Starting phenix.real_space_refine
on Mon Sep 23 15:36:35 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrf_0260/09_2024/6hrf_0260.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrf_0260/09_2024/6hrf_0260.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrf_0260/09_2024/6hrf_0260.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrf_0260/09_2024/6hrf_0260.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrf_0260/09_2024/6hrf_0260.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrf_0260/09_2024/6hrf_0260.cif"
  }
  resolution = 3.3
  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=   0.002 sd=   0.008
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       6      5.16       5
     C    2202      2.51       5
     N     648      2.21       5
     O     666      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 3522
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 587
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 3, 'TRANS': 73}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 2.26, per 1000 atoms: 0.64
  Number of scatterers: 3522
  At special positions: 0
  Unit cell: (115.44, 118.56, 37.44, 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       6     16.00
     O     666      8.00
     N     648      7.00
     C    2202      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: 0.76
  Conformation dependent library (CDL) restraints added in 432.1 milliseconds
  

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  804

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 18 sheets defined
      0.0% alpha, 31.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 310
    Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314
      removed outlier: 6.632A  pdb=" N   VAL A 313 " --> pdb=" O   ASP C 314 " (cutoff:3.500A)
      removed outlier: 6.654A  pdb=" N   VAL C 313 " --> pdb=" O   ASP E 314 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 322
      removed outlier: 7.197A  pdb=" N   THR A 319 " --> pdb=" O   SER C 320 " (cutoff:3.500A)
      removed outlier: 8.139A  pdb=" N   CYS C 322 " --> pdb=" O   THR A 319 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LYS A 321 " --> pdb=" O   CYS C 322 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   THR C 319 " --> pdb=" O   SER E 320 " (cutoff:3.500A)
      removed outlier: 8.149A  pdb=" N   CYS E 322 " --> pdb=" O   THR C 319 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   LYS C 321 " --> pdb=" O   CYS E 322 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 330
      removed outlier: 6.810A  pdb=" N   HIS A 329 " --> pdb=" O   HIS C 330 " (cutoff:3.500A)
      removed outlier: 6.858A  pdb=" N   HIS C 329 " --> pdb=" O   HIS E 330 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 339 through 341
    Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 353
      removed outlier: 6.691A  pdb=" N   GLN A 351 " --> pdb=" O   SER C 352 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   GLN C 351 " --> pdb=" O   SER E 352 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 359
      removed outlier: 7.330A  pdb=" N   SER A 356 " --> pdb=" O   LEU C 357 " (cutoff:3.500A)
      removed outlier: 8.223A  pdb=" N   ASN C 359 " --> pdb=" O   SER A 356 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   ASP A 358 " --> pdb=" O   ASN C 359 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   SER C 356 " --> pdb=" O   LEU E 357 " (cutoff:3.500A)
      removed outlier: 8.137A  pdb=" N   ASN E 359 " --> pdb=" O   SER C 356 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   ASP C 358 " --> pdb=" O   ASN E 359 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 371
    Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 378
      removed outlier: 6.549A  pdb=" N   LYS A 375 " --> pdb=" O   LEU C 376 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   PHE C 378 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.424A  pdb=" N   THR A 377 " --> pdb=" O   PHE C 378 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   LYS C 375 " --> pdb=" O   LEU E 376 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   PHE E 378 " --> pdb=" O   LYS C 375 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   THR C 377 " --> pdb=" O   PHE E 378 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 305 through 310
    Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314
      removed outlier: 6.558A  pdb=" N   VAL B 313 " --> pdb=" O   ASP D 314 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   VAL D 313 " --> pdb=" O   ASP F 314 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'B' and resid 318 through 322
      removed outlier: 7.138A  pdb=" N   THR B 319 " --> pdb=" O   SER D 320 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   CYS D 322 " --> pdb=" O   THR B 319 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   LYS B 321 " --> pdb=" O   CYS D 322 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   THR D 319 " --> pdb=" O   SER F 320 " (cutoff:3.500A)
      removed outlier: 8.095A  pdb=" N   CYS F 322 " --> pdb=" O   THR D 319 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   LYS D 321 " --> pdb=" O   CYS F 322 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 329 through 330
      removed outlier: 6.873A  pdb=" N   HIS B 329 " --> pdb=" O   HIS D 330 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   HIS D 329 " --> pdb=" O   HIS F 330 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 339 through 341
      removed outlier: 3.550A  pdb=" N   LYS B 340 " --> pdb=" O   VAL D 339 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   SER D 341 " --> pdb=" O   LYS B 340 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   SER F 341 " --> pdb=" O   LYS D 340 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 351 through 353
      removed outlier: 6.764A  pdb=" N   GLN B 351 " --> pdb=" O   SER D 352 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   GLN D 351 " --> pdb=" O   SER F 352 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'B' and resid 356 through 359
      removed outlier: 7.381A  pdb=" N   SER B 356 " --> pdb=" O   LEU D 357 " (cutoff:3.500A)
      removed outlier: 8.257A  pdb=" N   ASN D 359 " --> pdb=" O   SER B 356 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   ASP B 358 " --> pdb=" O   ASN D 359 " (cutoff:3.500A)
      removed outlier: 7.292A  pdb=" N   SER D 356 " --> pdb=" O   LEU F 357 " (cutoff:3.500A)
      removed outlier: 8.169A  pdb=" N   ASN F 359 " --> pdb=" O   SER D 356 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   ASP D 358 " --> pdb=" O   ASN F 359 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'B' and resid 369 through 371
    Processing sheet with id=AB9, first strand: chain 'B' and resid 374 through 378
      removed outlier: 6.610A  pdb=" N   LYS B 375 " --> pdb=" O   LEU D 376 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   PHE D 378 " --> pdb=" O   LYS B 375 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   THR B 377 " --> pdb=" O   PHE D 378 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   LYS D 375 " --> pdb=" O   LEU F 376 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   PHE F 378 " --> pdb=" O   LYS D 375 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   THR D 377 " --> pdb=" O   PHE F 378 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9

