Starting phenix.real_space_refine
on Fri Aug 22 21:36:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pxb_18002/08_2025/8pxb_18002.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pxb_18002/08_2025/8pxb_18002.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pxb_18002/08_2025/8pxb_18002.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pxb_18002/08_2025/8pxb_18002.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pxb_18002/08_2025/8pxb_18002.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pxb_18002/08_2025/8pxb_18002.map"
  }
  resolution = 3.6
  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=   0.004 sd=   0.051
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      50      5.16       5
     C    5388      2.51       5
     N    1280      2.21       5
     O    1384      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  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: 8102
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 4051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 509, 4051
          Classifications: {'peptide': 509}
          Link IDs: {'PTRANS': 18, 'TRANS': 490}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 509, 4051
          Classifications: {'peptide': 509}
          Link IDs: {'PTRANS': 18, 'TRANS': 490}
          Chain breaks: 1
  Time building chain proxies: 2.25, per 1000 atoms: 0.28
  Number of scatterers: 8102
  At special positions: 0
  Unit cell: (80.925, 106.862, 88.1875, 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      50     16.00
     O    1384      8.00
     N    1280      7.00
     C    5388      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: 0.72
  Conformation dependent library (CDL) restraints added in 499.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1892

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 1 sheets defined
      72.5% alpha, 2.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'B' and resid 19 through 45
      removed outlier: 4.045A  pdb=" N   GLU B  23 " --> pdb=" O   GLN B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 68
      removed outlier: 3.591A  pdb=" N   TYR B  68 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 121
    Processing helix  chain 'B' and resid 132 through 137
    Processing helix  chain 'B' and resid 138 through 149
      removed outlier: 3.729A  pdb=" N   ILE B 142 " --> pdb=" O   LEU B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 192
      removed outlier: 4.380A  pdb=" N   THR B 170 " --> pdb=" O   ALA B 166 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ALA B 171 " --> pdb=" O   PHE B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 211
    Processing helix  chain 'B' and resid 216 through 227
    Processing helix  chain 'B' and resid 229 through 257
      removed outlier: 3.558A  pdb=" N   TYR B 233 " --> pdb=" O   ASP B 229 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ASP B 244 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ALA B 245 " --> pdb=" O   VAL B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 303
    Processing helix  chain 'B' and resid 304 through 307
      removed outlier: 3.824A  pdb=" N   GLU B 307 " --> pdb=" O   LYS B 304 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 304 through 307'
    Processing helix  chain 'B' and resid 308 through 330
    Processing helix  chain 'B' and resid 333 through 349
      removed outlier: 3.594A  pdb=" N   ALA B 337 " --> pdb=" O   THR B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 352
      No H-bonds generated for 'chain 'B' and resid 350 through 352'
    Processing helix  chain 'B' and resid 354 through 381
      removed outlier: 3.711A  pdb=" N   MET B 359 " --> pdb=" O   LEU B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 422
      removed outlier: 3.618A  pdb=" N   ILE B 412 " --> pdb=" O   ARG B 408 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   TYR B 413 " --> pdb=" O   ALA B 409 " (cutoff:3.500A)
      Proline residue:  B 414  - end of helix
      removed outlier: 3.807A  pdb=" N   GLY B 422 " --> pdb=" O   LEU B 418 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 438
    Processing helix  chain 'B' and resid 442 through 452
      removed outlier: 3.901A  pdb=" N   PHE B 446 " --> pdb=" O   GLY B 442 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   ASP B 452 " --> pdb=" O   LEU B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 487
      removed outlier: 3.647A  pdb=" N   TRP B 474 " --> pdb=" O   PHE B 470 " (cutoff:3.500A)
      removed outlier: 5.212A  pdb=" N   THR B 481 " --> pdb=" O   GLY B 477 " (cutoff:3.500A)
      Proline residue:  B 482  - end of helix
    Processing helix  chain 'B' and resid 524 through 535
    Processing helix  chain 'B' and resid 535 through 541
      removed outlier: 3.869A  pdb=" N   ILE B 539 " --> pdb=" O   TYR B 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 45
      removed outlier: 3.990A  pdb=" N   GLU A  23 " --> pdb=" O   GLN A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 68
      removed outlier: 3.518A  pdb=" N   TYR A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 121
    Processing helix  chain 'A' and resid 132 through 137
    Processing helix  chain 'A' and resid 138 through 149
      removed outlier: 3.717A  pdb=" N   ILE A 142 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 192
      removed outlier: 4.380A  pdb=" N   THR A 170 " --> pdb=" O   ALA A 166 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA A 171 " --> pdb=" O   PHE A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 211
    Processing helix  chain 'A' and resid 216 through 227
    Processing helix  chain 'A' and resid 229 through 257
      removed outlier: 3.561A  pdb=" N   TYR A 233 " --> pdb=" O   ASP A 229 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ASP A 244 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ALA A 245 " --> pdb=" O   VAL A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 303
    Processing helix  chain 'A' and resid 304 through 307
      removed outlier: 3.761A  pdb=" N   GLU A 307 " --> pdb=" O   LYS A 304 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 304 through 307'
    Processing helix  chain 'A' and resid 308 through 330
    Processing helix  chain 'A' and resid 333 through 349
      removed outlier: 3.628A  pdb=" N   ALA A 337 " --> pdb=" O   THR A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 352
      No H-bonds generated for 'chain 'A' and resid 350 through 352'
    Processing helix  chain 'A' and resid 354 through 381
      removed outlier: 3.706A  pdb=" N   MET A 359 " --> pdb=" O   LEU A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 422
      removed outlier: 3.586A  pdb=" N   ILE A 412 " --> pdb=" O   ARG A 408 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   TYR A 413 " --> pdb=" O   ALA A 409 " (cutoff:3.500A)
      Proline residue:  A 414  - end of helix
      removed outlier: 3.778A  pdb=" N   GLY A 422 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 438
    Processing helix  chain 'A' and resid 442 through 452
      removed outlier: 3.902A  pdb=" N   PHE A 446 " --> pdb=" O   GLY A 442 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ASP A 452 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 487
      removed outlier: 3.645A  pdb=" N   TRP A 474 " --> pdb=" O   PHE A 470 " (cutoff:3.500A)
      removed outlier: 5.214A  pdb=" N   THR A 481 " --> pdb=" O   GLY A 477 " (cutoff:3.500A)
      Proline residue:  A 482  - end of helix
    Processing helix  chain 'A' and resid 524 through 535
    Processing helix  chain 'A' and resid 535 through 541
      removed outlier: 3.874A  pdb=" N   ILE A 539 " --> pdb=" O   TYR A 535 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 97
      removed outlier: 7.373A  pdb=" N   VAL B 101 " --> pdb=" O   GLU A 109 " (cutoff:3.500A)
      removed outlier: 5.291A  pdb=" N   GLU A 109 " --> pdb=" O   VAL B 101 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   GLU B 103 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LYS B 107 " --> pdb=" O   GLU A 103 " (cutoff:3.500A)
      removed outlier: 7.401A  pdb=" N   GLU A 103 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 5.542A  pdb=" N   GLU B 109 " --> pdb=" O   VAL A 101 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   VAL A 101 " --> pdb=" O   GLU B 109 " (cutoff:3.500A)

    539 hydrogen bonds defined for protein.
