Starting phenix.real_space_refine
on Fri May  9 15:33:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8oth_17179/05_2025/8oth_17179.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8oth_17179/05_2025/8oth_17179.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8oth_17179/05_2025/8oth_17179.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8oth_17179/05_2025/8oth_17179.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8oth_17179/05_2025/8oth_17179.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8oth_17179/05_2025/8oth_17179.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 2.70, per 1000 atoms: 0.94
  Number of scatterers: 2870
  At special positions: 0
  Unit cell: (135.464, 109.032, 33.04, 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: 0.67
  Conformation dependent library (CDL) restraints added in 372.2 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, 42.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 306 through 310
      removed outlier: 6.991A  pdb=" N   GLN A 307 " --> pdb=" O   ILE D 308 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   TYR D 310 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   VAL A 309 " --> pdb=" O   TYR D 310 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314
      removed outlier: 6.819A  pdb=" N   VAL A 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 319 through 328
      removed outlier: 6.803A  pdb=" N   THR A 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 8.459A  pdb=" N   CYS D 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   LYS A 321 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   SER D 324 " --> pdb=" O   LYS A 321 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   GLY A 323 " --> pdb=" O   SER D 324 " (cutoff:3.500A)
      removed outlier: 9.877A  pdb=" N   GLY D 326 " --> pdb=" O   GLY A 323 " (cutoff:3.500A)
      removed outlier: 8.985A  pdb=" N   LEU A 325 " --> pdb=" O   GLY D 326 " (cutoff:3.500A)
      removed outlier: 9.514A  pdb=" N   ILE D 328 " --> pdb=" O   LEU A 325 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ASN A 327 " --> pdb=" O   ILE D 328 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   SER A 324 " --> pdb=" O   GLY E 323 " (cutoff:3.500A)
      removed outlier: 6.871A  pdb=" N   LEU E 325 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   GLY A 326 " --> pdb=" O   LEU E 325 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   ASN E 327 " --> pdb=" O   GLY A 326 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 337 through 339
      removed outlier: 6.481A  pdb=" N   VAL A 337 " --> pdb=" O   GLU E 338 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 342 through 345
      removed outlier: 6.926A  pdb=" N   LYS A 343 " --> pdb=" O   GLU D 342 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   GLU A 342 " --> pdb=" O   LYS E 343 " (cutoff:3.500A)
      removed outlier: 8.332A  pdb=" N   ASP E 345 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   LEU A 344 " --> pdb=" O   ASP E 345 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 350 through 357
      removed outlier: 6.460A  pdb=" N   VAL A 350 " --> pdb=" O   GLN E 351 " (cutoff:3.500A)
      removed outlier: 8.416A  pdb=" N   LYS E 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   SER A 352 " --> pdb=" O   LYS E 353 " (cutoff:3.500A)
      removed outlier: 8.221A  pdb=" N   GLY E 355 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   ILE A 354 " --> pdb=" O   GLY E 355 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   LEU E 357 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   SER A 356 " --> pdb=" O   LEU E 357 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 369 through 373
      removed outlier: 6.781A  pdb=" N   LYS A 369 " --> pdb=" O   LYS D 370 " (cutoff:3.500A)
      removed outlier: 8.281A  pdb=" N   GLU D 372 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ILE A 371 " --> pdb=" O   GLU D 372 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 376 through 378
      removed outlier: 6.498A  pdb=" N   LEU A 376 " --> pdb=" O   THR E 377 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 306 through 310
      removed outlier: 6.991A  pdb=" N   GLN B 307 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   TYR C 310 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   VAL B 309 " --> pdb=" O   TYR C 310 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 313 through 314
      removed outlier: 6.820A  pdb=" N   VAL B 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 319 through 328
      removed outlier: 6.803A  pdb=" N   THR B 319 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 8.458A  pdb=" N   CYS C 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   LYS B 321 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   SER C 324 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   GLY B 323 " --> pdb=" O   SER C 324 " (cutoff:3.500A)
      removed outlier: 9.876A  pdb=" N   GLY C 326 " --> pdb=" O   GLY B 323 " (cutoff:3.500A)
      removed outlier: 8.985A  pdb=" N   LEU B 325 " --> pdb=" O   GLY C 326 " (cutoff:3.500A)
      removed outlier: 9.513A  pdb=" N   ILE C 328 " --> pdb=" O   LEU B 325 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ASN B 327 " --> pdb=" O   ILE C 328 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 337 through 339
    Processing sheet with id=AB4, first strand: chain 'B' and resid 342 through 345
      removed outlier: 6.926A  pdb=" N   LYS B 343 " --> pdb=" O   GLU C 342 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 350 through 357
    Processing sheet with id=AB6, first strand: chain 'B' and resid 369 through 373
      removed outlier: 6.780A  pdb=" N   LYS B 369 " --> pdb=" O   LYS C 370 " (cutoff:3.500A)
      removed outlier: 8.281A  pdb=" N   GLU C 372 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ILE B 371 " --> pdb=" O   GLU C 372 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'B' and resid 376 through 378