    33 hydrogen bonds defined for protein.
    99 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: 0.77

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 630
        1.32 -     1.44: 788
        1.44 -     1.55: 2027
        1.55 -     1.67: 125
        1.67 -     1.79: 6
  Bond restraints: 3576
  Sorted by residual:
  bond pdb=" C   LYS E 311 "
       pdb=" N   PRO E 312 "
    ideal  model  delta    sigma   weight residual
    1.333  1.386 -0.053 1.17e-02 7.31e+03 2.07e+01
  bond pdb=" C   LYS B 311 "
       pdb=" N   PRO B 312 "
    ideal  model  delta    sigma   weight residual
    1.333  1.386 -0.053 1.17e-02 7.31e+03 2.04e+01
  bond pdb=" C   LYS C 311 "
       pdb=" N   PRO C 312 "
    ideal  model  delta    sigma   weight residual
    1.333  1.385 -0.053 1.17e-02 7.31e+03 2.03e+01
  bond pdb=" N   ARG B 349 "
       pdb=" CA  ARG B 349 "
    ideal  model  delta    sigma   weight residual
    1.457  1.529 -0.071 1.58e-02 4.01e+03 2.03e+01
  bond pdb=" C   LYS A 311 "
       pdb=" N   PRO A 312 "
    ideal  model  delta    sigma   weight residual
    1.333  1.385 -0.053 1.17e-02 7.31e+03 2.02e+01
  ... (remaining 3571 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 4011
        1.38 -     2.76: 519
        2.76 -     4.14: 163
        4.14 -     5.51: 71
        5.51 -     6.89: 18
  Bond angle restraints: 4782
  Sorted by residual:
  angle pdb=" N   SER F 352 "
        pdb=" CA  SER F 352 "
        pdb=" C   SER F 352 "
      ideal   model   delta    sigma   weight residual
     108.99  114.69   -5.70 1.57e+00 4.06e-01 1.32e+01
  angle pdb=" N   SER A 352 "
        pdb=" CA  SER A 352 "
        pdb=" C   SER A 352 "
      ideal   model   delta    sigma   weight residual
     108.99  114.69   -5.70 1.57e+00 4.06e-01 1.32e+01
  angle pdb=" N   SER E 352 "
        pdb=" CA  SER E 352 "
        pdb=" C   SER E 352 "
      ideal   model   delta    sigma   weight residual
     108.99  114.69   -5.70 1.57e+00 4.06e-01 1.32e+01
  angle pdb=" N   SER C 352 "
        pdb=" CA  SER C 352 "
        pdb=" C   SER C 352 "
      ideal   model   delta    sigma   weight residual
     108.99  114.69   -5.70 1.57e+00 4.06e-01 1.32e+01
  angle pdb=" N   SER D 352 "
        pdb=" CA  SER D 352 "
        pdb=" C   SER D 352 "
      ideal   model   delta    sigma   weight residual
     108.99  114.68   -5.69 1.57e+00 4.06e-01 1.31e+01
  ... (remaining 4777 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.36: 1896
       13.36 -    26.71: 174
       26.71 -    40.06: 72
       40.06 -    53.41: 24
       53.41 -    66.76: 12
  Dihedral angle restraints: 2178
    sinusoidal: 912
      harmonic: 1266
  Sorted by residual:
  dihedral pdb=" CB  LYS B 353 "
           pdb=" CG  LYS B 353 "
           pdb=" CD  LYS B 353 "
           pdb=" CE  LYS B 353 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -101.76   41.76     3      1.50e+01 4.44e-03 7.48e+00
  dihedral pdb=" CB  LYS A 353 "
           pdb=" CG  LYS A 353 "
           pdb=" CD  LYS A 353 "
           pdb=" CE  LYS A 353 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -101.73   41.73     3      1.50e+01 4.44e-03 7.47e+00
  dihedral pdb=" CB  LYS D 353 "
           pdb=" CG  LYS D 353 "
           pdb=" CD  LYS D 353 "
           pdb=" CE  LYS D 353 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -101.72   41.72     3      1.50e+01 4.44e-03 7.47e+00
  ... (remaining 2175 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 227
       0.050 -    0.099: 142
       0.099 -    0.149: 81
       0.149 -    0.198: 72
       0.198 -    0.248: 12
  Chirality restraints: 534
  Sorted by residual:
  chirality pdb=" CA  ILE D 328 "
            pdb=" N   ILE D 328 "
            pdb=" C   ILE D 328 "
            pdb=" CB  ILE D 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.68   -0.25 2.00e-01 2.50e+01 1.54e+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    2.68   -0.25 2.00e-01 2.50e+01 1.54e+00
  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    2.68   -0.25 2.00e-01 2.50e+01 1.53e+00
  ... (remaining 531 not shown)