    1611 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: 1.21

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2442
        1.34 -     1.46: 2105
        1.46 -     1.58: 3705
        1.58 -     1.69: 0
        1.69 -     1.81: 86
  Bond restraints: 8338
  Sorted by residual:
  bond pdb=" CA  ASN A 430 "
       pdb=" CB  ASN A 430 "
    ideal  model  delta    sigma   weight residual
    1.530  1.544 -0.014 1.69e-02 3.50e+03 7.07e-01
  bond pdb=" N   GLU B 454 "
       pdb=" CA  GLU B 454 "
    ideal  model  delta    sigma   weight residual
    1.460  1.471 -0.011 1.42e-02 4.96e+03 6.46e-01
  bond pdb=" CA  ASN B 430 "
       pdb=" CB  ASN B 430 "
    ideal  model  delta    sigma   weight residual
    1.530  1.543 -0.013 1.69e-02 3.50e+03 6.12e-01
  bond pdb=" N   SER A 258 "
       pdb=" CA  SER A 258 "
    ideal  model  delta    sigma   weight residual
    1.463  1.456  0.007 8.80e-03 1.29e+04 6.02e-01
  bond pdb=" N   GLU A 454 "
       pdb=" CA  GLU A 454 "
    ideal  model  delta    sigma   weight residual
    1.460  1.471 -0.011 1.42e-02 4.96e+03 5.83e-01
  ... (remaining 8333 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 11155
        1.45 -     2.90: 122
        2.90 -     4.35: 25
        4.35 -     5.80: 16
        5.80 -     7.24: 2
  Bond angle restraints: 11320
  Sorted by residual:
  angle pdb=" C   TRP A 429 "
        pdb=" N   ASN A 430 "
        pdb=" CA  ASN A 430 "
      ideal   model   delta    sigma   weight residual
     121.54  128.78   -7.24 1.91e+00 2.74e-01 1.44e+01
  angle pdb=" C   TRP B 429 "
        pdb=" N   ASN B 430 "
        pdb=" CA  ASN B 430 "
      ideal   model   delta    sigma   weight residual
     121.54  128.75   -7.21 1.91e+00 2.74e-01 1.42e+01
  angle pdb=" N   ILE B 115 "
        pdb=" CA  ILE B 115 "
        pdb=" C   ILE B 115 "
      ideal   model   delta    sigma   weight residual
     112.29  109.17    3.12 9.40e-01 1.13e+00 1.10e+01
  angle pdb=" N   ILE A 115 "
        pdb=" CA  ILE A 115 "
        pdb=" C   ILE A 115 "
      ideal   model   delta    sigma   weight residual
     112.29  109.21    3.08 9.40e-01 1.13e+00 1.08e+01
  angle pdb=" N   PHE B 155 "
        pdb=" CA  PHE B 155 "
        pdb=" CB  PHE B 155 "
      ideal   model   delta    sigma   weight residual
     113.65  110.30    3.35 1.47e+00 4.63e-01 5.19e+00
  ... (remaining 11315 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.98: 4305
        9.98 -    19.95: 307
       19.95 -    29.93: 90
       29.93 -    39.91: 41
       39.91 -    49.88: 21
  Dihedral angle restraints: 4764
    sinusoidal: 1818
      harmonic: 2946
  Sorted by residual:
  dihedral pdb=" CA  GLU A  51 "
           pdb=" CB  GLU A  51 "
           pdb=" CG  GLU A  51 "
           pdb=" CD  GLU A  51 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -109.88   49.88     3      1.50e+01 4.44e-03 8.83e+00
  dihedral pdb=" CA  GLU B  51 "
           pdb=" CB  GLU B  51 "
           pdb=" CG  GLU B  51 "
           pdb=" CD  GLU B  51 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -107.90   47.90     3      1.50e+01 4.44e-03 8.56e+00
  dihedral pdb=" CA  GLN A  19 "
           pdb=" CB  GLN A  19 "
           pdb=" CG  GLN A  19 "
           pdb=" CD  GLN A  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  106.95  -46.95     3      1.50e+01 4.44e-03 8.42e+00
  ... (remaining 4761 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 772
       0.024 -    0.048: 307
       0.048 -    0.072: 127
       0.072 -    0.097: 45
       0.097 -    0.121: 25
  Chirality restraints: 1276
  Sorted by residual:
  chirality pdb=" CA  ILE B  97 "
            pdb=" N   ILE B  97 "
            pdb=" C   ILE B  97 "
            pdb=" CB  ILE B  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.64e-01
  chirality pdb=" CA  ILE B 110 "
            pdb=" N   ILE B 110 "
            pdb=" C   ILE B 110 "
            pdb=" CB  ILE B 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.44e-01
  chirality pdb=" CA  ILE A  97 "
            pdb=" N   ILE A  97 "
            pdb=" C   ILE A  97 "
            pdb=" CB  ILE A  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.43e-01
  ... (remaining 1273 not shown)

  Planarity restraints: 1402
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 140 "   -0.022 5.00e-02 4.00e+02   3.32e-02 1.76e+00
        pdb=" N   PRO A 141 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 141 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 141 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 140 "    0.022 5.00e-02 4.00e+02   3.28e-02 1.72e+00
        pdb=" N   PRO B 141 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO B 141 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 141 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 139 "    0.020 5.00e-02 4.00e+02   2.98e-02 1.42e+00
        pdb=" N   PRO A 140 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 140 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 140 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1399 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1848
        2.79 -     3.32: 8135
        3.32 -     3.84: 13236
        3.84 -     4.37: 14142
        4.37 -     4.90: 25290
  Nonbonded interactions: 62651
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 370 "
            pdb=" ND2 ASN A 374 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" O   PHE B 370 "
            pdb=" ND2 ASN B 374 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" O   TRP B 429 "
            pdb=" ND2 ASN B 430 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" O   TRP A 429 "
            pdb=" ND2 ASN A 430 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" OE2 GLU A 312 "
            pdb=" OG  SER A 357 "
     model   vdw
     2.279 3.040
  ... (remaining 62646 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
}

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 group one per residue
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:             0.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.450
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6505
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      :  0.002   0.024   8338  Z= 0.094
  Angle     :  0.446   7.244  11320  Z= 0.252
  Chirality :  0.035   0.121   1276
  Planarity :  0.003   0.033   1402
  Dihedral  :  9.092  49.883   2872
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  6.15 %
    Favored  : 93.39 %
  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:  2.65 (0.28), residues: 1010
  helix:  3.00 (0.19), residues: 696
  sheet:  3.48 (0.82), residues: 24
  loop : -1.76 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  47 
 TYR   0.004   0.001   TYR A 165 
 PHE   0.008   0.001   PHE A 278 
 TRP   0.003   0.000   TRP B 429 
 HIS   0.002   0.000   HIS B  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00163 ( 8338)
  covalent geometry    : angle       0.44608 (11320)
  hydrogen bonds       : bond        0.09018 (  539)
  hydrogen bonds       : angle       3.54284 ( 1611)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 326