    40 hydrogen bonds defined for protein.
    120 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: 727
        1.34 -     1.46: 657
        1.46 -     1.58: 1526
        1.58 -     1.70: 0
        1.70 -     1.82: 5
  Bond restraints: 2915
  Sorted by residual:
  bond pdb=" CG  HIS B 330 "
       pdb=" CD2 HIS B 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.322  0.032 1.10e-02 8.26e+03 8.21e+00
  bond pdb=" CG  HIS C 330 "
       pdb=" CD2 HIS C 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.323  0.031 1.10e-02 8.26e+03 8.00e+00
  bond pdb=" CG  HIS A 330 "
       pdb=" CD2 HIS A 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.323  0.031 1.10e-02 8.26e+03 7.92e+00
  bond pdb=" CG  HIS D 330 "
       pdb=" CD2 HIS D 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.323  0.031 1.10e-02 8.26e+03 7.80e+00
  bond pdb=" CG  HIS E 330 "
       pdb=" CD2 HIS E 330 "
    ideal  model  delta    sigma   weight residual
    1.354  1.323  0.031 1.10e-02 8.26e+03 7.75e+00
  ... (remaining 2910 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 3025
        1.76 -     3.52: 767
        3.52 -     5.28: 83
        5.28 -     7.04: 20
        7.04 -     8.80: 5
  Bond angle restraints: 3900
  Sorted by residual:
  angle pdb=" C   HIS D 362 "
        pdb=" CA  HIS D 362 "
        pdb=" CB  HIS D 362 "
      ideal   model   delta    sigma   weight residual
     110.22  119.02   -8.80 1.67e+00 3.59e-01 2.78e+01
  angle pdb=" C   HIS B 362 "
        pdb=" CA  HIS B 362 "
        pdb=" CB  HIS B 362 "
      ideal   model   delta    sigma   weight residual
     110.22  119.02   -8.80 1.67e+00 3.59e-01 2.77e+01
  angle pdb=" C   HIS C 362 "
        pdb=" CA  HIS C 362 "
        pdb=" CB  HIS C 362 "
      ideal   model   delta    sigma   weight residual
     110.22  119.01   -8.79 1.67e+00 3.59e-01 2.77e+01
  angle pdb=" C   HIS A 362 "
        pdb=" CA  HIS A 362 "
        pdb=" CB  HIS A 362 "
      ideal   model   delta    sigma   weight residual
     110.22  119.00   -8.78 1.67e+00 3.59e-01 2.77e+01
  angle pdb=" C   HIS E 362 "
        pdb=" CA  HIS E 362 "
        pdb=" CB  HIS E 362 "
      ideal   model   delta    sigma   weight residual
     110.22  119.00   -8.78 1.67e+00 3.59e-01 2.76e+01
  ... (remaining 3895 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.74: 1540
       14.74 -    29.48: 190
       29.48 -    44.21: 40
       44.21 -    58.95: 5
       58.95 -    73.69: 5
  Dihedral angle restraints: 1780
    sinusoidal: 745
      harmonic: 1035
  Sorted by residual:
  dihedral pdb=" CA  VAL D 318 "
           pdb=" C   VAL D 318 "
           pdb=" N   THR D 319 "
           pdb=" CA  THR D 319 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.07  -29.93     0      5.00e+00 4.00e-02 3.58e+01
  dihedral pdb=" CA  VAL C 318 "
           pdb=" C   VAL C 318 "
           pdb=" N   THR C 319 "
           pdb=" CA  THR C 319 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.07  -29.93     0      5.00e+00 4.00e-02 3.58e+01
  dihedral pdb=" CA  VAL B 318 "
           pdb=" C   VAL B 318 "
           pdb=" N   THR B 319 "
           pdb=" CA  THR B 319 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.10  -29.90     0      5.00e+00 4.00e-02 3.57e+01
  ... (remaining 1777 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 162
       0.052 -    0.103: 166
       0.103 -    0.155: 82
       0.155 -    0.206: 25
       0.206 -    0.258: 5
  Chirality restraints: 440
  Sorted by residual:
  chirality pdb=" CA  ILE C 328 "
            pdb=" N   ILE C 328 "
            pdb=" C   ILE C 328 "
            pdb=" CB  ILE C 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CA  ILE B 328 "
            pdb=" N   ILE B 328 "
            pdb=" C   ILE B 328 "
            pdb=" CB  ILE B 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CA  ILE A 328 "
            pdb=" N   ILE A 328 "
            pdb=" C   ILE A 328 "
            pdb=" CB  ILE A 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.69   -0.26 2.00e-01 2.50e+01 1.65e+00
  ... (remaining 437 not shown)

  Planarity restraints: 495
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 363 "   -0.022 2.00e-02 2.50e+03   4.33e-02 1.87e+01
        pdb=" C   VAL D 363 "    0.075 2.00e-02 2.50e+03
        pdb=" O   VAL D 363 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   PRO D 364 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 363 "    0.022 2.00e-02 2.50e+03   4.32e-02 1.87e+01
        pdb=" C   VAL B 363 "   -0.075 2.00e-02 2.50e+03
        pdb=" O   VAL B 363 "    0.027 2.00e-02 2.50e+03
        pdb=" N   PRO B 364 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 363 "   -0.022 2.00e-02 2.50e+03   4.32e-02 1.87e+01
        pdb=" C   VAL A 363 "    0.075 2.00e-02 2.50e+03
        pdb=" O   VAL A 363 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   PRO A 364 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 492 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 598
        2.81 -     3.33: 2681
        3.33 -     3.85: 4409
        3.85 -     4.38: 4732
        4.38 -     4.90: 8981
  Nonbonded interactions: 21401
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 316 "
            pdb=" NZ  LYS C 370 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" OG  SER E 316 "
            pdb=" NZ  LYS E 370 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" OG  SER A 316 "
            pdb=" NZ  LYS A 370 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" OG  SER D 316 "
            pdb=" NZ  LYS D 370 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" OG  SER B 316 "
            pdb=" NZ  LYS B 370 "
     model   vdw
     2.287 3.120
  ... (remaining 21396 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:             2.710
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.140
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
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      :  0.009   0.041   2915  Z= 0.574
  Angle     :  1.555   8.805   3900  Z= 1.013
  Chirality :  0.092   0.258    440
  Planarity :  0.011   0.054    495
  Dihedral  : 14.035  73.685   1120
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.59 %
    Favored  : 90.41 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 10.61 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.34 (0.29), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.30 (0.22), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.004   HIS C 329 
 PHE   0.017   0.004   PHE D 346 
 TYR   0.035   0.013   TYR E 310 
 ARG   0.004   0.002   ARG E 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21931 (   40)
  hydrogen bonds       : angle       8.76015 (  120)
  covalent geometry    : bond        0.00865 ( 2915)
  covalent geometry    : angle       1.55466 ( 3900)