  Planarity restraints: 612
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN E 368 "    0.013 2.00e-02 2.50e+03   2.55e-02 6.53e+00
        pdb=" C   ASN E 368 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   ASN E 368 "    0.017 2.00e-02 2.50e+03
        pdb=" N   LYS E 369 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 368 "    0.013 2.00e-02 2.50e+03   2.55e-02 6.53e+00
        pdb=" C   ASN A 368 "   -0.044 2.00e-02 2.50e+03
        pdb=" O   ASN A 368 "    0.017 2.00e-02 2.50e+03
        pdb=" N   LYS A 369 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 368 "   -0.013 2.00e-02 2.50e+03   2.55e-02 6.53e+00
        pdb=" C   ASN B 368 "    0.044 2.00e-02 2.50e+03
        pdb=" O   ASN B 368 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LYS B 369 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 609 not shown)

  Histogram of nonbonded interaction distances:
        2.63 -     3.08: 2011
        3.08 -     3.54: 3350
        3.54 -     3.99: 5016
        3.99 -     4.45: 4850
        4.45 -     4.90: 9434
  Nonbonded interactions: 24661
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 316 "
            pdb=" NZ  LYS B 370 "
     model   vdw
     2.627 3.120
  nonbonded pdb=" OG  SER D 316 "
            pdb=" NZ  LYS D 370 "
     model   vdw
     2.628 3.120
  nonbonded pdb=" OG  SER A 316 "
            pdb=" NZ  LYS A 370 "
     model   vdw
     2.628 3.120
  nonbonded pdb=" OG  SER C 316 "
            pdb=" NZ  LYS C 370 "
     model   vdw
     2.628 3.120
  nonbonded pdb=" OG  SER E 316 "
            pdb=" NZ  LYS E 370 "
     model   vdw
     2.628 3.120
  ... (remaining 24656 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             1.510
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.780
  Find NCS groups from input model:        0.130
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
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      :  0.016   0.071   3576  Z= 1.101
  Angle     :  1.247   6.892   4782  Z= 0.750
  Chirality :  0.093   0.248    534
  Planarity :  0.010   0.038    612
  Dihedral  : 13.679  66.761   1374
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.33 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  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: -4.08 (0.28), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.21), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS E 362 
 PHE   0.027   0.008   PHE C 346 
 TYR   0.033   0.014   TYR C 310 
 ARG   0.010   0.003   ARG B 349 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.413 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8535 (mtmt) cc_final: 0.7769 (mmmt)
REVERT: A  317 LYS cc_start: 0.8622 (ptpt) cc_final: 0.8154 (ptpp)
REVERT: A  349 ARG cc_start: 0.7460 (mtt-85) cc_final: 0.7108 (mtm180)
REVERT: A  353 LYS cc_start: 0.7858 (ttmt) cc_final: 0.7648 (tttm)
REVERT: B  311 LYS cc_start: 0.9014 (mtmt) cc_final: 0.8307 (mmmt)
REVERT: C  317 LYS cc_start: 0.7974 (ptpt) cc_final: 0.7508 (ptpp)
REVERT: C  343 LYS cc_start: 0.8134 (mttp) cc_final: 0.7818 (ttmm)
REVERT: C  349 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7740 (mtm-85)
REVERT: D  327 ASN cc_start: 0.7756 (p0) cc_final: 0.7370 (p0)
REVERT: E  317 LYS cc_start: 0.8162 (ptpt) cc_final: 0.7763 (ptpp)
REVERT: E  349 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7920 (mtm180)
REVERT: E  361 THR cc_start: 0.9083 (m) cc_final: 0.8877 (t)
REVERT: E  379 ARG cc_start: 0.7195 (mtt180) cc_final: 0.6404 (ptt-90)
REVERT: F  310 TYR cc_start: 0.8833 (t80) cc_final: 0.8616 (t80)
REVERT: F  311 LYS cc_start: 0.8914 (mtmt) cc_final: 0.8439 (mtpt)
REVERT: F  327 ASN cc_start: 0.8104 (p0) cc_final: 0.7629 (p0)
REVERT: F  379 ARG cc_start: 0.6578 (mtt180) cc_final: 0.5019 (mtm110)
  outliers start: 0
  outliers final: 0
  residues processed: 147
  average time/residue: 0.3149
  time to fit residues: 50.9713
Evaluate side-chains
  87 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 21 optimal weight:    7.9990
   chunk 32 optimal weight:    5.9990
   chunk 12 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN
C 329 HIS
C 336 GLN
** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 336 GLN
F 362 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.4518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3576  Z= 0.357
  Angle     :  0.688   6.420   4782  Z= 0.352
  Chirality :  0.050   0.147    534
  Planarity :  0.004   0.029    612
  Dihedral  :  5.354  13.725    474
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 12.44 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.78 (0.29), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.87 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.013   0.002   HIS C 330 
 PHE   0.010   0.002   PHE B 378 
 TYR   0.015   0.002   TYR D 310 
 ARG   0.006   0.001   ARG C 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8231 (mmtm)
REVERT: A  317 LYS cc_start: 0.8718 (ptpt) cc_final: 0.8194 (ptpp)
REVERT: A  338 GLU cc_start: 0.7413 (mp0) cc_final: 0.6980 (tm-30)
REVERT: A  349 ARG cc_start: 0.8195 (mtt-85) cc_final: 0.7652 (mtm180)
REVERT: A  353 LYS cc_start: 0.8047 (ttmt) cc_final: 0.7540 (tppt)
REVERT: B  311 LYS cc_start: 0.9131 (mtmt) cc_final: 0.8413 (mmtt)
REVERT: B  336 GLN cc_start: 0.8040 (pp30) cc_final: 0.7772 (pp30)
REVERT: C  338 GLU cc_start: 0.8042 (mp0) cc_final: 0.7232 (tm-30)
REVERT: C  349 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7451 (mtm-85)
REVERT: D  327 ASN cc_start: 0.8065 (p0) cc_final: 0.7655 (p0)
REVERT: E  342 GLU cc_start: 0.2774 (pm20) cc_final: 0.2270 (pm20)
REVERT: E  343 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7229 (mtmm)
REVERT: E  349 ARG cc_start: 0.8096 (mtt-85) cc_final: 0.7829 (mtm180)
REVERT: E  379 ARG cc_start: 0.7425 (mtt180) cc_final: 0.6662 (ptt-90)
REVERT: F  311 LYS cc_start: 0.9009 (mtmt) cc_final: 0.8673 (mtpt)
REVERT: F  327 ASN cc_start: 0.8210 (p0) cc_final: 0.7877 (p0)
REVERT: F  379 ARG cc_start: 0.6740 (mtt180) cc_final: 0.5850 (mtm180)
  outliers start: 7
  outliers final: 6
  residues processed: 110
  average time/residue: 0.2468
  time to fit residues: 30.6794
Evaluate side-chains
  104 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain D residue  377 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain E residue  350 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 25 optimal weight:   20.0000
   chunk 10 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   chunk 41 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0770
   chunk 30 optimal weight:    5.9990
   chunk 28 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   overall best weight:    3.2146

