Starting phenix.real_space_refine
on Sun Apr  5 02:07:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mcr_63803/04_2026/9mcr_63803.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mcr_63803/04_2026/9mcr_63803.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mcr_63803/04_2026/9mcr_63803.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mcr_63803/04_2026/9mcr_63803.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mcr_63803/04_2026/9mcr_63803.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mcr_63803/04_2026/9mcr_63803.map"
  }
  resolution = 2.41
  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=   0.001 sd=   0.201
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      28      5.16       5
     C    4784      2.51       5
     N    1102      2.21       5
     O    1194      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7108
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 470, 3554
          Classifications: {'peptide': 470}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 447}
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.53, per 1000 atoms: 0.36
  Number of scatterers: 7108
  At special positions: 0
  Unit cell: (81.084, 112.772, 78.288, 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      28     16.00
     O    1194      8.00
     N    1102      7.00
     C    4784      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: 0.75
  Conformation dependent library (CDL) restraints added in 257.8 milliseconds
  

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1688

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 0 sheets defined
      82.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 91 through 108
      removed outlier: 3.752A  pdb=" N   PHE A 107 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 135
    Processing helix  chain 'A' and resid 138 through 153
    Processing helix  chain 'A' and resid 157 through 162
    Processing helix  chain 'A' and resid 163 through 166
      removed outlier: 4.193A  pdb=" N   GLY A 166 " --> pdb=" O   SER A 163 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 163 through 166'
    Processing helix  chain 'A' and resid 167 through 187
      removed outlier: 3.547A  pdb=" N   TRP A 171 " --> pdb=" O   ASP A 167 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLY A 182 " --> pdb=" O   PHE A 178 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   PHE A 183 " --> pdb=" O   PHE A 179 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ILE A 184 " --> pdb=" O   ALA A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 201
      removed outlier: 3.838A  pdb=" N   GLN A 195 " --> pdb=" O   ARG A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 218
      removed outlier: 3.742A  pdb=" N   LEU A 211 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 232
      removed outlier: 3.560A  pdb=" N   ILE A 232 " --> pdb=" O   ARG A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 244
    Processing helix  chain 'A' and resid 256 through 263
      removed outlier: 3.696A  pdb=" N   LEU A 262 " --> pdb=" O   SER A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 272
    Processing helix  chain 'A' and resid 281 through 293
    Processing helix  chain 'A' and resid 298 through 325
      removed outlier: 4.940A  pdb=" N   VAL A 308 " --> pdb=" O   LYS A 304 " (cutoff:3.500A)
      Proline residue:  A 309  - end of helix
      Proline residue:  A 318  - end of helix
    Processing helix  chain 'A' and resid 334 through 347
      removed outlier: 3.595A  pdb=" N   MET A 346 " --> pdb=" O   LYS A 342 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   GLY A 347 " --> pdb=" O   LEU A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 369
    Processing helix  chain 'A' and resid 376 through 391
    Processing helix  chain 'A' and resid 395 through 401
    Processing helix  chain 'A' and resid 402 through 425
      removed outlier: 3.695A  pdb=" N   TRP A 406 " --> pdb=" O   GLU A 402 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ASN A 423 " --> pdb=" O   ALA A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 440
    Processing helix  chain 'A' and resid 445 through 459