*********************** 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
  75 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.8220 (mttt) cc_final: 0.7703 (mptt)
REVERT: A  369 LYS cc_start: 0.8381 (mttt) cc_final: 0.7869 (mtpt)
REVERT: A  378 PHE cc_start: 0.8163 (t80) cc_final: 0.7901 (t80)
REVERT: B  311 LYS cc_start: 0.7562 (mtmt) cc_final: 0.7060 (mmmt)
REVERT: B  321 LYS cc_start: 0.6802 (ttmt) cc_final: 0.6294 (tttt)
REVERT: B  347 LYS cc_start: 0.8459 (mttt) cc_final: 0.7975 (mptt)
REVERT: B  349 ARG cc_start: 0.8767 (mtt180) cc_final: 0.7743 (mmm160)
REVERT: B  369 LYS cc_start: 0.8429 (mttt) cc_final: 0.7920 (mtpt)
REVERT: C  321 LYS cc_start: 0.7545 (ttmt) cc_final: 0.7317 (ttmt)
REVERT: C  349 ARG cc_start: 0.8804 (mtt180) cc_final: 0.7529 (pmt-80)
REVERT: C  369 LYS cc_start: 0.8546 (mttt) cc_final: 0.8133 (mtpt)
REVERT: D  321 LYS cc_start: 0.7550 (ttmt) cc_final: 0.7238 (ttmt)
REVERT: D  347 LYS cc_start: 0.8559 (mttt) cc_final: 0.8321 (mptt)
REVERT: D  349 ARG cc_start: 0.8801 (mtt180) cc_final: 0.7559 (pmt-80)
REVERT: D  369 LYS cc_start: 0.8627 (mttt) cc_final: 0.8040 (mtmt)
REVERT: E  311 LYS cc_start: 0.7622 (mtmt) cc_final: 0.7126 (mmmt)
REVERT: E  321 LYS cc_start: 0.6808 (ttmt) cc_final: 0.6372 (ttpt)
REVERT: E  347 LYS cc_start: 0.8389 (mttt) cc_final: 0.7987 (mptt)
REVERT: E  349 ARG cc_start: 0.8725 (mtt180) cc_final: 0.7761 (mmp-170)
REVERT: E  369 LYS cc_start: 0.8373 (mttt) cc_final: 0.7844 (mtpt)
  outliers start: 5
  outliers final: 0
  residues processed: 75
  average time/residue: 0.3015
  time to fit residues: 24.9542
Evaluate side-chains
  52 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 9 optimal weight:    0.6980
   chunk 17 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 31 optimal weight:    8.9990
   chunk 21 optimal weight:    8.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 362 HIS
B 362 HIS
C 330 HIS
C 362 HIS
D 330 HIS
D 362 HIS
E 362 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.156438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.126103 restraints weight = 3447.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.4314 rms_B_bonded: 2.65
r_work: 0.4211 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.4109 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.4109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2915  Z= 0.190
  Angle     :  0.627   5.266   3900  Z= 0.325
  Chirality :  0.050   0.131    440
  Planarity :  0.004   0.029    495
  Dihedral  :  5.934  21.050    385
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 13.94 %
    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 (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: -4.02 (0.29), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.05 (0.22), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS A 330 
 PHE   0.006   0.001   PHE C 346 
 TYR   0.017   0.004   TYR A 310 
 ARG   0.001   0.000   ARG C 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02902 (   40)
  hydrogen bonds       : angle       5.90323 (  120)
  covalent geometry    : bond        0.00403 ( 2915)
  covalent geometry    : angle       0.62746 ( 3900)

*********************** 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
  83 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.8034 (mttt) cc_final: 0.7554 (mptt)
REVERT: A  375 LYS cc_start: 0.7780 (tttt) cc_final: 0.7241 (mttt)
REVERT: B  311 LYS cc_start: 0.7638 (mtmt) cc_final: 0.6896 (mmtt)
REVERT: B  321 LYS cc_start: 0.6855 (ttmt) cc_final: 0.6637 (ttmt)
REVERT: B  347 LYS cc_start: 0.8117 (mttt) cc_final: 0.7568 (mptt)
REVERT: B  349 ARG cc_start: 0.8397 (mtt180) cc_final: 0.7426 (mmp-170)
REVERT: B  369 LYS cc_start: 0.7859 (mttt) cc_final: 0.7152 (mtpt)
REVERT: B  375 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7325 (mttt)
REVERT: C  321 LYS cc_start: 0.7480 (ttmt) cc_final: 0.7139 (ttmt)
REVERT: C  349 ARG cc_start: 0.8564 (mtt180) cc_final: 0.7098 (pmt-80)
REVERT: C  375 LYS cc_start: 0.8300 (ttmt) cc_final: 0.7955 (mttt)
REVERT: D  321 LYS cc_start: 0.7412 (ttmt) cc_final: 0.6927 (ttmt)
REVERT: D  347 LYS cc_start: 0.8389 (mttt) cc_final: 0.8119 (mptt)
REVERT: D  369 LYS cc_start: 0.8196 (mttt) cc_final: 0.7496 (mtpt)
REVERT: D  375 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7859 (mttt)
REVERT: E  311 LYS cc_start: 0.7742 (mtmt) cc_final: 0.7051 (mmtt)
REVERT: E  331 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8213 (mttm)
REVERT: E  347 LYS cc_start: 0.8165 (mttt) cc_final: 0.7615 (mptt)
REVERT: E  349 ARG cc_start: 0.8467 (mtt180) cc_final: 0.7377 (mmm160)
REVERT: E  369 LYS cc_start: 0.7596 (mttt) cc_final: 0.6933 (mtpt)
  outliers start: 8
  outliers final: 6
  residues processed: 75
  average time/residue: 0.2962
  time to fit residues: 24.5650
Evaluate side-chains
  60 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain E residue  318 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0470
   chunk 22 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   chunk 8 optimal weight:    9.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.7280

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.159309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.128575 restraints weight = 3305.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.4350 rms_B_bonded: 2.67
r_work: 0.4242 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.4136 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.4136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   2915  Z= 0.114
  Angle     :  0.511   4.496   3900  Z= 0.263
  Chirality :  0.048   0.119    440
  Planarity :  0.004   0.049    495
  Dihedral  :  4.807  17.612    385
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 19.70 %
    Favored  : 78.48 %
  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: -3.35 (0.31), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.55 (0.24), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS A 330 
 PHE   0.004   0.001   PHE C 346 
 TYR   0.017   0.004   TYR A 310 
 ARG   0.001   0.000   ARG A 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01855 (   40)
  hydrogen bonds       : angle       4.87393 (  120)
  covalent geometry    : bond        0.00247 ( 2915)
  covalent geometry    : angle       0.51110 ( 3900)