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

Flipped N/Q/H residues before XYZ refinement:
** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN
** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 368 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.5319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3576  Z= 0.287
  Angle     :  0.653   6.199   4782  Z= 0.320
  Chirality :  0.048   0.132    534
  Planarity :  0.003   0.024    612
  Dihedral  :  4.911  14.663    474
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 15.92 %
    Favored  : 81.34 %
  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: -3.65 (0.30), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.23), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS E 330 
 PHE   0.010   0.002   PHE F 346 
 TYR   0.022   0.003   TYR A 310 
 ARG   0.006   0.001   ARG C 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8807 (mtmt) cc_final: 0.8227 (mmtm)
REVERT: A  317 LYS cc_start: 0.8707 (ptpt) cc_final: 0.8186 (ptpp)
REVERT: A  349 ARG cc_start: 0.8172 (mtt-85) cc_final: 0.7826 (mtm180)
REVERT: B  311 LYS cc_start: 0.9079 (mtmt) cc_final: 0.8355 (mmtt)
REVERT: C  336 GLN cc_start: 0.8447 (mp10) cc_final: 0.8170 (mp10)
REVERT: C  338 GLU cc_start: 0.8033 (mp0) cc_final: 0.7287 (tm-30)
REVERT: C  349 ARG cc_start: 0.7931 (mtt-85) cc_final: 0.7453 (mtm-85)
REVERT: D  327 ASN cc_start: 0.8086 (p0) cc_final: 0.7761 (p0)
REVERT: E  342 GLU cc_start: 0.2538 (pm20) cc_final: 0.1982 (pm20)
REVERT: E  343 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7175 (mtmm)
REVERT: E  349 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7757 (mtm180)
REVERT: E  379 ARG cc_start: 0.7442 (mtt180) cc_final: 0.6584 (ptt-90)
REVERT: F  311 LYS cc_start: 0.8985 (mtmt) cc_final: 0.8680 (mtpt)
REVERT: F  316 SER cc_start: 0.9328 (p) cc_final: 0.9048 (p)
REVERT: F  327 ASN cc_start: 0.8178 (p0) cc_final: 0.7947 (p0)
REVERT: F  379 ARG cc_start: 0.6984 (mtt180) cc_final: 0.5926 (mtm180)
  outliers start: 11
  outliers final: 8
  residues processed: 112
  average time/residue: 0.2467
  time to fit residues: 31.2930
Evaluate side-chains
  111 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  311 LYS
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  343 LYS
Chi-restraints excluded: chain E residue  350 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 18 optimal weight:    7.9990
   chunk 25 optimal weight:   20.0000
   chunk 38 optimal weight:    0.1980
   chunk 40 optimal weight:    0.4980
   chunk 20 optimal weight:    7.9990
   chunk 36 optimal weight:    0.0770
   chunk 10 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.9542

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

Flipped N/Q/H residues before XYZ refinement:
** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN
D 307 GLN
** D 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 336 GLN
F 368 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.5675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3576  Z= 0.267
  Angle     :  0.657   8.544   4782  Z= 0.312
  Chirality :  0.047   0.134    534
  Planarity :  0.003   0.024    612
  Dihedral  :  4.690  14.546    474
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 18.16 %
    Favored  : 79.60 %
  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: -3.59 (0.29), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.73 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E 330 
 PHE   0.011   0.002   PHE F 346 
 TYR   0.018   0.002   TYR A 310 
 ARG   0.006   0.000   ARG C 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8188 (mmtm)
REVERT: A  317 LYS cc_start: 0.8705 (ptpt) cc_final: 0.8173 (ptpp)