    Processing helix  chain 'A' and resid 460 through 464
    Processing helix  chain 'A' and resid 467 through 485
      removed outlier: 6.502A  pdb=" N   THR A 476 " --> pdb=" O   GLY A 472 " (cutoff:3.500A)
      removed outlier: 5.456A  pdb=" N   ALA A 477 " --> pdb=" O   ALA A 473 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL A 481 " --> pdb=" O   ALA A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 503
      removed outlier: 3.930A  pdb=" N   ASN A 501 " --> pdb=" O   ALA A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 506
      No H-bonds generated for 'chain 'A' and resid 504 through 506'
    Processing helix  chain 'A' and resid 513 through 519
    Processing helix  chain 'A' and resid 524 through 545
    Processing helix  chain 'A' and resid 545 through 554
    Processing helix  chain 'B' and resid 91 through 108
      removed outlier: 3.752A  pdb=" N   PHE B 107 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 135
    Processing helix  chain 'B' and resid 138 through 153
    Processing helix  chain 'B' and resid 157 through 162
    Processing helix  chain 'B' and resid 163 through 166
      removed outlier: 4.193A  pdb=" N   GLY B 166 " --> pdb=" O   SER B 163 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 163 through 166'
    Processing helix  chain 'B' and resid 167 through 187
      removed outlier: 3.547A  pdb=" N   TRP B 171 " --> pdb=" O   ASP B 167 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLY B 182 " --> pdb=" O   PHE B 178 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   PHE B 183 " --> pdb=" O   PHE B 179 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ILE B 184 " --> pdb=" O   ALA B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 201
      removed outlier: 3.838A  pdb=" N   GLN B 195 " --> pdb=" O   ARG B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 218
      removed outlier: 3.742A  pdb=" N   LEU B 211 " --> pdb=" O   LEU B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 224 through 232
      removed outlier: 3.560A  pdb=" N   ILE B 232 " --> pdb=" O   ARG B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 244
    Processing helix  chain 'B' and resid 256 through 263
      removed outlier: 3.697A  pdb=" N   LEU B 262 " --> pdb=" O   SER B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 272
    Processing helix  chain 'B' and resid 281 through 293
    Processing helix  chain 'B' and resid 298 through 325
      removed outlier: 4.940A  pdb=" N   VAL B 308 " --> pdb=" O   LYS B 304 " (cutoff:3.500A)
      Proline residue:  B 309  - end of helix
      Proline residue:  B 318  - end of helix
    Processing helix  chain 'B' and resid 334 through 347
      removed outlier: 3.595A  pdb=" N   MET B 346 " --> pdb=" O   LYS B 342 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   GLY B 347 " --> pdb=" O   LEU B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 369
    Processing helix  chain 'B' and resid 376 through 391
    Processing helix  chain 'B' and resid 395 through 401
    Processing helix  chain 'B' and resid 402 through 425
      removed outlier: 3.696A  pdb=" N   TRP B 406 " --> pdb=" O   GLU B 402 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ASN B 423 " --> pdb=" O   ALA B 419 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 440
    Processing helix  chain 'B' and resid 445 through 459
    Processing helix  chain 'B' and resid 460 through 464
    Processing helix  chain 'B' and resid 467 through 485
      removed outlier: 6.503A  pdb=" N   THR B 476 " --> pdb=" O   GLY B 472 " (cutoff:3.500A)
      removed outlier: 5.456A  pdb=" N   ALA B 477 " --> pdb=" O   ALA B 473 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   VAL B 481 " --> pdb=" O   ALA B 477 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 503
      removed outlier: 3.931A  pdb=" N   ASN B 501 " --> pdb=" O   ALA B 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 506
      No H-bonds generated for 'chain 'B' and resid 504 through 506'
    Processing helix  chain 'B' and resid 513 through 519
    Processing helix  chain 'B' and resid 524 through 545
    Processing helix  chain 'B' and resid 545 through 554

    510 hydrogen bonds defined for protein.
