Starting phenix.real_space_refine
on Fri Aug 22 13:02:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8oth_17179/08_2025/8oth_17179.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8oth_17179/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8oth_17179/08_2025/8oth_17179.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8oth_17179/08_2025/8oth_17179.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8oth_17179/08_2025/8oth_17179.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8oth_17179/08_2025/8oth_17179.map"
  }
  resolution = 3.4
  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 35 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: 0.70, per 1000 atoms: 0.24
  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: 0.20
  Conformation dependent library (CDL) restraints added in 113.1 milliseconds
  
  Enol-peptide restraints added in 953.7 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, 42.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  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: 0.30

  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: 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: 0.01
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:             3.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.700
  Find NCS groups from input model:        0.030
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.180
-------------------------------------------------------------------------------
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 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: -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
 ARG   0.004   0.002   ARG E 349 
 TYR   0.035   0.013   TYR E 310 
 PHE   0.017   0.004   PHE D 346 
 HIS   0.011   0.004   HIS C 329 

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

*********************** 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  : 0.123 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.8220 (mttt) cc_final: 0.7704 (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: 0.7971 (mptt)
REVERT: B  349 ARG cc_start: 0.8767 (mtt180) cc_final: 0.7744 (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: 0.7534 (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: 0.8320 (mptt)
REVERT: D  349 ARG cc_start: 0.8801 (mtt180) cc_final: 0.7561 (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: 0.7762 (mmp-170)
REVERT: E  369 LYS cc_start: 0.8373 (mttt) cc_final: 0.7845 (mtpt)
  outliers start: 5
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1387
  time to fit residues: 11.4101
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  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0040
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   overall best weight:    0.6994

-------------------------------------------------------------------------------
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 = 0.4670 r_free = 0.4670 target = 0.163736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.132538 restraints weight = 3368.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.4384 rms_B_bonded: 2.71
r_work: 0.4284 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.4182 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   2915  Z= 0.106
  Angle     :  0.567   4.704   3900  Z= 0.286
  Chirality :  0.048   0.132    440
  Planarity :  0.003   0.026    495
  Dihedral  :  5.408  17.818    385
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 12.42 %
    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: -4.01 (0.30), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.05 (0.23), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 379 
 TYR   0.014   0.003   TYR A 310 
 PHE   0.004   0.001   PHE D 378 
 HIS   0.005   0.002   HIS A 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 2915)
  covalent geometry    : angle       0.56668 ( 3900)
  hydrogen bonds       : bond        0.02215 (   40)
  hydrogen bonds       : angle       5.76224 (  120)

*********************** 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
  75 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.101 
Fit side-chains
REVERT: A  348 ASP cc_start: 0.8436 (t0) cc_final: 0.8097 (t0)
REVERT: A  375 LYS cc_start: 0.7746 (tttt) cc_final: 0.7224 (mttt)
REVERT: B  311 LYS cc_start: 0.7611 (mtmt) cc_final: 0.6857 (mmtt)
REVERT: B  345 ASP cc_start: 0.7775 (m-30) cc_final: 0.6745 (t0)
REVERT: B  369 LYS cc_start: 0.7662 (mttt) cc_final: 0.6996 (mtpt)
REVERT: B  375 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7387 (mttt)
REVERT: C  345 ASP cc_start: 0.8199 (m-30) cc_final: 0.7424 (t0)
REVERT: C  375 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7952 (mttt)
REVERT: D  321 LYS cc_start: 0.7382 (ttmt) cc_final: 0.6912 (ttmt)
REVERT: D  347 LYS cc_start: 0.8330 (mttt) cc_final: 0.8125 (mptt)
REVERT: D  369 LYS cc_start: 0.8073 (mttt) cc_final: 0.7338 (mtmt)
REVERT: D  375 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7863 (mttt)
REVERT: E  311 LYS cc_start: 0.7682 (mtmt) cc_final: 0.7024 (mmtt)
REVERT: E  321 LYS cc_start: 0.6432 (ttmt) cc_final: 0.5712 (tttt)
REVERT: E  345 ASP cc_start: 0.7685 (m-30) cc_final: 0.6701 (t0)
REVERT: E  349 ARG cc_start: 0.8444 (mtt180) cc_final: 0.7363 (mmm160)
REVERT: E  369 LYS cc_start: 0.7458 (mttt) cc_final: 0.6888 (mtpt)
REVERT: E  375 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7525 (mttt)
  outliers start: 8
  outliers final: 6
  residues processed: 68
  average time/residue: 0.1001
  time to fit residues: 7.6536
Evaluate side-chains
  61 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain E residue  375 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 22 optimal weight:    9.9990
   chunk 23 optimal weight:    0.6980
   chunk 19 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 8 optimal weight:    8.9990
   chunk 1 optimal weight:    1.9990
   chunk 30 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0670
   overall best weight:    2.3524