REVERT: A  349 ARG cc_start: 0.8157 (mtt-85) cc_final: 0.7524 (mtm180)
REVERT: A  368 ASN cc_start: 0.8806 (m-40) cc_final: 0.8577 (m110)
REVERT: B  311 LYS cc_start: 0.9066 (mtmt) cc_final: 0.8331 (mmtt)
REVERT: C  338 GLU cc_start: 0.8113 (mp0) cc_final: 0.7267 (tm-30)
REVERT: C  349 ARG cc_start: 0.7900 (mtt-85) cc_final: 0.7408 (mtm-85)
REVERT: D  327 ASN cc_start: 0.8183 (p0) cc_final: 0.7721 (p0)
REVERT: E  349 ARG cc_start: 0.8097 (mtt-85) cc_final: 0.7769 (mtm180)
REVERT: E  379 ARG cc_start: 0.7551 (mtt180) cc_final: 0.6482 (ptt-90)
REVERT: F  311 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8665 (mtpt)
REVERT: F  316 SER cc_start: 0.9347 (p) cc_final: 0.9059 (p)
REVERT: F  338 GLU cc_start: 0.8124 (mp0) cc_final: 0.7697 (pm20)
REVERT: F  379 ARG cc_start: 0.7076 (mtt180) cc_final: 0.5996 (mtm180)
  outliers start: 9
  outliers final: 7
  residues processed: 112
  average time/residue: 0.2349
  time to fit residues: 29.9916
Evaluate side-chains
  106 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  350 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 23 optimal weight:    9.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 329 HIS
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 307 GLN
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 327 ASN
F 368 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.6370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   3576  Z= 0.378
  Angle     :  0.724   6.995   4782  Z= 0.353
  Chirality :  0.049   0.137    534
  Planarity :  0.004   0.024    612
  Dihedral  :  5.164  15.444    474
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 18.91 %
    Favored  : 77.61 %
  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: -3.66 (0.29), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.78 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS C 330 
 PHE   0.017   0.002   PHE B 378 
 TYR   0.018   0.003   TYR A 310 
 ARG   0.005   0.001   ARG C 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.410 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8864 (mtmt) cc_final: 0.8227 (mmtm)
REVERT: A  317 LYS cc_start: 0.8753 (ptpt) cc_final: 0.8227 (ptpp)
REVERT: A  338 GLU cc_start: 0.7552 (mp0) cc_final: 0.7314 (mp0)
REVERT: A  349 ARG cc_start: 0.8034 (mtt-85) cc_final: 0.7327 (mtm180)
REVERT: B  311 LYS cc_start: 0.9052 (mtmt) cc_final: 0.8334 (mmtt)
REVERT: C  336 GLN cc_start: 0.8544 (mp10) cc_final: 0.8197 (mp10)
REVERT: C  338 GLU cc_start: 0.8036 (mp0) cc_final: 0.7336 (tm-30)
REVERT: C  349 ARG cc_start: 0.7779 (mtt-85) cc_final: 0.7254 (mtm-85)
REVERT: D  327 ASN cc_start: 0.8222 (p0) cc_final: 0.7792 (p0)
REVERT: E  342 GLU cc_start: 0.2469 (OUTLIER) cc_final: 0.1847 (pm20)
REVERT: E  349 ARG cc_start: 0.8099 (mtt-85) cc_final: 0.7749 (mtm180)
REVERT: E  379 ARG cc_start: 0.7608 (mtt180) cc_final: 0.6543 (ptt-90)
REVERT: F  327 ASN cc_start: 0.7787 (OUTLIER) cc_final: 0.7439 (p0)
REVERT: F  338 GLU cc_start: 0.8381 (mp0) cc_final: 0.8099 (pm20)
REVERT: F  380 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6523 (mp0)
  outliers start: 14
  outliers final: 10
  residues processed: 109
  average time/residue: 0.2047
  time to fit residues: 25.8753
Evaluate side-chains
  110 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  342 GLU
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain F residue  327 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 40 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 3 optimal weight:    9.9990
   chunk 13 optimal weight:    0.1980
   chunk 21 optimal weight:    3.9990
   chunk 39 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 23 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    4.0388