*********************** 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
  62 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.7933 (mttt) cc_final: 0.7400 (mptt)
REVERT: A  375 LYS cc_start: 0.7782 (tttt) cc_final: 0.7277 (mttt)
REVERT: B  311 LYS cc_start: 0.7754 (mtmt) cc_final: 0.7009 (mmtt)
REVERT: B  347 LYS cc_start: 0.7960 (mttt) cc_final: 0.7429 (mptt)
REVERT: B  349 ARG cc_start: 0.8401 (mtt180) cc_final: 0.7295 (mmp-170)
REVERT: B  369 LYS cc_start: 0.7783 (mttt) cc_final: 0.7077 (mtpt)
REVERT: B  375 LYS cc_start: 0.7842 (ttmt) cc_final: 0.7405 (mttt)
REVERT: C  347 LYS cc_start: 0.8399 (mptt) cc_final: 0.7744 (mptt)
REVERT: C  349 ARG cc_start: 0.8635 (mtt180) cc_final: 0.7130 (pmt-80)
REVERT: C  369 LYS cc_start: 0.8126 (mttt) cc_final: 0.7487 (mtpt)
REVERT: C  375 LYS cc_start: 0.8297 (ttmt) cc_final: 0.7960 (mttt)
REVERT: D  321 LYS cc_start: 0.7375 (ttmt) cc_final: 0.6876 (ttmt)
REVERT: D  347 LYS cc_start: 0.8338 (mttt) cc_final: 0.8039 (mptt)
REVERT: D  369 LYS cc_start: 0.8135 (mttt) cc_final: 0.7486 (mtpt)
REVERT: D  375 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7845 (mttt)
REVERT: E  311 LYS cc_start: 0.7696 (mtmt) cc_final: 0.7000 (mmtt)
REVERT: E  331 LYS cc_start: 0.8540 (mtmt) cc_final: 0.8168 (mttm)
REVERT: E  347 LYS cc_start: 0.8104 (mttt) cc_final: 0.7515 (mptt)
REVERT: E  349 ARG cc_start: 0.8492 (mtt180) cc_final: 0.7348 (mmm160)
REVERT: E  369 LYS cc_start: 0.7524 (mttt) cc_final: 0.6852 (mtpt)
REVERT: E  375 LYS cc_start: 0.8114 (tppt) cc_final: 0.7609 (mttt)
  outliers start: 6
  outliers final: 6
  residues processed: 56
  average time/residue: 0.3272
  time to fit residues: 20.3643
Evaluate side-chains
  57 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain E residue  318 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    0.7980
   chunk 19 optimal weight:    6.9990
   chunk 24 optimal weight:    6.9990
   chunk 14 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 34 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 17 optimal weight:    9.9990
   chunk 4 optimal weight:    8.9990
   overall best weight:    3.8986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4913 r_free = 0.4913 target = 0.292757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.5140 r_free = 0.5140 target = 0.243428 restraints weight = 3425.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.4383 rms_B_bonded: 1.26
r_work: 0.4313 rms_B_bonded: 1.31 restraints_weight: 0.5000
r_work: 0.4247 rms_B_bonded: 2.16 restraints_weight: 0.2500
r_work (final): 0.4247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   2915  Z= 0.223
  Angle     :  0.600   6.882   3900  Z= 0.313
  Chirality :  0.049   0.132    440
  Planarity :  0.005   0.051    495
  Dihedral  :  5.167  19.190    385
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 19.09 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.32), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.38 (0.25), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.003   HIS B 330 
 PHE   0.005   0.002   PHE D 346 
 TYR   0.018   0.005   TYR A 310 
 ARG   0.001   0.000   ARG B 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02111 (   40)
  hydrogen bonds       : angle       4.80178 (  120)
  covalent geometry    : bond        0.00490 ( 2915)
  covalent geometry    : angle       0.60042 ( 3900)

*********************** 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
  72 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.8152 (mttt) cc_final: 0.7667 (mptt)
REVERT: A  375 LYS cc_start: 0.8033 (tttt) cc_final: 0.7590 (mttt)
REVERT: B  311 LYS cc_start: 0.7781 (mtmt) cc_final: 0.7079 (mmtt)
REVERT: B  347 LYS cc_start: 0.8198 (mttt) cc_final: 0.7722 (mptt)
REVERT: B  349 ARG cc_start: 0.8421 (mtt180) cc_final: 0.7461 (mmm160)
REVERT: B  369 LYS cc_start: 0.7956 (mttt) cc_final: 0.7234 (mtpt)
REVERT: B  375 LYS cc_start: 0.7926 (ttmt) cc_final: 0.7534 (mttt)
REVERT: C  321 LYS cc_start: 0.7359 (ttmt) cc_final: 0.7127 (ttmt)
REVERT: C  347 LYS cc_start: 0.8523 (mptt) cc_final: 0.7887 (mptt)
REVERT: C  349 ARG cc_start: 0.8598 (mtt180) cc_final: 0.7310 (pmt-80)
REVERT: C  369 LYS cc_start: 0.8147 (mttt) cc_final: 0.7461 (mtpt)
REVERT: C  375 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7917 (mttt)
REVERT: D  321 LYS cc_start: 0.7594 (ttmt) cc_final: 0.7127 (ttmt)
REVERT: D  322 CYS cc_start: 0.8279 (t) cc_final: 0.8027 (t)
REVERT: D  347 LYS cc_start: 0.8410 (mttt) cc_final: 0.8188 (mptt)
REVERT: D  348 ASP cc_start: 0.6279 (t0) cc_final: 0.5757 (p0)
REVERT: D  369 LYS cc_start: 0.8186 (mttt) cc_final: 0.7484 (mtpt)
REVERT: D  375 LYS cc_start: 0.8200 (ttmt) cc_final: 0.7904 (mttt)
REVERT: E  311 LYS cc_start: 0.7903 (mtmt) cc_final: 0.7151 (mmtt)
REVERT: E  331 LYS cc_start: 0.8583 (mtmt) cc_final: 0.8227 (mttm)
REVERT: E  347 LYS cc_start: 0.8317 (mttt) cc_final: 0.7799 (mptt)
REVERT: E  349 ARG cc_start: 0.8547 (mtt180) cc_final: 0.7598 (mmm160)
REVERT: E  369 LYS cc_start: 0.7782 (mttt) cc_final: 0.7027 (mtpt)
REVERT: E  375 LYS cc_start: 0.8115 (tppt) cc_final: 0.7653 (mttt)
  outliers start: 9
  outliers final: 7
  residues processed: 64
  average time/residue: 0.3466
  time to fit residues: 24.3884
Evaluate side-chains
  67 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  318 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 7 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 18 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 26 optimal weight:    7.9990
   chunk 34 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   overall best weight:    5.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4855 r_free = 0.4855 target = 0.287033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 91)----------------|
| r_work = 0.5074 r_free = 0.5074 target = 0.238191 restraints weight = 3471.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.4333 rms_B_bonded: 1.06
r_work: 0.4262 rms_B_bonded: 1.14 restraints_weight: 0.5000
r_work: 0.4203 rms_B_bonded: 1.84 restraints_weight: 0.2500
r_work (final): 0.4203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.3484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042   2915  Z= 0.323
  Angle     :  0.706   6.536   3900  Z= 0.378
  Chirality :  0.052   0.137    440
  Planarity :  0.006   0.057    495
  Dihedral  :  5.685  20.957    385
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 18.79 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.25 (0.32), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.47 (0.25), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS B 330 
 PHE   0.007   0.002   PHE D 346 
 TYR   0.019   0.006   TYR A 310 
 ARG   0.001   0.000   ARG A 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02627 (   40)
  hydrogen bonds       : angle       5.14606 (  120)
  covalent geometry    : bond        0.00714 ( 2915)
  covalent geometry    : angle       0.70554 ( 3900)