-------------------------------------------------------------------------------
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 = 0.4618 r_free = 0.4618 target = 0.158769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.127596 restraints weight = 3406.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.4337 rms_B_bonded: 2.68
r_work: 0.4231 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.4123 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.4123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2915  Z= 0.144
  Angle     :  0.524   4.427   3900  Z= 0.271
  Chirality :  0.048   0.126    440
  Planarity :  0.004   0.048    495
  Dihedral  :  4.855  18.378    385
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 20.00 %
    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 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: -3.36 (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
 ARG   0.001   0.000   ARG D 349 
 TYR   0.019   0.004   TYR A 310 
 PHE   0.006   0.002   PHE D 346 
 HIS   0.007   0.002   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 2915)
  covalent geometry    : angle       0.52388 ( 3900)
  hydrogen bonds       : bond        0.01961 (   40)
  hydrogen bonds       : angle       4.79932 (  120)

*********************** 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
  70 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.8170 (mptt) cc_final: 0.7598 (mptt)
REVERT: A  375 LYS cc_start: 0.7958 (tttt) cc_final: 0.7483 (mttt)
REVERT: B  311 LYS cc_start: 0.7672 (mtmt) cc_final: 0.6975 (mmtt)
REVERT: B  347 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7434 (mptt)
REVERT: B  349 ARG cc_start: 0.8424 (mtt180) cc_final: 0.7318 (mmp-170)
REVERT: B  369 LYS cc_start: 0.7828 (mttt) cc_final: 0.7146 (mtpt)
REVERT: B  375 LYS cc_start: 0.7861 (ttmt) cc_final: 0.7411 (mttt)
REVERT: C  347 LYS cc_start: 0.8305 (mptt) cc_final: 0.8080 (mptt)
REVERT: C  369 LYS cc_start: 0.8113 (mttt) cc_final: 0.7499 (mtpt)
REVERT: C  375 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7957 (mttt)
REVERT: D  321 LYS cc_start: 0.7463 (ttmt) cc_final: 0.7014 (ttmt)
REVERT: D  347 LYS cc_start: 0.8344 (mttt) cc_final: 0.8070 (mptt)
REVERT: D  369 LYS cc_start: 0.8148 (mttt) cc_final: 0.7506 (mtpt)
REVERT: D  375 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7850 (mttt)
REVERT: E  311 LYS cc_start: 0.7761 (mtmt) cc_final: 0.7093 (mmtt)
REVERT: E  347 LYS cc_start: 0.8113 (mttp) cc_final: 0.7636 (mptt)
REVERT: E  349 ARG cc_start: 0.8490 (mtt180) cc_final: 0.7367 (mmm160)
REVERT: E  369 LYS cc_start: 0.7556 (mttt) cc_final: 0.6897 (mtpt)
REVERT: E  375 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7708 (mttt)
  outliers start: 6
  outliers final: 5
  residues processed: 64
  average time/residue: 0.1549
  time to fit residues: 10.8307
Evaluate side-chains
  60 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
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  347 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    0.6980
   chunk 33 optimal weight:    9.9990
   chunk 18 optimal weight:    3.9990
   chunk 4 optimal weight:    9.9990
   chunk 21 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   overall best weight:    3.9388