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

Flipped N/Q/H residues before XYZ refinement:
** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.6666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3576  Z= 0.336
  Angle     :  0.685   7.156   4782  Z= 0.331
  Chirality :  0.048   0.135    534
  Planarity :  0.003   0.025    612
  Dihedral  :  4.882  15.259    474
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 20.15 %
    Favored  : 76.37 %
  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: -3.65 (0.28), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.77 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 374 
 PHE   0.013   0.002   PHE B 378 
 TYR   0.016   0.002   TYR A 310 
 ARG   0.005   0.001   ARG C 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.439 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8224 (mmtm)
REVERT: A  317 LYS cc_start: 0.8737 (ptpt) cc_final: 0.8217 (ptpp)
REVERT: A  349 ARG cc_start: 0.7946 (mtt-85) cc_final: 0.7304 (mtm180)
REVERT: B  311 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8301 (mmtm)
REVERT: C  338 GLU cc_start: 0.8007 (mp0) cc_final: 0.7334 (tm-30)
REVERT: C  349 ARG cc_start: 0.7827 (mtt-85) cc_final: 0.7304 (mtm-85)
REVERT: D  327 ASN cc_start: 0.8200 (p0) cc_final: 0.7838 (p0)
REVERT: D  336 GLN cc_start: 0.8552 (mp-120) cc_final: 0.8342 (mp10)
REVERT: E  349 ARG cc_start: 0.8053 (mtt-85) cc_final: 0.7736 (mtm180)
REVERT: F  311 LYS cc_start: 0.9002 (mtmt) cc_final: 0.8675 (mtpt)
REVERT: F  327 ASN cc_start: 0.7808 (p0) cc_final: 0.7467 (p0)
  outliers start: 14
  outliers final: 11
  residues processed: 108
  average time/residue: 0.2062
  time to fit residues: 25.7493
Evaluate side-chains
  108 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  319 THR
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  350 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 25 optimal weight:   20.0000
   chunk 24 optimal weight:    7.9990
   chunk 18 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9990
   chunk 12 optimal weight:   10.0000
   chunk 7 optimal weight:    8.9990
   chunk 27 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 327 ASN
** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.6857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3576  Z= 0.238
  Angle     :  0.675   7.755   4782  Z= 0.322
  Chirality :  0.047   0.162    534
  Planarity :  0.003   0.024    612
  Dihedral  :  4.444  14.776    474
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 22.89 %
    Favored  : 74.63 %
  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: -3.56 (0.29), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.000   HIS B 374 
 PHE   0.009   0.001   PHE F 346 
 TYR   0.013   0.002   TYR D 310 
 ARG   0.004   0.000   ARG C 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
REVERT: A  311 LYS cc_start: 0.8844 (mtmt) cc_final: 0.8191 (mmtm)
REVERT: A  317 LYS cc_start: 0.8733 (ptpt) cc_final: 0.8209 (ptpp)
REVERT: A  349 ARG cc_start: 0.7999 (mtt-85) cc_final: 0.7382 (mtm180)
REVERT: B  311 LYS cc_start: 0.9014 (mtmt) cc_final: 0.8275 (mmtt)
REVERT: C  336 GLN cc_start: 0.8565 (mp10) cc_final: 0.8237 (mp10)
REVERT: C  338 GLU cc_start: 0.8026 (mp0) cc_final: 0.7300 (tm-30)
REVERT: C  349 ARG cc_start: 0.7776 (mtt-85) cc_final: 0.7268 (mtm-85)
REVERT: D  327 ASN cc_start: 0.8262 (p0) cc_final: 0.7900 (p0)
REVERT: D  349 ARG cc_start: 0.6068 (tpm170) cc_final: 0.5669 (ttp-110)
REVERT: E  349 ARG cc_start: 0.8097 (mtt-85) cc_final: 0.7760 (mtm180)
REVERT: F  316 SER cc_start: 0.9435 (p) cc_final: 0.9144 (p)
REVERT: F  349 ARG cc_start: 0.2565 (ppt170) cc_final: 0.2282 (ppt170)
  outliers start: 10
  outliers final: 8
  residues processed: 107
  average time/residue: 0.2101
  time to fit residues: 26.2585
Evaluate side-chains
  107 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  350 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0570
   chunk 34 optimal weight:    7.9990
   overall best weight:    1.7304