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   37 THR cc_start: 0.7926 (p) cc_final: 0.7450 (p)
REVERT: A  180 ILE cc_start: 0.8279 (mt) cc_final: 0.7987 (mt)
REVERT: A  378 CYS cc_start: 0.6785 (t) cc_final: 0.5598 (t)
REVERT: A  420 ASN cc_start: 0.7178 (m-40) cc_final: 0.6910 (m-40)
  outliers start: 4
  outliers final: 0
  residues processed: 326
  average time/residue: 0.0863
  time to fit residues: 39.1067
Evaluate side-chains
  212 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 432 GLN
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 363 GLN
A 432 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.085679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.068195 restraints weight = 36399.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.069974 restraints weight = 25254.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.071195 restraints weight = 19287.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.072205 restraints weight = 15890.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.073164 restraints weight = 13440.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.4297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   8338  Z= 0.241
  Angle     :  0.752  11.535  11320  Z= 0.389
  Chirality :  0.046   0.166   1276
  Planarity :  0.004   0.026   1402
  Dihedral  :  3.846  16.324   1078
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 19.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 17.17 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.27), residues: 1010
  helix:  1.99 (0.19), residues: 700
  sheet:  4.67 (0.86), residues: 24
  loop : -2.10 (0.38), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  47 
 TYR   0.025   0.002   TYR A  68 
 PHE   0.023   0.003   PHE A 201 
 TRP   0.017   0.002   TRP B 474 
 HIS   0.005   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 8338)
  covalent geometry    : angle       0.75175 (11320)
  hydrogen bonds       : bond        0.04194 (  539)
  hydrogen bonds       : angle       4.44389 ( 1611)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 212
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 LEU cc_start: 0.9696 (mt) cc_final: 0.9231 (tt)
REVERT: B   28 ASN cc_start: 0.9733 (m110) cc_final: 0.9439 (m110)
REVERT: B  184 PHE cc_start: 0.8892 (m-80) cc_final: 0.8245 (m-10)
REVERT: B  211 MET cc_start: 0.9406 (tpp) cc_final: 0.9125 (tpp)
REVERT: B  310 MET cc_start: 0.9203 (tpp) cc_final: 0.8712 (tmm)
REVERT: B  365 PHE cc_start: 0.9127 (m-80) cc_final: 0.8812 (m-80)
REVERT: B  434 MET cc_start: 0.9302 (tpp) cc_final: 0.9064 (tpp)
REVERT: B  452 ASP cc_start: 0.8625 (t0) cc_final: 0.8404 (t0)
REVERT: B  483 MET cc_start: 0.9383 (tpp) cc_final: 0.9132 (tpp)
REVERT: A  360 ARG cc_start: 0.8928 (ttm110) cc_final: 0.8634 (ttm110)
REVERT: A  365 PHE cc_start: 0.9263 (m-80) cc_final: 0.8955 (m-80)
REVERT: A  373 GLU cc_start: 0.8810 (pt0) cc_final: 0.8527 (pt0)
REVERT: A  374 ASN cc_start: 0.9458 (m-40) cc_final: 0.8924 (m110)
REVERT: A  378 CYS cc_start: 0.9231 (t) cc_final: 0.8820 (m)
REVERT: A  454 GLU cc_start: 0.6919 (pp20) cc_final: 0.6627 (tp30)
  outliers start: 29
  outliers final: 21
  residues processed: 226
  average time/residue: 0.0728
  time to fit residues: 23.5684
Evaluate side-chains
  197 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 176
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  175 ILE
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  332 LEU
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  430 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    7.9990
   chunk 16 optimal weight:    0.8980
   chunk 85 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   chunk 81 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0270
   chunk 57 optimal weight:    8.9990
   chunk 72 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.7038

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

Flipped N/Q/H residues before XYZ refinement:
B  18 HIS
B 243 ASN
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 374 ASN
B 430 ASN
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.087100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.068636 restraints weight = 34031.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.070461 restraints weight = 23761.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.071870 restraints weight = 18192.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.072835 restraints weight = 14800.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.073695 restraints weight = 12680.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.4596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8338  Z= 0.133
  Angle     :  0.702  10.322  11320  Z= 0.348
  Chirality :  0.044   0.274   1276
  Planarity :  0.003   0.033   1402
  Dihedral  :  3.697  16.252   1078
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 18.79 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.27), residues: 1010
  helix:  1.71 (0.19), residues: 702
  sheet:  4.78 (0.85), residues: 24
  loop : -2.01 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 360 
 TYR   0.019   0.001   TYR A  68 
 PHE   0.031   0.002   PHE B 377 
 TRP   0.010   0.001   TRP A  39 
 HIS   0.005   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8338)
  covalent geometry    : angle       0.70166 (11320)
  hydrogen bonds       : bond        0.03779 (  539)
  hydrogen bonds       : angle       4.12343 ( 1611)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 223
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 LEU cc_start: 0.9691 (mt) cc_final: 0.9066 (tp)
REVERT: B   28 ASN cc_start: 0.9707 (m110) cc_final: 0.9321 (m-40)
REVERT: B   64 LEU cc_start: 0.9578 (tp) cc_final: 0.9364 (pp)
REVERT: B  132 GLU cc_start: 0.8273 (pt0) cc_final: 0.7967 (pp20)
REVERT: B  133 ILE cc_start: 0.9598 (mt) cc_final: 0.8977 (mp)
REVERT: B  188 MET cc_start: 0.8255 (tmm) cc_final: 0.7963 (tmm)
REVERT: B  332 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7495 (pp)
REVERT: B  411 ASN cc_start: 0.9066 (t0) cc_final: 0.8579 (m-40)
REVERT: B  434 MET cc_start: 0.9306 (tpp) cc_final: 0.8981 (tpp)
REVERT: B  452 ASP cc_start: 0.8606 (t0) cc_final: 0.8345 (t0)
REVERT: B  483 MET cc_start: 0.9363 (tpp) cc_final: 0.9039 (tpp)
REVERT: A   67 ARG cc_start: 0.9110 (tpt90) cc_final: 0.8570 (tmm160)
REVERT: A  127 MET cc_start: 0.7232 (tpp) cc_final: 0.6879 (tpp)
REVERT: A  134 PHE cc_start: 0.8601 (m-80) cc_final: 0.8358 (m-80)
REVERT: A  148 TYR cc_start: 0.8967 (t80) cc_final: 0.7118 (t80)
REVERT: A  321 TRP cc_start: 0.9069 (OUTLIER) cc_final: 0.8652 (t60)
REVERT: A  373 GLU cc_start: 0.8583 (pt0) cc_final: 0.8338 (pt0)
REVERT: A  374 ASN cc_start: 0.9400 (m-40) cc_final: 0.8858 (m110)
REVERT: A  380 MET cc_start: 0.9361 (mtt) cc_final: 0.8920 (mtp)
REVERT: A  420 ASN cc_start: 0.8680 (m-40) cc_final: 0.8447 (m-40)
REVERT: A  454 GLU cc_start: 0.6969 (pp20) cc_final: 0.6761 (tp30)
REVERT: A  483 MET cc_start: 0.9394 (tpp) cc_final: 0.9014 (tpp)
  outliers start: 18
  outliers final: 9
  residues processed: 232
  average time/residue: 0.0717
  time to fit residues: 24.2141