*********************** 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
  74 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.8229 (mttt) cc_final: 0.7728 (mptt)
REVERT: A  348 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8076 (t70)
REVERT: A  375 LYS cc_start: 0.8065 (tttt) cc_final: 0.7606 (mttt)
REVERT: B  311 LYS cc_start: 0.7855 (mtmt) cc_final: 0.7130 (mmtt)
REVERT: B  347 LYS cc_start: 0.8294 (mttt) cc_final: 0.7787 (mptt)
REVERT: B  348 ASP cc_start: 0.8441 (t70) cc_final: 0.8041 (t70)
REVERT: B  349 ARG cc_start: 0.8462 (mtt180) cc_final: 0.7523 (mmm160)
REVERT: B  369 LYS cc_start: 0.8190 (mttt) cc_final: 0.7414 (mtpt)
REVERT: B  375 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7587 (mttt)
REVERT: B  379 ARG cc_start: 0.7091 (tmt-80) cc_final: 0.6674 (ttp80)
REVERT: C  347 LYS cc_start: 0.8575 (mptt) cc_final: 0.7863 (mptt)
REVERT: C  349 ARG cc_start: 0.8577 (mtt180) cc_final: 0.7232 (pmt-80)
REVERT: C  369 LYS cc_start: 0.8248 (mttt) cc_final: 0.7631 (mtpt)
REVERT: D  322 CYS cc_start: 0.8280 (t) cc_final: 0.8043 (t)
REVERT: D  348 ASP cc_start: 0.7148 (t0) cc_final: 0.6486 (p0)
REVERT: D  369 LYS cc_start: 0.8342 (mttt) cc_final: 0.7590 (mtpt)
REVERT: E  311 LYS cc_start: 0.7957 (mtmt) cc_final: 0.7192 (mmtt)
REVERT: E  347 LYS cc_start: 0.8414 (mttt) cc_final: 0.7941 (mptt)
REVERT: E  349 ARG cc_start: 0.8565 (mtt180) cc_final: 0.7661 (mmm160)
REVERT: E  369 LYS cc_start: 0.7966 (mttt) cc_final: 0.7227 (mtpt)
REVERT: E  375 LYS cc_start: 0.8141 (tppt) cc_final: 0.7632 (mttt)
  outliers start: 12
  outliers final: 10
  residues processed: 64
  average time/residue: 0.3081
  time to fit residues: 21.7026
Evaluate side-chains
  69 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain C residue  311 LYS
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  318 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   chunk 4 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 28 optimal weight:    7.9990
   chunk 31 optimal weight:    3.9990
   chunk 8 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    2.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4908 r_free = 0.4908 target = 0.293399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.5134 r_free = 0.5134 target = 0.245360 restraints weight = 3442.466|
|-----------------------------------------------------------------------------|
r_work (start): 0.4413 rms_B_bonded: 1.07
r_work: 0.4342 rms_B_bonded: 1.12 restraints_weight: 0.5000
r_work: 0.4282 rms_B_bonded: 1.85 restraints_weight: 0.2500
r_work (final): 0.4282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.3725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   2915  Z= 0.164
  Angle     :  0.592   8.676   3900  Z= 0.295
  Chirality :  0.048   0.122    440
  Planarity :  0.005   0.052    495
  Dihedral  :  4.919  17.586    385
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 19.70 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.84 (0.35), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.15 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS B 330 
 PHE   0.008   0.001   PHE E 378 
 TYR   0.015   0.004   TYR A 310 
 ARG   0.001   0.000   ARG C 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01794 (   40)
  hydrogen bonds       : angle       4.72772 (  120)
  covalent geometry    : bond        0.00358 ( 2915)
  covalent geometry    : angle       0.59239 ( 3900)