-------------------------------------------------------------------------------
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 = 0.4907 r_free = 0.4907 target = 0.292554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.5125 r_free = 0.5125 target = 0.244945 restraints weight = 3377.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.4409 rms_B_bonded: 1.04
r_work: 0.4338 rms_B_bonded: 1.11 restraints_weight: 0.5000
r_work: 0.4275 rms_B_bonded: 1.82 restraints_weight: 0.2500
r_work (final): 0.4275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.3333

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= 0.226
  Angle     :  0.596   4.948   3900  Z= 0.314
  Chirality :  0.049   0.132    440
  Planarity :  0.005   0.053    495
  Dihedral  :  5.184  19.516    385
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 21.21 %
    Favored  : 76.06 %
  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: -3.07 (0.33), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (0.25), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 379 
 TYR   0.017   0.004   TYR A 310 
 PHE   0.006   0.002   PHE A 346 
 HIS   0.009   0.003   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 2915)
  covalent geometry    : angle       0.59570 ( 3900)
  hydrogen bonds       : bond        0.02124 (   40)
  hydrogen bonds       : angle       4.72995 (  120)

*********************** 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
  74 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A  347 LYS cc_start: 0.8480 (mptt) cc_final: 0.7930 (mptt)
REVERT: A  348 ASP cc_start: 0.8543 (t70) cc_final: 0.8136 (t0)
REVERT: A  375 LYS cc_start: 0.8016 (tttt) cc_final: 0.7589 (mttt)
REVERT: B  311 LYS cc_start: 0.7767 (mtmt) cc_final: 0.7078 (mmtt)
REVERT: B  347 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7670 (mptt)
REVERT: B  349 ARG cc_start: 0.8414 (mtt180) cc_final: 0.7513 (mmm160)
REVERT: B  369 LYS cc_start: 0.7970 (mttt) cc_final: 0.7256 (mtpt)
REVERT: B  375 LYS cc_start: 0.7908 (ttmt) cc_final: 0.7525 (mttt)
REVERT: B  379 ARG cc_start: 0.7069 (tmt-80) cc_final: 0.6471 (ttp80)
REVERT: C  347 LYS cc_start: 0.8453 (mptt) cc_final: 0.7676 (mptt)
REVERT: C  369 LYS cc_start: 0.8102 (mttt) cc_final: 0.7454 (mtpt)
REVERT: C  375 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7899 (mttt)
REVERT: D  322 CYS cc_start: 0.8303 (t) cc_final: 0.8067 (t)
REVERT: D  348 ASP cc_start: 0.4920 (t0) cc_final: 0.4679 (p0)
REVERT: D  369 LYS cc_start: 0.8170 (mttt) cc_final: 0.7484 (mtpt)
REVERT: D  375 LYS cc_start: 0.8194 (ttmt) cc_final: 0.7904 (mttt)
REVERT: E  311 LYS cc_start: 0.7870 (mtmt) cc_final: 0.7126 (mmtt)
REVERT: E  347 LYS cc_start: 0.8286 (mttp) cc_final: 0.7909 (mptt)
REVERT: E  349 ARG cc_start: 0.8513 (mtt180) cc_final: 0.7566 (mmm160)
REVERT: E  369 LYS cc_start: 0.7759 (mttt) cc_final: 0.7027 (mtpt)
REVERT: E  375 LYS cc_start: 0.8176 (ttmt) cc_final: 0.7730 (mttt)
  outliers start: 9
  outliers final: 8
  residues processed: 65
  average time/residue: 0.1384
  time to fit residues: 9.8554
Evaluate side-chains
  67 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
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 B residue  347 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 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 26 optimal weight:    0.8980
   chunk 13 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 21 optimal weight:    8.9990
   chunk 8 optimal weight:    9.9990
   overall best weight:    4.5788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4873 r_free = 0.4873 target = 0.289744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.5097 r_free = 0.5097 target = 0.239826 restraints weight = 3407.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.4339 rms_B_bonded: 1.27
r_work: 0.4267 rms_B_bonded: 1.32 restraints_weight: 0.5000
r_work: 0.4201 rms_B_bonded: 2.19 restraints_weight: 0.2500
r_work (final): 0.4201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.3554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   2915  Z= 0.252
  Angle     :  0.633   6.035   3900  Z= 0.335
  Chirality :  0.050   0.133    440
  Planarity :  0.005   0.054    495
  Dihedral  :  5.288  19.399    385
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 21.82 %
    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 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: -3.04 (0.33), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.31 (0.25), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 379 
 TYR   0.019   0.005   TYR A 310 
 PHE   0.005   0.002   PHE D 346 
 HIS   0.009   0.003   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00554 ( 2915)
  covalent geometry    : angle       0.63284 ( 3900)
  hydrogen bonds       : bond        0.02250 (   40)
  hydrogen bonds       : angle       4.87844 (  120)