    1518 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: 1.11

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1991
        1.34 -     1.45: 1482
        1.45 -     1.57: 3803
        1.57 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 7324
  Sorted by residual:
  bond pdb=" CB  PHE A 265 "
       pdb=" CG  PHE A 265 "
    ideal  model  delta    sigma   weight residual
    1.502  1.447  0.055 2.30e-02 1.89e+03 5.82e+00
  bond pdb=" CB  PHE B 265 "
       pdb=" CG  PHE B 265 "
    ideal  model  delta    sigma   weight residual
    1.502  1.447  0.055 2.30e-02 1.89e+03 5.66e+00
  bond pdb=" CG1 ILE B 270 "
       pdb=" CD1 ILE B 270 "
    ideal  model  delta    sigma   weight residual
    1.513  1.433  0.080 3.90e-02 6.57e+02 4.22e+00
  bond pdb=" CG1 ILE A 270 "
       pdb=" CD1 ILE A 270 "
    ideal  model  delta    sigma   weight residual
    1.513  1.433  0.080 3.90e-02 6.57e+02 4.21e+00
  bond pdb=" CD2 PHE B 265 "
       pdb=" CE2 PHE B 265 "
    ideal  model  delta    sigma   weight residual
    1.382  1.321  0.061 3.00e-02 1.11e+03 4.16e+00
  ... (remaining 7319 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.63: 9816
        2.63 -     5.27: 172
        5.27 -     7.90: 26
        7.90 -    10.54: 6
       10.54 -    13.17: 2
  Bond angle restraints: 10022
  Sorted by residual:
  angle pdb=" C   PHE A 265 "
        pdb=" N   GLN A 266 "
        pdb=" CA  GLN A 266 "
      ideal   model   delta    sigma   weight residual
     120.71  115.17    5.54 1.67e+00 3.59e-01 1.10e+01
  angle pdb=" C   PHE B 265 "
        pdb=" N   GLN B 266 "
        pdb=" CA  GLN B 266 "
      ideal   model   delta    sigma   weight residual
     120.71  115.17    5.54 1.67e+00 3.59e-01 1.10e+01
  angle pdb=" C   THR B 153 "
        pdb=" N   LYS B 154 "
        pdb=" CA  LYS B 154 "
      ideal   model   delta    sigma   weight residual
     122.40  126.82   -4.42 1.45e+00 4.76e-01 9.29e+00
  angle pdb=" C   THR A 153 "
        pdb=" N   LYS A 154 "
        pdb=" CA  LYS A 154 "
      ideal   model   delta    sigma   weight residual
     122.40  126.78   -4.38 1.45e+00 4.76e-01 9.13e+00
  angle pdb=" C   CYS B 264 "
        pdb=" N   PHE B 265 "
        pdb=" CA  PHE B 265 "
      ideal   model   delta    sigma   weight residual
     122.15  113.83    8.32 2.83e+00 1.25e-01 8.64e+00
  ... (remaining 10017 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 3810
       17.95 -    35.90: 242
       35.90 -    53.85: 46
       53.85 -    71.79: 4
       71.79 -    89.74: 4
  Dihedral angle restraints: 4106
    sinusoidal: 1452
      harmonic: 2654
  Sorted by residual:
  dihedral pdb=" CA  LEU A 262 "
           pdb=" C   LEU A 262 "
           pdb=" N   THR A 263 "
           pdb=" CA  THR A 263 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.78  -27.22     0      5.00e+00 4.00e-02 2.96e+01
  dihedral pdb=" CA  LEU B 262 "
           pdb=" C   LEU B 262 "
           pdb=" N   THR B 263 "
           pdb=" CA  THR B 263 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.80  -27.20     0      5.00e+00 4.00e-02 2.96e+01
  dihedral pdb=" CA  SER A 272 "
           pdb=" C   SER A 272 "
           pdb=" N   SER A 273 "
           pdb=" CA  SER A 273 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.60   22.40     0      5.00e+00 4.00e-02 2.01e+01
  ... (remaining 4103 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 768
       0.048 -    0.096: 309
       0.096 -    0.143: 81
       0.143 -    0.191: 16
       0.191 -    0.239: 4
  Chirality restraints: 1178
  Sorted by residual:
  chirality pdb=" CA  PHE A 265 "
            pdb=" N   PHE A 265 "
            pdb=" C   PHE A 265 "
            pdb=" CB  PHE A 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CA  PHE B 265 "
            pdb=" N   PHE B 265 "
            pdb=" C   PHE B 265 "
            pdb=" CB  PHE B 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CG  LEU A 211 "
            pdb=" CB  LEU A 211 "
            pdb=" CD1 LEU A 211 "
            pdb=" CD2 LEU A 211 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.79    0.20 2.00e-01 2.50e+01 9.90e-01
  ... (remaining 1175 not shown)

  Planarity restraints: 1204
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 265 "    0.029 2.00e-02 2.50e+03   1.92e-02 6.46e+00
        pdb=" CG  PHE B 265 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 265 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 265 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 265 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 265 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 265 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 265 "   -0.029 2.00e-02 2.50e+03   1.90e-02 6.33e+00
        pdb=" CG  PHE A 265 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 265 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 265 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 265 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 265 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 265 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 137 "   -0.038 5.00e-02 4.00e+02   5.71e-02 5.22e+00
        pdb=" N   PRO B 138 "    0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO B 138 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 138 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 1201 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2228
        2.81 -     3.34: 6503
        3.34 -     3.86: 12729
        3.86 -     4.38: 15130
        4.38 -     4.90: 25417
  Nonbonded interactions: 62007
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 259 "
            pdb=" OG1 THR A 263 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" O   TRP B 259 "
            pdb=" OG1 THR B 263 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   THR A 263 "
            pdb=" OG1 THR A 267 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" O   THR B 263 "
            pdb=" OG1 THR B 267 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" NH2 ARG A 228 "
            pdb=" O   ALA A 278 "
     model   vdw
     2.362 3.120
  ... (remaining 62002 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.620
  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:6.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.080   7324  Z= 0.299
  Angle     :  0.892  13.174  10022  Z= 0.465
  Chirality :  0.054   0.239   1178
  Planarity :  0.007   0.057   1204
  Dihedral  : 12.738  89.742   2418
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  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 are not related in a simple way.