*********************** 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
  73 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.8215 (mttt) cc_final: 0.7758 (mptt)
REVERT: A  348 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8002 (t70)
REVERT: A  375 LYS cc_start: 0.7982 (tttt) cc_final: 0.7596 (mttt)
REVERT: B  311 LYS cc_start: 0.7870 (mtmt) cc_final: 0.7159 (mmtt)
REVERT: B  347 LYS cc_start: 0.8088 (mttt) cc_final: 0.7695 (mptt)
REVERT: B  348 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7957 (t70)
REVERT: B  349 ARG cc_start: 0.8475 (mtt180) cc_final: 0.7554 (mmp-170)
REVERT: B  369 LYS cc_start: 0.8146 (mttt) cc_final: 0.7354 (mtpt)
REVERT: B  375 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7509 (mttt)
REVERT: B  379 ARG cc_start: 0.7040 (tmt-80) cc_final: 0.6657 (ttp80)
REVERT: C  322 CYS cc_start: 0.8225 (t) cc_final: 0.7911 (t)
REVERT: C  347 LYS cc_start: 0.8543 (mptt) cc_final: 0.7873 (mptt)
REVERT: C  349 ARG cc_start: 0.8574 (mtt180) cc_final: 0.7266 (pmt-80)
REVERT: C  369 LYS cc_start: 0.8228 (mttt) cc_final: 0.7541 (ttmt)
REVERT: C  375 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7974 (mttt)
REVERT: D  322 CYS cc_start: 0.8116 (t) cc_final: 0.7892 (t)
REVERT: D  348 ASP cc_start: 0.7217 (t0) cc_final: 0.6592 (p0)
REVERT: D  369 LYS cc_start: 0.8345 (mttt) cc_final: 0.7597 (mtpt)
REVERT: D  375 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7909 (mttt)
REVERT: E  311 LYS cc_start: 0.7944 (mtmt) cc_final: 0.7173 (mmtt)
REVERT: E  331 LYS cc_start: 0.8504 (mtpt) cc_final: 0.7957 (mttp)
REVERT: E  347 LYS cc_start: 0.8374 (mttt) cc_final: 0.7933 (mptt)
REVERT: E  349 ARG cc_start: 0.8598 (mtt180) cc_final: 0.7661 (mmm160)
REVERT: E  369 LYS cc_start: 0.7986 (mttt) cc_final: 0.7253 (mtpt)
REVERT: E  375 LYS cc_start: 0.8100 (tppt) cc_final: 0.7646 (mttt)
  outliers start: 12
  outliers final: 8
  residues processed: 63
  average time/residue: 0.2978
  time to fit residues: 20.7224
Evaluate side-chains
  71 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  318 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 14 optimal weight:    7.9990
   chunk 20 optimal weight:    8.9990
   chunk 4 optimal weight:    6.9990
   chunk 8 optimal weight:    9.9990
   overall best weight:    4.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4875 r_free = 0.4875 target = 0.289460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.5100 r_free = 0.5100 target = 0.240415 restraints weight = 3522.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.4370 rms_B_bonded: 1.09
r_work: 0.4299 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.4239 rms_B_bonded: 1.86 restraints_weight: 0.2500
r_work (final): 0.4239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.3822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   2915  Z= 0.232
  Angle     :  0.642   8.324   3900  Z= 0.328
  Chirality :  0.050   0.126    440
  Planarity :  0.005   0.054    495
  Dihedral  :  5.168  18.837    385
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 20.30 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.82 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (0.27), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS B 330 
 PHE   0.006   0.001   PHE D 346 
 TYR   0.017   0.005   TYR A 310 
 ARG   0.001   0.000   ARG A 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02116 (   40)
  hydrogen bonds       : angle       4.78734 (  120)
  covalent geometry    : bond        0.00512 ( 2915)
  covalent geometry    : angle       0.64239 ( 3900)

*********************** 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
  76 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.7041 (ttmt) cc_final: 0.6665 (ttmt)
REVERT: A  347 LYS cc_start: 0.8289 (mttt) cc_final: 0.7802 (mptt)
REVERT: A  348 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8022 (t70)
REVERT: A  369 LYS cc_start: 0.8333 (mttt) cc_final: 0.7463 (mtpt)
REVERT: A  375 LYS cc_start: 0.7962 (tttt) cc_final: 0.7593 (mttt)
REVERT: B  311 LYS cc_start: 0.7898 (mtmt) cc_final: 0.7179 (mmtt)
REVERT: B  347 LYS cc_start: 0.8181 (mttt) cc_final: 0.7729 (mptt)
REVERT: B  348 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.7954 (t70)
REVERT: B  349 ARG cc_start: 0.8439 (mtt180) cc_final: 0.7507 (mmm160)
REVERT: B  369 LYS cc_start: 0.8163 (mttt) cc_final: 0.7385 (mtpt)
REVERT: B  375 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7526 (mttt)
REVERT: B  379 ARG cc_start: 0.7052 (tmt-80) cc_final: 0.6687 (ttp80)
REVERT: C  322 CYS cc_start: 0.8214 (t) cc_final: 0.7897 (t)
REVERT: C  347 LYS cc_start: 0.8543 (mptt) cc_final: 0.7829 (mptt)
REVERT: C  349 ARG cc_start: 0.8568 (mtt180) cc_final: 0.7267 (pmt-80)
REVERT: C  369 LYS cc_start: 0.8275 (mttt) cc_final: 0.7566 (ttmt)
REVERT: C  375 LYS cc_start: 0.8293 (ttmt) cc_final: 0.8000 (mttt)
REVERT: D  322 CYS cc_start: 0.8166 (t) cc_final: 0.7936 (t)
REVERT: E  311 LYS cc_start: 0.8016 (mtmt) cc_final: 0.7243 (mmtt)
REVERT: E  331 LYS cc_start: 0.8578 (mtpt) cc_final: 0.8025 (mttm)
REVERT: E  347 LYS cc_start: 0.8426 (mttt) cc_final: 0.7946 (mptt)
REVERT: E  349 ARG cc_start: 0.8546 (mtt180) cc_final: 0.7653 (mmm160)
REVERT: E  369 LYS cc_start: 0.8060 (mttt) cc_final: 0.7300 (mtpt)
REVERT: E  375 LYS cc_start: 0.8161 (tppt) cc_final: 0.7640 (mttt)
  outliers start: 11
  outliers final: 8
  residues processed: 67
  average time/residue: 0.3153
  time to fit residues: 23.2849
Evaluate side-chains
  75 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  318 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 28 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 29 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   overall best weight:    1.9786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4930 r_free = 0.4930 target = 0.295712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.5105 r_free = 0.5105 target = 0.249046 restraints weight = 3472.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.4458 rms_B_bonded: 1.37
r_work: 0.4357 rms_B_bonded: 1.49 restraints_weight: 0.5000
r_work: 0.4289 rms_B_bonded: 2.48 restraints_weight: 0.2500
r_work (final): 0.4289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.3949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.016   2915  Z= 0.122
  Angle     :  0.564   8.967   3900  Z= 0.272
  Chirality :  0.048   0.119    440
  Planarity :  0.004   0.052    495
  Dihedral  :  4.553  16.103    385
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 21.21 %
    Favored  : 75.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.56 (0.37), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.94 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS B 330 
 PHE   0.003   0.001   PHE D 346 
 TYR   0.013   0.003   TYR E 310 
 ARG   0.001   0.000   ARG C 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01501 (   40)
  hydrogen bonds       : angle       4.51671 (  120)
  covalent geometry    : bond        0.00265 ( 2915)
  covalent geometry    : angle       0.56352 ( 3900)