Evaluate side-chains
  208 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 197
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  243 ASN
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  321 TRP
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  430 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 38 optimal weight:    6.9990
   chunk 17 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9980
   chunk 92 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 83 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** 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 = 0.3983 r_free = 0.3983 target = 0.086965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.068505 restraints weight = 35714.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.070271 restraints weight = 24896.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.071678 restraints weight = 19109.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.072780 restraints weight = 15499.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.073557 restraints weight = 13169.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.4951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8338  Z= 0.137
  Angle     :  0.720  11.896  11320  Z= 0.353
  Chirality :  0.044   0.242   1276
  Planarity :  0.003   0.034   1402
  Dihedral  :  3.716  15.692   1078
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 15.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 20.07 %
    Favored  : 77.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.27), residues: 1010
  helix:  1.61 (0.19), residues: 702
  sheet:  4.92 (0.87), residues: 24
  loop : -2.06 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 451 
 TYR   0.012   0.001   TYR A  58 
 PHE   0.025   0.002   PHE A 266 
 TRP   0.015   0.001   TRP A  39 
 HIS   0.003   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8338)
  covalent geometry    : angle       0.72017 (11320)
  hydrogen bonds       : bond        0.03833 (  539)
  hydrogen bonds       : angle       4.17491 ( 1611)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 214
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 LEU cc_start: 0.9674 (mt) cc_final: 0.9183 (tp)
REVERT: B   28 ASN cc_start: 0.9693 (m110) cc_final: 0.9431 (m110)
REVERT: B   58 TYR cc_start: 0.8986 (m-10) cc_final: 0.8470 (m-10)
REVERT: B   62 MET cc_start: 0.9472 (mmp) cc_final: 0.9027 (tpt)
REVERT: B   64 LEU cc_start: 0.9622 (tp) cc_final: 0.9402 (pp)
REVERT: B  127 MET cc_start: 0.6708 (tpp) cc_final: 0.6068 (tpp)
REVERT: B  132 GLU cc_start: 0.8181 (pt0) cc_final: 0.7819 (pp20)
REVERT: B  310 MET cc_start: 0.9077 (tpp) cc_final: 0.8783 (tmm)
REVERT: B  332 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7453 (pp)
REVERT: B  377 PHE cc_start: 0.9438 (m-80) cc_final: 0.9230 (m-10)
REVERT: B  378 CYS cc_start: 0.9051 (m) cc_final: 0.8813 (m)
REVERT: B  434 MET cc_start: 0.9316 (tpp) cc_final: 0.8874 (tpp)
REVERT: B  452 ASP cc_start: 0.8707 (t0) cc_final: 0.8466 (t0)
REVERT: B  483 MET cc_start: 0.9370 (tpp) cc_final: 0.8944 (tpp)
REVERT: A   58 TYR cc_start: 0.8691 (m-10) cc_final: 0.8481 (m-10)
REVERT: A   67 ARG cc_start: 0.9135 (tpt90) cc_final: 0.8526 (tmm160)
REVERT: A  127 MET cc_start: 0.7215 (tpp) cc_final: 0.6789 (tpp)
REVERT: A  134 PHE cc_start: 0.8677 (m-80) cc_final: 0.8351 (m-80)
REVERT: A  199 PHE cc_start: 0.7217 (m-80) cc_final: 0.6945 (m-80)
REVERT: A  310 MET cc_start: 0.8944 (tpp) cc_final: 0.8635 (tmm)
REVERT: A  350 TYR cc_start: 0.8710 (t80) cc_final: 0.8469 (t80)
REVERT: A  373 GLU cc_start: 0.8640 (pt0) cc_final: 0.8344 (pt0)
REVERT: A  374 ASN cc_start: 0.9351 (m-40) cc_final: 0.8927 (m110)
REVERT: A  380 MET cc_start: 0.9512 (mtt) cc_final: 0.9050 (mtp)
REVERT: A  420 ASN cc_start: 0.8716 (m-40) cc_final: 0.8489 (m-40)
REVERT: A  483 MET cc_start: 0.9444 (tpp) cc_final: 0.9061 (tpp)
  outliers start: 17
  outliers final: 9
  residues processed: 225
  average time/residue: 0.0744
  time to fit residues: 24.6206
Evaluate side-chains
  201 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 191
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  430 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 90 optimal weight:    9.9990
   chunk 84 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 57 optimal weight:   40.0000
   chunk 3 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9980
   chunk 49 optimal weight:    5.9990
   chunk 77 optimal weight:    7.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
B 243 ASN
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.083850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.066262 restraints weight = 36627.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.067987 restraints weight = 25234.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.069328 restraints weight = 19257.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.070346 restraints weight = 15610.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.071130 restraints weight = 13230.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.5551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8338  Z= 0.158
  Angle     :  0.733   9.284  11320  Z= 0.366
  Chirality :  0.045   0.187   1276
  Planarity :  0.004   0.033   1402
  Dihedral  :  3.895  21.767   1078
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 17.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.53 %
    Favored  : 76.57 %
  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:  0.98 (0.27), residues: 1010
  helix:  1.54 (0.19), residues: 702
  sheet:  4.83 (0.86), residues: 24
  loop : -2.10 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 451 
 TYR   0.011   0.001   TYR A  58 
 PHE   0.039   0.002   PHE A 365 
 TRP   0.022   0.002   TRP A  39 
 HIS   0.003   0.001   HIS A 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 8338)
  covalent geometry    : angle       0.73291 (11320)
  hydrogen bonds       : bond        0.03935 (  539)
  hydrogen bonds       : angle       4.41597 ( 1611)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 207
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 LEU cc_start: 0.9683 (mt) cc_final: 0.9170 (tp)
REVERT: B   28 ASN cc_start: 0.9679 (m110) cc_final: 0.9333 (m110)
REVERT: B   64 LEU cc_start: 0.9603 (tp) cc_final: 0.9378 (pp)
REVERT: B  127 MET cc_start: 0.6922 (tpp) cc_final: 0.6691 (mmt)
REVERT: B  132 GLU cc_start: 0.8140 (pt0) cc_final: 0.7670 (pp20)
REVERT: B  133 ILE cc_start: 0.9650 (mt) cc_final: 0.9288 (mp)
REVERT: B  184 PHE cc_start: 0.8842 (m-80) cc_final: 0.8584 (m-80)
REVERT: B  318 LEU cc_start: 0.9609 (mm) cc_final: 0.9341 (mm)
REVERT: B  332 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7427 (pp)
REVERT: B  365 PHE cc_start: 0.9165 (m-80) cc_final: 0.8946 (m-80)
REVERT: B  378 CYS cc_start: 0.8945 (m) cc_final: 0.8720 (m)
REVERT: B  452 ASP cc_start: 0.8809 (t0) cc_final: 0.8444 (t0)
REVERT: B  483 MET cc_start: 0.9376 (tpp) cc_final: 0.9035 (tpp)
REVERT: A   67 ARG cc_start: 0.9147 (tpt90) cc_final: 0.8680 (tpt90)
REVERT: A  127 MET cc_start: 0.7341 (tpp) cc_final: 0.6909 (tpp)