  whole: -5.35 (0.17), residues: 936
  helix: -3.71 (0.09), residues: 748
  sheet:  None (None), residues: 0
  loop : -1.34 (0.40), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 228 
 TYR   0.016   0.002   TYR B 459 
 PHE   0.038   0.003   PHE B 265 
 TRP   0.017   0.003   TRP A 411 
 HIS   0.013   0.005   HIS B 461 

Details of bonding type rmsd
  covalent geometry    : bond        0.00734 ( 7324)
  covalent geometry    : angle       0.89182 (10022)
  hydrogen bonds       : bond        0.25448 (  510)
  hydrogen bonds       : angle       9.51590 ( 1518)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A  342 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7701 (mtpp)
REVERT: A  346 MET cc_start: 0.8509 (mtm) cc_final: 0.8170 (mtp)
REVERT: A  353 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8070 (mt-10)
REVERT: A  474 MET cc_start: 0.9041 (mtt) cc_final: 0.8657 (mtt)
REVERT: B  474 MET cc_start: 0.8982 (mtt) cc_final: 0.8646 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.6225
  time to fit residues: 65.3772
Evaluate side-chains
  77 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.1980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.4980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 120 GLN
A 195 GLN
A 287 ASN
A 340 GLN
A 423 ASN
A 461 HIS
B 120 GLN
B 195 GLN
B 287 ASN
B 340 GLN
B 423 ASN
B 461 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.118444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.105958 restraints weight = 8495.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 1.18
r_work: 0.2963 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7324  Z= 0.131
  Angle     :  0.596   9.547  10022  Z= 0.299
  Chirality :  0.041   0.144   1178
  Planarity :  0.005   0.045   1204
  Dihedral  :  4.974  23.456    980
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  8.40 %
    Favored  : 91.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.09 (0.25), residues: 936
  helix: -0.58 (0.17), residues: 750
  sheet:  None (None), residues: 0
  loop : -0.55 (0.45), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 228 
 TYR   0.011   0.001   TYR A 459 
 PHE   0.017   0.001   PHE B 233 
 TRP   0.016   0.002   TRP A 411 
 HIS   0.002   0.001   HIS B 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 7324)
  covalent geometry    : angle       0.59639 (10022)
  hydrogen bonds       : bond        0.04468 (  510)
  hydrogen bonds       : angle       4.93072 ( 1518)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 0.253 
Fit side-chains
REVERT: B  349 MET cc_start: 0.8890 (mtp) cc_final: 0.8625 (mtm)
  outliers start: 3
  outliers final: 1
  residues processed: 90
  average time/residue: 0.7268
  time to fit residues: 68.3386
Evaluate side-chains
  75 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 74
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  437 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 89 optimal weight:    0.0870
   chunk 45 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 85 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 15 optimal weight:    5.9990
   chunk 91 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 78 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.5964

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.106821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.093532 restraints weight = 8605.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 1.20
r_work: 0.2848 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.2754 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7324  Z= 0.179
  Angle     :  0.624   9.612  10022  Z= 0.311
  Chirality :  0.045   0.150   1178
  Planarity :  0.005   0.037   1204
  Dihedral  :  5.044  25.067    980
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  9.78 %
    Favored  : 89.53 %
  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 are not related in a simple way.