*********************** 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
  74 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.8118 (mttt) cc_final: 0.7591 (mptt)
REVERT: A  348 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7920 (t70)
REVERT: A  375 LYS cc_start: 0.7916 (tttt) cc_final: 0.7550 (mttt)
REVERT: B  311 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7113 (mmtt)
REVERT: B  347 LYS cc_start: 0.8019 (mttt) cc_final: 0.7602 (mptt)
REVERT: B  348 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7934 (t70)
REVERT: B  349 ARG cc_start: 0.8430 (mtt180) cc_final: 0.7461 (mmm160)
REVERT: B  369 LYS cc_start: 0.8135 (mttt) cc_final: 0.7377 (mtpt)
REVERT: B  375 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7504 (mttt)
REVERT: B  379 ARG cc_start: 0.6999 (tmt-80) cc_final: 0.6651 (ttp80)
REVERT: C  322 CYS cc_start: 0.8093 (t) cc_final: 0.7781 (t)
REVERT: C  347 LYS cc_start: 0.8526 (mptt) cc_final: 0.7833 (mptt)
REVERT: C  369 LYS cc_start: 0.8282 (mttt) cc_final: 0.7574 (ttmt)
REVERT: C  375 LYS cc_start: 0.8281 (ttmt) cc_final: 0.8012 (mttt)
REVERT: D  322 CYS cc_start: 0.7979 (t) cc_final: 0.7759 (t)
REVERT: D  375 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7924 (mttt)
REVERT: E  311 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7138 (mmtt)
REVERT: E  331 LYS cc_start: 0.8514 (mtpt) cc_final: 0.7975 (mttm)
REVERT: E  347 LYS cc_start: 0.8278 (mttt) cc_final: 0.7828 (mptt)
REVERT: E  349 ARG cc_start: 0.8582 (mtt180) cc_final: 0.7588 (mmm160)
REVERT: E  369 LYS cc_start: 0.8026 (mttt) cc_final: 0.7284 (mtpt)
REVERT: E  375 LYS cc_start: 0.8153 (tppt) cc_final: 0.7668 (mttt)
  outliers start: 12
  outliers final: 8
  residues processed: 64
  average time/residue: 0.2808
  time to fit residues: 19.9047
Evaluate side-chains
  68 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  318 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 29 optimal weight:    6.9990
   chunk 14 optimal weight:    0.2980
   chunk 18 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 26 optimal weight:    9.9990
   chunk 34 optimal weight:    0.0570
   chunk 22 optimal weight:   10.0000
   overall best weight:    3.2704

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4894 r_free = 0.4894 target = 0.292169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.5090 r_free = 0.5090 target = 0.243737 restraints weight = 3471.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.4401 rms_B_bonded: 1.41
r_work: 0.4312 rms_B_bonded: 1.38 restraints_weight: 0.5000
r_work: 0.4245 rms_B_bonded: 2.28 restraints_weight: 0.2500
r_work (final): 0.4245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.4111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   2915  Z= 0.184
  Angle     :  0.597   8.500   3900  Z= 0.300
  Chirality :  0.049   0.124    440
  Planarity :  0.005   0.053    495
  Dihedral  :  4.758  17.377    385
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 22.73 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.57 (0.38), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.95 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS B 330 
 PHE   0.005   0.001   PHE D 346 
 TYR   0.016   0.004   TYR A 310 
 ARG   0.001   0.000   ARG E 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01774 (   40)
  hydrogen bonds       : angle       4.55919 (  120)
  covalent geometry    : bond        0.00405 ( 2915)
  covalent geometry    : angle       0.59673 ( 3900)