*********************** 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
  73 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.6943 (ttmt) cc_final: 0.6583 (ttmt)
REVERT: A  347 LYS cc_start: 0.8392 (mptt) cc_final: 0.7857 (mptt)
REVERT: A  369 LYS cc_start: 0.8266 (mttt) cc_final: 0.7412 (mtpt)
REVERT: A  375 LYS cc_start: 0.8056 (tttt) cc_final: 0.7609 (mttt)
REVERT: B  311 LYS cc_start: 0.7756 (mtmt) cc_final: 0.7029 (mmtt)
REVERT: B  347 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7560 (mptt)
REVERT: B  349 ARG cc_start: 0.8485 (mtt180) cc_final: 0.7495 (mmm160)
REVERT: B  369 LYS cc_start: 0.8103 (mttt) cc_final: 0.7343 (mtpt)
REVERT: B  375 LYS cc_start: 0.7927 (ttmt) cc_final: 0.7537 (mttt)
REVERT: C  347 LYS cc_start: 0.8526 (mptt) cc_final: 0.7717 (mptt)
REVERT: C  369 LYS cc_start: 0.8197 (mttt) cc_final: 0.7593 (mtpt)
REVERT: C  375 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7912 (mttt)
REVERT: D  322 CYS cc_start: 0.8241 (t) cc_final: 0.7995 (t)
REVERT: D  348 ASP cc_start: 0.5505 (t0) cc_final: 0.5172 (p0)
REVERT: D  369 LYS cc_start: 0.8245 (mttt) cc_final: 0.7530 (mtpt)
REVERT: D  375 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7936 (mttt)
REVERT: E  311 LYS cc_start: 0.7882 (mtmt) cc_final: 0.7108 (mmtt)
REVERT: E  347 LYS cc_start: 0.8250 (mttp) cc_final: 0.7840 (mptt)
REVERT: E  349 ARG cc_start: 0.8576 (mtt180) cc_final: 0.7609 (mmm160)
REVERT: E  369 LYS cc_start: 0.7941 (mttt) cc_final: 0.7173 (mtpt)
REVERT: E  375 LYS cc_start: 0.8166 (ttmt) cc_final: 0.7715 (mttt)
  outliers start: 10
  outliers final: 9
  residues processed: 65
  average time/residue: 0.1314
  time to fit residues: 9.3907
Evaluate side-chains
  71 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
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 B residue  347 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  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 34 optimal weight:    0.9980
   chunk 8 optimal weight:   20.0000
   chunk 21 optimal weight:    9.9990
   chunk 26 optimal weight:    0.0870
   chunk 11 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 15 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.2162