REVERT: A  199 PHE cc_start: 0.7287 (m-80) cc_final: 0.7053 (m-80)
REVERT: A  310 MET cc_start: 0.8854 (tpp) cc_final: 0.8605 (tmm)
REVERT: A  321 TRP cc_start: 0.9134 (t60) cc_final: 0.8582 (t60)
REVERT: A  350 TYR cc_start: 0.8752 (t80) cc_final: 0.8407 (t80)
REVERT: A  364 LEU cc_start: 0.9732 (tt) cc_final: 0.9474 (pp)
REVERT: A  365 PHE cc_start: 0.9037 (m-80) cc_final: 0.8820 (m-80)
REVERT: A  374 ASN cc_start: 0.9396 (m-40) cc_final: 0.8903 (m110)
REVERT: A  380 MET cc_start: 0.9550 (mtt) cc_final: 0.9122 (mtp)
REVERT: A  432 GLN cc_start: 0.9160 (mt0) cc_final: 0.8947 (mp10)
  outliers start: 25
  outliers final: 13
  residues processed: 219
  average time/residue: 0.0744
  time to fit residues: 23.8615
Evaluate side-chains
  212 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 198
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  142 ILE
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  430 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 55 optimal weight:    8.9990
   chunk 96 optimal weight:    0.3980
   chunk 5 optimal weight:    0.0970
   chunk 60 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 93 optimal weight:    8.9990
   chunk 61 optimal weight:    0.0980
   chunk 94 optimal weight:    0.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  28 ASN
A 243 ASN
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.089761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.072901 restraints weight = 34609.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.074744 restraints weight = 24059.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.076192 restraints weight = 18341.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.077167 restraints weight = 14737.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.078209 restraints weight = 12492.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.5638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8338  Z= 0.134
  Angle     :  0.798  13.282  11320  Z= 0.378
  Chirality :  0.045   0.162   1276
  Planarity :  0.004   0.052   1402
  Dihedral  :  3.808  15.099   1078
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 15.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 22.16 %
    Favored  : 75.29 %
  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:  0.89 (0.27), residues: 1010
  helix:  1.48 (0.19), residues: 694
  sheet:  4.91 (0.87), residues: 24
  loop : -2.04 (0.35), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  47 
 TYR   0.013   0.001   TYR A  58 
 PHE   0.037   0.002   PHE A 223 
 TRP   0.027   0.001   TRP A  39 
 HIS   0.003   0.000   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 8338)
  covalent geometry    : angle       0.79814 (11320)
  hydrogen bonds       : bond        0.04002 (  539)
  hydrogen bonds       : angle       4.31366 ( 1611)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 221
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 LEU cc_start: 0.9666 (mt) cc_final: 0.9124 (tp)
REVERT: B   28 ASN cc_start: 0.9664 (m110) cc_final: 0.9272 (m110)
REVERT: B   29 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7347 (t80)
REVERT: B   41 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8073 (t80)
REVERT: B   64 LEU cc_start: 0.9585 (tp) cc_final: 0.9349 (pp)
REVERT: B  127 MET cc_start: 0.6726 (tpp) cc_final: 0.6413 (mmm)
REVERT: B  181 MET cc_start: 0.8921 (tmm) cc_final: 0.8499 (ppp)
REVERT: B  207 PHE cc_start: 0.9254 (t80) cc_final: 0.9037 (t80)
REVERT: B  332 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7479 (pp)
REVERT: B  365 PHE cc_start: 0.9155 (m-80) cc_final: 0.8793 (m-80)
REVERT: B  378 CYS cc_start: 0.8834 (m) cc_final: 0.8612 (m)
REVERT: B  390 HIS cc_start: 0.7411 (t-90) cc_final: 0.7117 (t-90)
REVERT: B  452 ASP cc_start: 0.8819 (t0) cc_final: 0.8478 (t0)
REVERT: B  460 MET cc_start: 0.8786 (ptp) cc_final: 0.8547 (ptp)
REVERT: B  483 MET cc_start: 0.9352 (tpp) cc_final: 0.9036 (tpp)
REVERT: A   41 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.8039 (t80)
REVERT: A  127 MET cc_start: 0.7222 (tpp) cc_final: 0.6871 (tpp)
REVERT: A  167 PHE cc_start: 0.9348 (m-10) cc_final: 0.9025 (m-80)
REVERT: A  199 PHE cc_start: 0.7138 (m-80) cc_final: 0.6823 (m-80)
REVERT: A  223 PHE cc_start: 0.9391 (m-80) cc_final: 0.8924 (m-80)
REVERT: A  310 MET cc_start: 0.8761 (tpp) cc_final: 0.8506 (tmm)
REVERT: A  321 TRP cc_start: 0.9005 (t60) cc_final: 0.8441 (t60)
REVERT: A  350 TYR cc_start: 0.8645 (t80) cc_final: 0.8251 (t80)
REVERT: A  364 LEU cc_start: 0.9639 (tt) cc_final: 0.9363 (pp)
REVERT: A  365 PHE cc_start: 0.9076 (m-80) cc_final: 0.8732 (m-80)
REVERT: A  374 ASN cc_start: 0.9303 (m-40) cc_final: 0.8840 (m110)
REVERT: A  380 MET cc_start: 0.9498 (mtt) cc_final: 0.9084 (mtp)
REVERT: A  483 MET cc_start: 0.9275 (mmm) cc_final: 0.8968 (mmp)
  outliers start: 22
  outliers final: 12
  residues processed: 234
  average time/residue: 0.0749
  time to fit residues: 25.5072
Evaluate side-chains
  219 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 203
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 PHE
Chi-restraints excluded: chain B residue   41 PHE
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  423 ARG
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   41 PHE
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  430 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 67 optimal weight:    9.9990
   chunk 48 optimal weight:    9.9990
   chunk 28 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 8 optimal weight:   10.0000
   chunk 98 optimal weight:   30.0000
   chunk 7 optimal weight:    9.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:
** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** 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 = 0.3930 r_free = 0.3930 target = 0.083683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.066113 restraints weight = 36501.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.067810 restraints weight = 25466.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.069132 restraints weight = 19488.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.070033 restraints weight = 15835.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.070916 restraints weight = 13537.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.6023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8338  Z= 0.162
  Angle     :  0.801  12.851  11320  Z= 0.390
  Chirality :  0.047   0.211   1276
  Planarity :  0.004   0.054   1402
  Dihedral  :  3.837  16.282   1078
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 18.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 24.48 %
    Favored  : 73.43 %
  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:  0.74 (0.27), residues: 1010
  helix:  1.34 (0.19), residues: 702
  sheet:  4.83 (0.87), residues: 24
  loop : -2.14 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  67 
 TYR   0.012   0.001   TYR A  58 
 PHE   0.039   0.002   PHE B 199 
 TRP   0.031   0.001   TRP A  39 
 HIS   0.003   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 8338)
  covalent geometry    : angle       0.80074 (11320)