*********************** 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
  74 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.7033 (ttmt) cc_final: 0.6705 (ttmt)
REVERT: A  347 LYS cc_start: 0.8226 (mttt) cc_final: 0.7659 (mptt)
REVERT: A  348 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7983 (t70)
REVERT: A  375 LYS cc_start: 0.7955 (tttt) cc_final: 0.7600 (mttt)
REVERT: B  311 LYS cc_start: 0.7887 (mtmt) cc_final: 0.7144 (mmtt)
REVERT: B  347 LYS cc_start: 0.8066 (mttt) cc_final: 0.7599 (mptt)
REVERT: B  348 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7942 (t70)
REVERT: B  349 ARG cc_start: 0.8396 (mtt180) cc_final: 0.7428 (mmm160)
REVERT: B  369 LYS cc_start: 0.8166 (mttt) cc_final: 0.7410 (mtpt)
REVERT: B  375 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7527 (mttt)
REVERT: B  379 ARG cc_start: 0.6999 (tmt-80) cc_final: 0.6648 (ttp80)
REVERT: C  322 CYS cc_start: 0.8176 (t) cc_final: 0.7857 (t)
REVERT: C  357 LEU cc_start: 0.8812 (mp) cc_final: 0.8560 (mp)
REVERT: C  369 LYS cc_start: 0.8318 (mttt) cc_final: 0.7598 (ttmt)
REVERT: C  375 LYS cc_start: 0.8284 (ttmt) cc_final: 0.8001 (mttt)
REVERT: D  322 CYS cc_start: 0.8142 (t) cc_final: 0.7897 (t)
REVERT: D  348 ASP cc_start: 0.7371 (t0) cc_final: 0.6683 (p0)
REVERT: D  375 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7917 (mttt)
REVERT: E  311 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7179 (mmtt)
REVERT: E  331 LYS cc_start: 0.8539 (mtpt) cc_final: 0.7975 (mttm)
REVERT: E  347 LYS cc_start: 0.8351 (mttt) cc_final: 0.7900 (mptt)
REVERT: E  349 ARG cc_start: 0.8549 (mtt180) cc_final: 0.7646 (mmm160)
REVERT: E  369 LYS cc_start: 0.8057 (mttt) cc_final: 0.7302 (mtpt)
REVERT: E  375 LYS cc_start: 0.8102 (tppt) cc_final: 0.7616 (mttt)
  outliers start: 11
  outliers final: 8
  residues processed: 65
  average time/residue: 0.2893
  time to fit residues: 20.7800
Evaluate side-chains
  74 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  318 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 2 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 16 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    2.7788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.293810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.5103 r_free = 0.5103 target = 0.246225 restraints weight = 3499.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.4429 rms_B_bonded: 1.35
r_work: 0.4341 rms_B_bonded: 1.33 restraints_weight: 0.5000
r_work: 0.4276 rms_B_bonded: 2.20 restraints_weight: 0.2500
r_work (final): 0.4276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.4155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2915  Z= 0.159
  Angle     :  0.595   9.106   3900  Z= 0.290
  Chirality :  0.049   0.123    440
  Planarity :  0.005   0.054    495
  Dihedral  :  4.616  16.429    385
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 22.12 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.49 (0.38), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.89 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS B 330 
 PHE   0.004   0.001   PHE D 346 
 TYR   0.014   0.003   TYR E 310 
 ARG   0.001   0.000   ARG C 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01650 (   40)
  hydrogen bonds       : angle       4.47699 (  120)
  covalent geometry    : bond        0.00347 ( 2915)
  covalent geometry    : angle       0.59505 ( 3900)

********************** 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
  74 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.6995 (ttmt) cc_final: 0.6642 (ttmt)
REVERT: A  347 LYS cc_start: 0.8193 (mttt) cc_final: 0.7642 (mptt)
REVERT: A  348 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7821 (t70)
REVERT: A  375 LYS cc_start: 0.7950 (tttt) cc_final: 0.7604 (mttt)
REVERT: B  311 LYS cc_start: 0.7920 (mtmt) cc_final: 0.7151 (mmtt)
REVERT: B  347 LYS cc_start: 0.8065 (mttt) cc_final: 0.7620 (mptt)
REVERT: B  348 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.7921 (t70)
REVERT: B  349 ARG cc_start: 0.8395 (mtt180) cc_final: 0.7419 (mmm160)
REVERT: B  369 LYS cc_start: 0.8192 (mttt) cc_final: 0.7427 (mtpt)
REVERT: B  375 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7516 (mttt)
REVERT: B  379 ARG cc_start: 0.6990 (tmt-80) cc_final: 0.6637 (ttp80)
REVERT: C  369 LYS cc_start: 0.8298 (mttt) cc_final: 0.7582 (ttmt)
REVERT: C  375 LYS cc_start: 0.8291 (ttmt) cc_final: 0.8003 (mttt)
REVERT: D  322 CYS cc_start: 0.8072 (t) cc_final: 0.7845 (t)
REVERT: D  348 ASP cc_start: 0.7368 (t0) cc_final: 0.6708 (p0)
REVERT: D  375 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7946 (mttt)
REVERT: E  311 LYS cc_start: 0.7941 (mtmt) cc_final: 0.7163 (mmtt)
REVERT: E  331 LYS cc_start: 0.8517 (mtpt) cc_final: 0.7969 (mttm)
REVERT: E  347 LYS cc_start: 0.8312 (mttt) cc_final: 0.7857 (mptt)
REVERT: E  349 ARG cc_start: 0.8543 (mtt180) cc_final: 0.7621 (mmm160)
REVERT: E  369 LYS cc_start: 0.8036 (mttt) cc_final: 0.7285 (mtpt)
REVERT: E  375 LYS cc_start: 0.8083 (tppt) cc_final: 0.7557 (mttt)
  outliers start: 13
  outliers final: 8
  residues processed: 65
  average time/residue: 0.2960
  time to fit residues: 21.2510
Evaluate side-chains
  72 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain B residue  318 VAL
Chi-restraints excluded: chain B residue  348 ASP
Chi-restraints excluded: chain B residue  375 LYS
Chi-restraints excluded: chain C residue  318 VAL
Chi-restraints excluded: chain C residue  324 SER
Chi-restraints excluded: chain D residue  318 VAL
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  318 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0570
   chunk 14 optimal weight:    0.1980
   overall best weight:    2.2504

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

Flipped N/Q/H residues before XYZ refinement:
D 336 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4925 r_free = 0.4925 target = 0.294965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 96)----------------|
| r_work = 0.5149 r_free = 0.5149 target = 0.246537 restraints weight = 3404.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.4435 rms_B_bonded: 1.09
r_work: 0.4370 rms_B_bonded: 1.13 restraints_weight: 0.5000
r_work: 0.4314 rms_B_bonded: 1.83 restraints_weight: 0.2500
r_work (final): 0.4314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.4245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2915  Z= 0.134
  Angle     :  0.563   9.233   3900  Z= 0.275
  Chirality :  0.048   0.120    440
  Planarity :  0.004   0.054    495
  Dihedral  :  4.470  15.971    385
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 23.03 %
    Favored  : 73.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.41 (0.38), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.83 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS B 330 
 PHE   0.005   0.001   PHE D 346 
 TYR   0.013   0.003   TYR A 310 
 ARG   0.001   0.000   ARG D 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01512 (   40)
  hydrogen bonds       : angle       4.39060 (  120)
  covalent geometry    : bond        0.00293 ( 2915)
  covalent geometry    : angle       0.56337 ( 3900)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1909.42 seconds
wall clock time: 34 minutes 4.37 seconds (2044.37 seconds total)