-------------------------------------------------------------------------------
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 = 0.5061 r_free = 0.5061 target = 0.363581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 109)---------------|
| r_work = 0.5400 r_free = 0.5400 target = 0.299269 restraints weight = 3844.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.4855 rms_B_bonded: 1.01
r_work: 0.5183 rms_B_bonded: 0.50 restraints_weight: 0.5000
r_work: 0.5168 rms_B_bonded: 0.74 restraints_weight: 0.2500
r_work: 0.4996 rms_B_bonded: 2.68 restraints_weight: 0.1250
r_work (final): 0.4996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.3825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.013   2915  Z= 0.089
  Angle     :  0.525   8.314   3900  Z= 0.256
  Chirality :  0.047   0.118    440
  Planarity :  0.004   0.049    495
  Dihedral  :  4.355  15.278    385
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 22.12 %
    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 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: -2.69 (0.36), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.04 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 349 
 TYR   0.013   0.003   TYR A 310 
 PHE   0.006   0.001   PHE E 378 
 HIS   0.007   0.002   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00193 ( 2915)
  covalent geometry    : angle       0.52464 ( 3900)
  hydrogen bonds       : bond        0.01312 (   40)
  hydrogen bonds       : angle       4.39983 (  120)

*********************** 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
  69 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A  321 LYS cc_start: 0.7783 (ttmt) cc_final: 0.7555 (ttmt)
REVERT: A  369 LYS cc_start: 0.8298 (mttt) cc_final: 0.7901 (mtpt)
REVERT: B  349 ARG cc_start: 0.8576 (mtt180) cc_final: 0.8348 (mmm160)
REVERT: B  369 LYS cc_start: 0.8327 (mttt) cc_final: 0.7951 (mtpt)
REVERT: C  369 LYS cc_start: 0.8033 (mttt) cc_final: 0.7657 (mtpt)
REVERT: D  369 LYS cc_start: 0.7822 (mttt) cc_final: 0.7613 (ttpt)
REVERT: E  369 LYS cc_start: 0.7965 (mttt) cc_final: 0.7696 (mtpt)
  outliers start: 9
  outliers final: 7
  residues processed: 61
  average time/residue: 0.1205
  time to fit residues: 8.1061
Evaluate side-chains
  45 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   chunk 29 optimal weight:    9.9990
   chunk 23 optimal weight:    9.9990
   chunk 8 optimal weight:    0.0030
   chunk 25 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 32 optimal weight:    8.9990
   overall best weight:    3.1998

-------------------------------------------------------------------------------
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 = 0.4565 r_free = 0.4565 target = 0.154424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.123930 restraints weight = 3538.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.4275 rms_B_bonded: 2.71
r_work: 0.4178 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.4074 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.4074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.4242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2915  Z= 0.186
  Angle     :  0.681   8.309   3900  Z= 0.337
  Chirality :  0.049   0.125    440
  Planarity :  0.004   0.050    495
  Dihedral  :  4.659  16.463    385
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 23.33 %
    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 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: -2.51 (0.37), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.91 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 349 
 TYR   0.016   0.004   TYR A 310 
 PHE   0.006   0.001   PHE D 346 
 HIS   0.007   0.002   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 2915)
  covalent geometry    : angle       0.68121 ( 3900)
  hydrogen bonds       : bond        0.01663 (   40)
  hydrogen bonds       : angle       4.42031 (  120)