  hydrogen bonds       : bond        0.03929 (  539)
  hydrogen bonds       : angle       4.43768 ( 1611)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 206
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 LEU cc_start: 0.9673 (mt) cc_final: 0.9140 (tp)
REVERT: B   28 ASN cc_start: 0.9674 (m110) cc_final: 0.9312 (m110)
REVERT: B   29 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.7332 (t80)
REVERT: B   41 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.8097 (t80)
REVERT: B   64 LEU cc_start: 0.9608 (tp) cc_final: 0.9363 (pp)
REVERT: B  127 MET cc_start: 0.7110 (tpp) cc_final: 0.6843 (mmt)
REVERT: B  204 CYS cc_start: 0.7934 (m) cc_final: 0.7336 (m)
REVERT: B  332 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7363 (pp)
REVERT: B  365 PHE cc_start: 0.9155 (m-80) cc_final: 0.8789 (m-80)
REVERT: B  378 CYS cc_start: 0.8939 (m) cc_final: 0.8688 (m)
REVERT: B  452 ASP cc_start: 0.8713 (t0) cc_final: 0.8362 (t0)
REVERT: B  483 MET cc_start: 0.9389 (tpp) cc_final: 0.9033 (tpp)
REVERT: A   41 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.7890 (t80)
REVERT: A  127 MET cc_start: 0.7472 (tpp) cc_final: 0.7123 (tpp)
REVERT: A  168 LEU cc_start: 0.9332 (mm) cc_final: 0.9087 (mm)
REVERT: A  199 PHE cc_start: 0.7403 (m-80) cc_final: 0.7035 (m-80)
REVERT: A  211 MET cc_start: 0.9335 (tpp) cc_final: 0.9120 (tpp)
REVERT: A  223 PHE cc_start: 0.9462 (m-80) cc_final: 0.8953 (m-80)
REVERT: A  310 MET cc_start: 0.8727 (tpp) cc_final: 0.8508 (tmm)
REVERT: A  321 TRP cc_start: 0.9078 (t60) cc_final: 0.8539 (t60)
REVERT: A  350 TYR cc_start: 0.8718 (t80) cc_final: 0.8282 (t80)
REVERT: A  351 ASN cc_start: 0.9263 (OUTLIER) cc_final: 0.8651 (p0)
REVERT: A  364 LEU cc_start: 0.9695 (tt) cc_final: 0.9467 (pp)
REVERT: A  365 PHE cc_start: 0.9052 (m-80) cc_final: 0.8624 (m-80)
REVERT: A  374 ASN cc_start: 0.9342 (m-40) cc_final: 0.8912 (m110)
REVERT: A  380 MET cc_start: 0.9504 (mtt) cc_final: 0.9115 (mtp)
REVERT: A  483 MET cc_start: 0.9446 (mmm) cc_final: 0.9089 (mmp)
  outliers start: 18
  outliers final: 13
  residues processed: 216
  average time/residue: 0.0765
  time to fit residues: 24.2201
Evaluate side-chains
  212 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 194
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 PHE
Chi-restraints excluded: chain B residue   41 PHE
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  423 ARG
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   41 PHE
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  430 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 59 optimal weight:   30.0000
   chunk 68 optimal weight:    0.2980
   chunk 56 optimal weight:    0.9980
   chunk 47 optimal weight:   10.0000
   chunk 24 optimal weight:    0.0060
   chunk 46 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 86 optimal weight:    0.7980
   chunk 78 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.5796

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

Flipped N/Q/H residues before XYZ refinement:
B 273 GLN
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.086563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.069032 restraints weight = 35124.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.070799 restraints weight = 24784.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.072252 restraints weight = 19055.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.073210 restraints weight = 15335.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.074103 restraints weight = 13075.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.6102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8338  Z= 0.140
  Angle     :  0.853  14.981  11320  Z= 0.402
  Chirality :  0.048   0.325   1276
  Planarity :  0.004   0.055   1402
  Dihedral  :  3.889  16.574   1078
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 16.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 25.41 %
    Favored  : 72.16 %
  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:  0.63 (0.26), residues: 1010
  helix:  1.24 (0.19), residues: 702
  sheet:  4.81 (0.87), residues: 24
  loop : -2.13 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  67 
 TYR   0.015   0.001   TYR A  58 
 PHE   0.033   0.002   PHE B 199 
 TRP   0.037   0.002   TRP B  39 
 HIS   0.003   0.000   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8338)
  covalent geometry    : angle       0.85344 (11320)
  hydrogen bonds       : bond        0.04014 (  539)
  hydrogen bonds       : angle       4.43806 ( 1611)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 208
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 LEU cc_start: 0.9663 (mt) cc_final: 0.9121 (tp)
REVERT: B   28 ASN cc_start: 0.9668 (m110) cc_final: 0.9271 (m110)
REVERT: B   29 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7213 (t80)
REVERT: B   41 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8139 (t80)
REVERT: B   64 LEU cc_start: 0.9606 (tp) cc_final: 0.9361 (pp)
REVERT: B  332 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7445 (pp)
REVERT: B  365 PHE cc_start: 0.9149 (m-80) cc_final: 0.8717 (m-80)
REVERT: B  378 CYS cc_start: 0.8891 (m) cc_final: 0.8643 (m)
REVERT: B  390 HIS cc_start: 0.7408 (t-90) cc_final: 0.7089 (t-90)
REVERT: B  452 ASP cc_start: 0.8722 (t0) cc_final: 0.8367 (t0)
REVERT: B  461 MET cc_start: 0.9271 (mmm) cc_final: 0.8820 (mtt)
REVERT: B  483 MET cc_start: 0.9334 (tpp) cc_final: 0.8996 (tpp)
REVERT: A   41 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7874 (t80)
REVERT: A   58 TYR cc_start: 0.8954 (m-10) cc_final: 0.8587 (m-10)
REVERT: A   62 MET cc_start: 0.9456 (mmp) cc_final: 0.8951 (tpt)
REVERT: A  127 MET cc_start: 0.7351 (tpp) cc_final: 0.7059 (tpp)
REVERT: A  132 GLU cc_start: 0.8371 (pm20) cc_final: 0.8099 (pm20)
REVERT: A  167 PHE cc_start: 0.9367 (m-10) cc_final: 0.9034 (m-80)
REVERT: A  168 LEU cc_start: 0.9322 (mm) cc_final: 0.9064 (mm)
REVERT: A  199 PHE cc_start: 0.7250 (m-80) cc_final: 0.6929 (m-80)
REVERT: A  211 MET cc_start: 0.9295 (tpp) cc_final: 0.9089 (tpp)
REVERT: A  223 PHE cc_start: 0.9404 (m-80) cc_final: 0.8928 (m-80)
REVERT: A  321 TRP cc_start: 0.8978 (t60) cc_final: 0.8418 (t60)
REVERT: A  350 TYR cc_start: 0.8538 (t80) cc_final: 0.8239 (t80)
REVERT: A  351 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8533 (p0)
REVERT: A  364 LEU cc_start: 0.9650 (tt) cc_final: 0.9359 (pp)
REVERT: A  365 PHE cc_start: 0.8881 (m-80) cc_final: 0.8469 (m-80)
REVERT: A  374 ASN cc_start: 0.9272 (m-40) cc_final: 0.8855 (m110)
REVERT: A  380 MET cc_start: 0.9483 (mtt) cc_final: 0.9137 (mtt)
REVERT: A  483 MET cc_start: 0.9446 (mmm) cc_final: 0.9059 (mmp)
  outliers start: 21
  outliers final: 12
  residues processed: 221
  average time/residue: 0.0730
  time to fit residues: 23.4839
Evaluate side-chains
  222 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 205
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 PHE
Chi-restraints excluded: chain B residue   41 PHE
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  332 LEU
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  423 ARG
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   41 PHE
