E  349 ARG cc_start: 0.8687 (mtt180) cc_final: 0.7387 (tpt90)
  outliers start: 4
  outliers final: 2
  residues processed: 85
  average time/residue: 0.6374
  time to fit residues: 55.2129
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  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  325 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0570
   chunk 14 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 24 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.9302

-------------------------------------------------------------------------------
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 = 0.3981 r_free = 0.3981 target = 0.129444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.114130 restraints weight = 3122.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3732 rms_B_bonded: 1.21
r_work: 0.3635 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.3561 rms_B_bonded: 2.41 restraints_weight: 0.2500
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8994
moved from start:          0.3360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2915  Z= 0.090
  Angle     :  0.542   7.002   3900  Z= 0.263
  Chirality :  0.049   0.127    440
  Planarity :  0.003   0.021    495
  Dihedral  :  4.784  13.846    385
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 2.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 16.67 %
    Favored  : 82.73 %
  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 aren not related in a simple way.
  whole: -1.60 (0.37), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.21 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 349 
 TYR   0.013   0.003   TYR E 310 
 PHE   0.006   0.001   PHE A 346 
 HIS   0.001   0.000   HIS D 362 

Details of bonding type rmsd
  covalent geometry    : bond        0.00194 ( 2915)
  covalent geometry    : angle       0.54231 ( 3900)
  hydrogen bonds       : bond        0.01898 (   63)
  hydrogen bonds       : angle       5.13939 (  189)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2021.60 seconds
wall clock time: 34 minutes 59.34 seconds (2099.34 seconds total)