*********************** 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
  53 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.097 
Fit side-chains
REVERT: A  375 LYS cc_start: 0.7940 (mttt) cc_final: 0.7272 (tppt)
REVERT: B  349 ARG cc_start: 0.8280 (mtt180) cc_final: 0.7127 (mmm160)
REVERT: B  375 LYS cc_start: 0.7657 (mttt) cc_final: 0.7184 (tppt)
REVERT: C  375 LYS cc_start: 0.8229 (mttt) cc_final: 0.7763 (tppt)
REVERT: D  348 ASP cc_start: 0.5700 (t0) cc_final: 0.5180 (p0)
REVERT: D  375 LYS cc_start: 0.8153 (mttt) cc_final: 0.7922 (tppt)
  outliers start: 10
  outliers final: 10
  residues processed: 46
  average time/residue: 0.0894
  time to fit residues: 4.6505
Evaluate side-chains
  52 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 21 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 3 optimal weight:    6.9990
   chunk 1 optimal weight:    8.9990
   chunk 18 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 20 optimal weight:    0.0670
   chunk 22 optimal weight:    6.9990
   chunk 5 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   overall best weight:    4.2124

-------------------------------------------------------------------------------
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 = 0.4539 r_free = 0.4539 target = 0.150870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.121167 restraints weight = 3605.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.4243 rms_B_bonded: 2.61
r_work: 0.4146 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.4042 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.4313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   2915  Z= 0.233
  Angle     :  0.690   8.546   3900  Z= 0.352
  Chirality :  0.050   0.128    440
  Planarity :  0.005   0.051    495
  Dihedral  :  5.040  17.932    385
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  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 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: -2.59 (0.37), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 379 
 TYR   0.015   0.005   TYR A 310 
 PHE   0.007   0.002   PHE D 346 
 HIS   0.008   0.002   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 ( 2915)
  covalent geometry    : angle       0.69015 ( 3900)
  hydrogen bonds       : bond        0.01987 (   40)
  hydrogen bonds       : angle       4.58805 (  120)

*********************** 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
  56 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A  348 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8068 (t70)
REVERT: A  375 LYS cc_start: 0.7976 (mttt) cc_final: 0.7397 (tppt)
REVERT: B  349 ARG cc_start: 0.8453 (mtt180) cc_final: 0.7396 (mmm160)
REVERT: B  375 LYS cc_start: 0.7737 (mttt) cc_final: 0.7263 (tppt)
REVERT: C  375 LYS cc_start: 0.8229 (mttt) cc_final: 0.7787 (tppt)
REVERT: D  348 ASP cc_start: 0.6261 (t0) cc_final: 0.5699 (p0)
REVERT: D  375 LYS cc_start: 0.8164 (mttt) cc_final: 0.7960 (tppt)
  outliers start: 11
  outliers final: 10
  residues processed: 47
  average time/residue: 0.1148
  time to fit residues: 6.1005
Evaluate side-chains
  56 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
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 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 29 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 24 optimal weight:    8.9990
   chunk 14 optimal weight:    0.4980
   chunk 1 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0070
   chunk 10 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.9004

-------------------------------------------------------------------------------
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 = 0.4599 r_free = 0.4599 target = 0.155621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.126071 restraints weight = 3505.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.4299 rms_B_bonded: 2.61
r_work: 0.4208 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.4105 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.4450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2915  Z= 0.120
  Angle     :  0.583   7.237   3900  Z= 0.289
  Chirality :  0.047   0.121    440
  Planarity :  0.004   0.053    495
  Dihedral  :  4.478  15.475    385
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 22.42 %
    Favored  : 74.24 %
  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: -2.47 (0.37), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.88 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 379 
 TYR   0.012   0.003   TYR A 310 
 PHE   0.003   0.001   PHE D 346 
 HIS   0.006   0.002   HIS E 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 2915)
  covalent geometry    : angle       0.58345 ( 3900)
  hydrogen bonds       : bond        0.01431 (   40)
  hydrogen bonds       : angle       4.33070 (  120)