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

Flipped N/Q/H residues before XYZ refinement:
** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.6937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3576  Z= 0.231
  Angle     :  0.678   8.117   4782  Z= 0.323
  Chirality :  0.047   0.172    534
  Planarity :  0.003   0.024    612
  Dihedral  :  4.201  14.079    474
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 22.39 %
    Favored  : 74.63 %
  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: -3.48 (0.29), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.64 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 329 
 PHE   0.007   0.001   PHE D 378 
 TYR   0.016   0.003   TYR F 310 
 ARG   0.004   0.001   ARG C 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.444 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8169 (mmtm)
REVERT: A  317 LYS cc_start: 0.8744 (ptpt) cc_final: 0.8229 (ptpp)
REVERT: A  349 ARG cc_start: 0.7998 (mtt-85) cc_final: 0.7426 (mtm180)
REVERT: A  353 LYS cc_start: 0.8334 (ttpt) cc_final: 0.8121 (ttpt)
REVERT: B  311 LYS cc_start: 0.9011 (mtmt) cc_final: 0.8272 (mmtt)
REVERT: B  337 VAL cc_start: 0.8533 (t) cc_final: 0.8101 (t)
REVERT: C  336 GLN cc_start: 0.8521 (mp10) cc_final: 0.8285 (mp10)
REVERT: C  338 GLU cc_start: 0.8038 (mp0) cc_final: 0.7244 (tm-30)
REVERT: C  349 ARG cc_start: 0.7795 (mtt-85) cc_final: 0.7306 (mtm-85)
REVERT: D  327 ASN cc_start: 0.8292 (p0) cc_final: 0.7976 (p0)
REVERT: D  349 ARG cc_start: 0.5499 (tpm170) cc_final: 0.5156 (ttp-110)
REVERT: D  372 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7750 (mp0)
REVERT: E  349 ARG cc_start: 0.8077 (mtt-85) cc_final: 0.7757 (mtm180)
REVERT: F  316 SER cc_start: 0.9363 (p) cc_final: 0.9066 (p)
  outliers start: 12
  outliers final: 10
  residues processed: 105
  average time/residue: 0.1917
  time to fit residues: 23.5899
Evaluate side-chains
  106 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  350 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.4980
   chunk 37 optimal weight:    0.1980
   chunk 24 optimal weight:   30.0000
   chunk 39 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 38 optimal weight:    7.9990
   chunk 33 optimal weight:    9.9990
   chunk 3 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.7008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   3576  Z= 0.236
  Angle     :  0.709   9.174   4782  Z= 0.338
  Chirality :  0.047   0.176    534
  Planarity :  0.003   0.026    612
  Dihedral  :  4.113  13.892    474
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 23.13 %
    Favored  : 74.13 %
  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: -3.39 (0.30), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.57 (0.23), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 329 
 PHE   0.008   0.001   PHE F 346 
 TYR   0.017   0.003   TYR F 310 
 ARG   0.004   0.000   ARG C 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.402 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8820 (mtmt) cc_final: 0.8110 (mmtm)
REVERT: A  317 LYS cc_start: 0.8694 (ptpt) cc_final: 0.8201 (ptpp)
REVERT: A  349 ARG cc_start: 0.7976 (mtt-85) cc_final: 0.7399 (mtm180)
REVERT: A  353 LYS cc_start: 0.8410 (ttpt) cc_final: 0.8183 (ttpt)
REVERT: B  311 LYS cc_start: 0.9008 (mtmt) cc_final: 0.8318 (mmtt)
REVERT: C  336 GLN cc_start: 0.8582 (mp10) cc_final: 0.8269 (mp10)
REVERT: C  338 GLU cc_start: 0.7996 (mp0) cc_final: 0.7205 (tm-30)
REVERT: C  349 ARG cc_start: 0.7745 (mtt-85) cc_final: 0.7281 (mtm-85)
REVERT: D  327 ASN cc_start: 0.8278 (p0) cc_final: 0.7962 (p0)
REVERT: D  336 GLN cc_start: 0.8351 (mp-120) cc_final: 0.8115 (mp10)
REVERT: D  349 ARG cc_start: 0.5538 (tpm170) cc_final: 0.5298 (ttp-110)
REVERT: D  372 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7743 (mp0)
REVERT: E  349 ARG cc_start: 0.8056 (mtt-85) cc_final: 0.7779 (mtm180)
REVERT: F  316 SER cc_start: 0.9356 (p) cc_final: 0.9050 (p)
  outliers start: 11
  outliers final: 11
  residues processed: 98
  average time/residue: 0.1934
  time to fit residues: 22.2022
Evaluate side-chains
  104 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  327 ASN
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  351 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 26 optimal weight:   20.0000
   chunk 35 optimal weight:    0.6980
   chunk 10 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   chunk 34 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    3.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.7275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   3576  Z= 0.352
  Angle     :  0.746   8.635   4782  Z= 0.362
  Chirality :  0.048   0.180    534
  Planarity :  0.003   0.027    612
  Dihedral  :  4.634  14.807    474
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 23.38 %
    Favored  : 74.13 %
  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: -3.54 (0.29), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.22), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F 329 
 PHE   0.013   0.002   PHE B 378 
 TYR   0.015   0.003   TYR A 310 
 ARG   0.004   0.001   ARG C 379 