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  430 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9980
   chunk 74 optimal weight:    6.9990
   chunk 64 optimal weight:    0.7980
   chunk 60 optimal weight:    0.0670
   chunk 24 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 80 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0170
   overall best weight:    0.4756

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

Flipped N/Q/H residues before XYZ refinement:
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** 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 = 0.3990 r_free = 0.3990 target = 0.087557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.069971 restraints weight = 34871.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.071747 restraints weight = 24676.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.073182 restraints weight = 18953.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.074169 restraints weight = 15269.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.075026 restraints weight = 13065.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.6248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8338  Z= 0.143
  Angle     :  0.882  14.203  11320  Z= 0.416
  Chirality :  0.049   0.256   1276
  Planarity :  0.004   0.055   1402
  Dihedral  :  3.938  15.681   1078
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 16.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 25.29 %
    Favored  : 72.74 %
  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:  0.48 (0.26), residues: 1010
  helix:  1.10 (0.19), residues: 702
  sheet:  4.85 (0.86), residues: 24
  loop : -2.11 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  67 
 TYR   0.012   0.001   TYR A  58 
 PHE   0.031   0.002   PHE B 223 
 TRP   0.038   0.002   TRP B  39 
 HIS   0.004   0.000   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8338)
  covalent geometry    : angle       0.88192 (11320)
  hydrogen bonds       : bond        0.04110 (  539)
  hydrogen bonds       : angle       4.48003 ( 1611)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 214
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 LEU cc_start: 0.9662 (mt) cc_final: 0.9190 (tp)
REVERT: B   28 ASN cc_start: 0.9642 (m110) cc_final: 0.9350 (m110)
REVERT: B   29 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7454 (t80)
REVERT: B   39 TRP cc_start: 0.8346 (t60) cc_final: 0.7897 (t60)
REVERT: B   41 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.8135 (t80)
REVERT: B   64 LEU cc_start: 0.9597 (tp) cc_final: 0.9346 (pp)
REVERT: B  167 PHE cc_start: 0.9310 (m-10) cc_final: 0.9000 (m-80)
REVERT: B  188 MET cc_start: 0.8697 (tmm) cc_final: 0.8371 (tmm)
REVERT: B  220 LEU cc_start: 0.9563 (pp) cc_final: 0.9294 (mp)
REVERT: B  312 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8075 (mp0)
REVERT: B  365 PHE cc_start: 0.9117 (m-80) cc_final: 0.8740 (m-80)
REVERT: B  378 CYS cc_start: 0.8875 (m) cc_final: 0.8580 (m)
REVERT: B  390 HIS cc_start: 0.7447 (t-90) cc_final: 0.7184 (t-90)
REVERT: B  451 ARG cc_start: 0.9446 (tpp-160) cc_final: 0.9197 (mmt90)
REVERT: B  452 ASP cc_start: 0.8858 (t0) cc_final: 0.8631 (t0)
REVERT: A   41 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7869 (t80)
REVERT: A   58 TYR cc_start: 0.8888 (m-10) cc_final: 0.8519 (m-10)
REVERT: A   62 MET cc_start: 0.9478 (mmp) cc_final: 0.8922 (tpt)
REVERT: A  127 MET cc_start: 0.7360 (tpp) cc_final: 0.7050 (tpp)
REVERT: A  132 GLU cc_start: 0.8281 (pm20) cc_final: 0.8009 (pm20)
REVERT: A  167 PHE cc_start: 0.9346 (m-10) cc_final: 0.8992 (m-80)
REVERT: A  168 LEU cc_start: 0.9309 (mm) cc_final: 0.9060 (mm)
REVERT: A  199 PHE cc_start: 0.7221 (m-80) cc_final: 0.6894 (m-80)
REVERT: A  211 MET cc_start: 0.9294 (tpp) cc_final: 0.9085 (tpp)
REVERT: A  223 PHE cc_start: 0.9371 (m-80) cc_final: 0.8937 (m-80)
REVERT: A  312 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7838 (mp0)
REVERT: A  350 TYR cc_start: 0.8516 (t80) cc_final: 0.8247 (t80)
REVERT: A  351 ASN cc_start: 0.9216 (OUTLIER) cc_final: 0.8548 (p0)
REVERT: A  364 LEU cc_start: 0.9631 (tt) cc_final: 0.9368 (pp)
REVERT: A  365 PHE cc_start: 0.8917 (m-80) cc_final: 0.8470 (m-80)
REVERT: A  374 ASN cc_start: 0.9227 (m-40) cc_final: 0.8985 (m-40)
REVERT: A  380 MET cc_start: 0.9477 (mtt) cc_final: 0.9143 (mtp)
REVERT: A  483 MET cc_start: 0.9461 (mmm) cc_final: 0.9059 (mmp)
  outliers start: 17
  outliers final: 13
  residues processed: 224
  average time/residue: 0.0736
  time to fit residues: 24.0570
Evaluate side-chains
  217 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 200
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 PHE
Chi-restraints excluded: chain B residue   41 PHE
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  423 ARG
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   41 PHE
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  218 THR
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  349 THR
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  430 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 29 optimal weight:    0.3980
   chunk 85 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 47 optimal weight:    0.2980
   chunk 89 optimal weight:    3.9990
   chunk 22 optimal weight:    9.9990
   chunk 28 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** 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 = 0.3943 r_free = 0.3943 target = 0.085157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.068167 restraints weight = 35811.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.069894 restraints weight = 24720.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.071305 restraints weight = 18740.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.072391 restraints weight = 15003.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.072980 restraints weight = 12566.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.6574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8338  Z= 0.157
  Angle     :  0.900  13.390  11320  Z= 0.430
  Chirality :  0.051   0.272   1276
  Planarity :  0.004   0.055   1402
  Dihedral  :  4.028  15.618   1078
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 18.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 25.75 %
    Favored  : 72.39 %
  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:  0.37 (0.26), residues: 1010
  helix:  0.98 (0.19), residues: 704
  sheet:  4.78 (0.87), residues: 24
  loop : -2.06 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 441 
 TYR   0.016   0.001   TYR B  58 
 PHE   0.048   0.002   PHE B 223 
 TRP   0.035   0.002   TRP B  39 
 HIS   0.005   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 8338)
  covalent geometry    : angle       0.90047 (11320)
  hydrogen bonds       : bond        0.04120 (  539)
  hydrogen bonds       : angle       4.59878 ( 1611)

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

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

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2020 Ramachandran restraints generated.