*********************** 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
  62 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A  348 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.7976 (t70)
REVERT: A  375 LYS cc_start: 0.7979 (mttt) cc_final: 0.7474 (tppt)
REVERT: B  349 ARG cc_start: 0.8413 (mtt180) cc_final: 0.7313 (mmm160)
REVERT: B  375 LYS cc_start: 0.7732 (mttt) cc_final: 0.7178 (tppt)
REVERT: C  375 LYS cc_start: 0.8213 (mttt) cc_final: 0.7963 (tppt)
REVERT: D  375 LYS cc_start: 0.8151 (mttt) cc_final: 0.7855 (ttmt)
REVERT: E  348 ASP cc_start: 0.8389 (t70) cc_final: 0.8030 (t70)
  outliers start: 11
  outliers final: 9
  residues processed: 53
  average time/residue: 0.1345
  time to fit residues: 7.9059
Evaluate side-chains
  59 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
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 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  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 18 optimal weight:    4.9990
   chunk 19 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.1588

-------------------------------------------------------------------------------
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 = 0.4592 r_free = 0.4592 target = 0.155977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.125945 restraints weight = 3513.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.4297 rms_B_bonded: 2.65
r_work: 0.4208 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.4106 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.4106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.4628

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= 0.134
  Angle     :  0.579   6.231   3900  Z= 0.291
  Chirality :  0.048   0.119    440
  Planarity :  0.004   0.053    495
  Dihedral  :  4.431  15.651    385
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 21.82 %
    Favored  : 74.55 %
  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: -2.47 (0.38), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.87 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 349 
 TYR   0.013   0.003   TYR A 310 
 PHE   0.004   0.001   PHE C 346 
 HIS   0.006   0.002   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 2915)
  covalent geometry    : angle       0.57851 ( 3900)
  hydrogen bonds       : bond        0.01409 (   40)
  hydrogen bonds       : angle       4.21125 (  120)

********************** 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
  58 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A  348 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8006 (t70)
REVERT: A  375 LYS cc_start: 0.7990 (mttt) cc_final: 0.7379 (tppt)
REVERT: B  348 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8042 (t70)
REVERT: B  349 ARG cc_start: 0.8420 (mtt180) cc_final: 0.7332 (mmm160)
REVERT: B  375 LYS cc_start: 0.7754 (mttt) cc_final: 0.7294 (ttmt)
REVERT: C  375 LYS cc_start: 0.8235 (mttt) cc_final: 0.7850 (tppt)
REVERT: D  375 LYS cc_start: 0.8173 (mttt) cc_final: 0.7965 (tppt)
REVERT: E  348 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.8026 (t70)
  outliers start: 12
  outliers final: 9
  residues processed: 48
  average time/residue: 0.1266
  time to fit residues: 6.8166
Evaluate side-chains
  56 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
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 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  318 VAL
Chi-restraints excluded: chain D residue  324 SER
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  348 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 35
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0060
   chunk 26 optimal weight:    0.6980
   chunk 13 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   chunk 30 optimal weight:    8.9990
   chunk 24 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9980
   overall best weight:    2.5400

-------------------------------------------------------------------------------
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 = 0.4587 r_free = 0.4587 target = 0.155443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.125720 restraints weight = 3508.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.4293 rms_B_bonded: 2.63
r_work: 0.4202 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.4100 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.4100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.4655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2915  Z= 0.150
  Angle     :  0.614   8.485   3900  Z= 0.302
  Chirality :  0.048   0.121    440
  Planarity :  0.004   0.053    495
  Dihedral  :  4.472  15.909    385
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 22.42 %
    Favored  : 74.24 %
  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: -2.47 (0.38), residues: 365
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.87 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 379 
 TYR   0.013   0.003   TYR A 310 
 PHE   0.005   0.001   PHE D 346 
 HIS   0.006   0.002   HIS B 330 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 2915)
  covalent geometry    : angle       0.61433 ( 3900)
  hydrogen bonds       : bond        0.01485 (   40)
  hydrogen bonds       : angle       4.29089 (  120)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1043.91 seconds
wall clock time: 18 minutes 44.53 seconds (1124.53 seconds total)