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.440 
Fit side-chains
REVERT: A  311 LYS cc_start: 0.8865 (mtmt) cc_final: 0.8215 (mmtm)
REVERT: A  317 LYS cc_start: 0.8708 (ptpt) cc_final: 0.8223 (ptpp)
REVERT: A  349 ARG cc_start: 0.7964 (mtt-85) cc_final: 0.7346 (mtm180)
REVERT: B  311 LYS cc_start: 0.8998 (mtmt) cc_final: 0.8253 (mmtm)
REVERT: C  336 GLN cc_start: 0.8594 (mp10) cc_final: 0.8247 (mp10)
REVERT: C  338 GLU cc_start: 0.7922 (mp0) cc_final: 0.7237 (tm-30)
REVERT: C  349 ARG cc_start: 0.7781 (mtt-85) cc_final: 0.7281 (mtm-85)
REVERT: D  327 ASN cc_start: 0.8300 (p0) cc_final: 0.7932 (p0)
REVERT: D  349 ARG cc_start: 0.5612 (tpm170) cc_final: 0.5142 (ttp-110)
REVERT: D  380 GLU cc_start: 0.6891 (mp0) cc_final: 0.6534 (mp0)
REVERT: E  349 ARG cc_start: 0.7971 (mtt-85) cc_final: 0.7703 (mtm180)
  outliers start: 10
  outliers final: 9
  residues processed: 104
  average time/residue: 0.1877
  time to fit residues: 22.9782
Evaluate side-chains
  108 residues out of total 402 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.558 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  352 SER
Chi-restraints excluded: chain B residue  368 ASN
Chi-restraints excluded: chain C residue  319 THR
Chi-restraints excluded: chain C residue  373 THR
Chi-restraints excluded: chain D residue  319 THR
Chi-restraints excluded: chain E residue  319 THR
Chi-restraints excluded: chain E residue  350 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 1 optimal weight:    6.9990
   chunk 24 optimal weight:   20.0000
   chunk 38 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 28 optimal weight:    0.0980
   chunk 26 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.140950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.118738 restraints weight = 5414.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3927 rms_B_bonded: 2.93
r_work: 0.3811 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.7264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   3576  Z= 0.236
  Angle     :  0.709   8.402   4782  Z= 0.341
  Chirality :  0.047   0.189    534
  Planarity :  0.003   0.025    612
  Dihedral  :  4.181  14.517    474
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 24.13 %
    Favored  : 73.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.40 (0.30), residues: 450
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.59 (0.23), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.000   HIS F 329 
 PHE   0.008   0.001   PHE D 378 
 TYR   0.017   0.003   TYR F 310 
 ARG   0.004   0.001   ARG D 379 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1242.19 seconds
wall clock time: 22 minutes 58.09 seconds (1378.09 seconds total)