    1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 197
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   24 LEU cc_start: 0.9651 (mt) cc_final: 0.9204 (tp)
REVERT: B   28 ASN cc_start: 0.9647 (m110) cc_final: 0.9336 (m110)
REVERT: B   29 PHE cc_start: 0.7694 (OUTLIER) cc_final: 0.7142 (t80)
REVERT: B   64 LEU cc_start: 0.9589 (tp) cc_final: 0.9349 (pp)
REVERT: B  188 MET cc_start: 0.8688 (tmm) cc_final: 0.8350 (tmm)
REVERT: B  207 PHE cc_start: 0.9445 (t80) cc_final: 0.9165 (t80)
REVERT: B  220 LEU cc_start: 0.9501 (pp) cc_final: 0.9093 (mp)
REVERT: B  365 PHE cc_start: 0.9037 (m-80) cc_final: 0.8686 (m-80)
REVERT: B  378 CYS cc_start: 0.8884 (m) cc_final: 0.8645 (m)
REVERT: B  390 HIS cc_start: 0.7345 (t-90) cc_final: 0.6749 (t-90)
REVERT: B  434 MET cc_start: 0.9383 (tpp) cc_final: 0.9174 (tpp)
REVERT: B  451 ARG cc_start: 0.9425 (tpp-160) cc_final: 0.9144 (mmt90)
REVERT: B  452 ASP cc_start: 0.9042 (t0) cc_final: 0.8707 (t0)
REVERT: B  460 MET cc_start: 0.8183 (ptp) cc_final: 0.7575 (ptp)
REVERT: B  461 MET cc_start: 0.9339 (mmm) cc_final: 0.9079 (tpt)
REVERT: A   41 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8033 (t80)
REVERT: A   58 TYR cc_start: 0.8938 (m-10) cc_final: 0.8552 (m-10)
REVERT: A   62 MET cc_start: 0.9508 (mmp) cc_final: 0.8952 (tpt)
REVERT: A  127 MET cc_start: 0.7643 (tpp) cc_final: 0.7238 (tpp)
REVERT: A  132 GLU cc_start: 0.8321 (pm20) cc_final: 0.8029 (pm20)
REVERT: A  168 LEU cc_start: 0.9335 (mm) cc_final: 0.9111 (mm)
REVERT: A  199 PHE cc_start: 0.7387 (m-80) cc_final: 0.7077 (m-80)
REVERT: A  223 PHE cc_start: 0.9394 (m-80) cc_final: 0.8931 (m-80)
REVERT: A  312 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7733 (mp0)
REVERT: A  350 TYR cc_start: 0.8580 (t80) cc_final: 0.8302 (t80)
REVERT: A  351 ASN cc_start: 0.9246 (OUTLIER) cc_final: 0.8594 (p0)
REVERT: A  364 LEU cc_start: 0.9656 (tt) cc_final: 0.9378 (pp)
REVERT: A  365 PHE cc_start: 0.9021 (m-80) cc_final: 0.8592 (m-80)
REVERT: A  374 ASN cc_start: 0.9299 (m-40) cc_final: 0.8907 (m110)
REVERT: A  380 MET cc_start: 0.9525 (mtt) cc_final: 0.9093 (mtp)
REVERT: A  460 MET cc_start: 0.8008 (ptp) cc_final: 0.7674 (ptp)
REVERT: A  483 MET cc_start: 0.9530 (mmm) cc_final: 0.9157 (mmp)
  outliers start: 16
  outliers final: 11
  residues processed: 206
  average time/residue: 0.0729
  time to fit residues: 22.0154
Evaluate side-chains
  207 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 193
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 PHE
Chi-restraints excluded: chain B residue  218 THR
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  336 VAL
Chi-restraints excluded: chain B residue  423 ARG
Chi-restraints excluded: chain B residue  450 ILE
Chi-restraints excluded: chain A residue   29 PHE
Chi-restraints excluded: chain A residue   41 PHE
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  203 ASP
Chi-restraints excluded: chain A residue  244 ASP
Chi-restraints excluded: chain A residue  336 VAL
Chi-restraints excluded: chain A residue  351 ASN
Chi-restraints excluded: chain A residue  430 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 48 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 92 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 79 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 58 optimal weight:   20.0000
   chunk 21 optimal weight:    0.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 459 GLN
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.086378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.069051 restraints weight = 35498.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.070835 restraints weight = 24619.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.072109 restraints weight = 18731.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.073261 restraints weight = 15346.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.074060 restraints weight = 12845.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.6677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8338  Z= 0.145
  Angle     :  0.912  13.725  11320  Z= 0.429
  Chirality :  0.051   0.357   1276
  Planarity :  0.004   0.052   1402
  Dihedral  :  4.047  15.131   1078
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 17.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 25.99 %
    Favored  : 72.16 %
  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:  0.34 (0.26), residues: 1010
  helix:  0.91 (0.19), residues: 714
  sheet:  4.77 (0.87), residues: 24
  loop : -2.01 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  67 
 TYR   0.012   0.001   TYR B  58 
 PHE   0.070   0.002   PHE B 223 
 TRP   0.041   0.002   TRP B  39 
 HIS   0.004   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8338)
  covalent geometry    : angle       0.91233 (11320)
  hydrogen bonds       : bond        0.04121 (  539)
  hydrogen bonds       : angle       4.59795 ( 1611)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1595.87 seconds
wall clock time: 28 minutes 22.68 seconds (1702.68 seconds total)