  whole:  0.41 (0.27), residues: 936
  helix:  0.50 (0.18), residues: 750
  sheet:  None (None), residues: 0
  loop : -0.18 (0.48), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 228 
 TYR   0.016   0.002   TYR A 459 
 PHE   0.024   0.002   PHE A 265 
 TRP   0.016   0.002   TRP A 411 
 HIS   0.003   0.001   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 7324)
  covalent geometry    : angle       0.62443 (10022)
  hydrogen bonds       : bond        0.04873 (  510)
  hydrogen bonds       : angle       4.70210 ( 1518)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.278 
Fit side-chains
REVERT: B  337 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7338 (mtpp)
REVERT: B  346 MET cc_start: 0.8496 (mtp) cc_final: 0.8258 (mtp)
REVERT: B  349 MET cc_start: 0.8847 (mtp) cc_final: 0.8604 (mtm)
  outliers start: 5
  outliers final: 3
  residues processed: 81
  average time/residue: 0.7791
  time to fit residues: 65.8531
Evaluate side-chains
  82 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  337 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 90 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 86 optimal weight:    3.9990
   chunk 50 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0870
   chunk 16 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.7764

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.109543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.096383 restraints weight = 8687.211|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 1.20
r_work: 0.2928 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7324  Z= 0.125
  Angle     :  0.558   9.257  10022  Z= 0.277
  Chirality :  0.042   0.144   1178
  Planarity :  0.004   0.033   1204
  Dihedral  :  4.755  22.461    980
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 10.47 %
    Favored  : 88.71 %
  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 are not related in a simple way.
  whole:  1.22 (0.27), residues: 936
  helix:  1.09 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -0.01 (0.47), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 228 
 TYR   0.011   0.001   TYR A 421 
 PHE   0.021   0.002   PHE A 233 
 TRP   0.017   0.001   TRP B 411 
 HIS   0.002   0.001   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 7324)
  covalent geometry    : angle       0.55791 (10022)
  hydrogen bonds       : bond        0.04016 (  510)
  hydrogen bonds       : angle       4.44199 ( 1518)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  337 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7330 (mtpp)
REVERT: A  345 LYS cc_start: 0.7214 (mmpt) cc_final: 0.6669 (tttp)
REVERT: B  320 LEU cc_start: 0.8131 (mt) cc_final: 0.7724 (tp)
REVERT: B  337 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7364 (mtpp)
REVERT: B  349 MET cc_start: 0.8820 (mtp) cc_final: 0.8619 (mtm)
  outliers start: 6
  outliers final: 1
  residues processed: 88
  average time/residue: 0.7310
  time to fit residues: 67.0631
Evaluate side-chains
  79 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 LYS
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  337 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.108377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.095169 restraints weight = 8628.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 1.19
r_work: 0.2989 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7324  Z= 0.145
  Angle     :  0.579   9.001  10022  Z= 0.288
  Chirality :  0.043   0.161   1178
  Planarity :  0.004   0.032   1204
  Dihedral  :  4.810  23.263    980
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 11.02 %
    Favored  : 87.74 %
  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 are not related in a simple way.
  whole:  1.51 (0.27), residues: 936
  helix:  1.28 (0.19), residues: 750
  sheet:  None (None), residues: 0
  loop :  0.19 (0.48), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 228 
 TYR   0.013   0.001   TYR A 459 
 PHE   0.022   0.002   PHE B 265 
 TRP   0.017   0.002   TRP A 411 
 HIS   0.002   0.001   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 7324)
  covalent geometry    : angle       0.57911 (10022)
  hydrogen bonds       : bond        0.04248 (  510)
  hydrogen bonds       : angle       4.41764 ( 1518)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  337 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7468 (mtpp)
REVERT: A  345 LYS cc_start: 0.7335 (mmpt) cc_final: 0.6803 (tttp)
REVERT: B  337 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7476 (mtpp)
  outliers start: 9
  outliers final: 3
  residues processed: 85
  average time/residue: 0.7366
  time to fit residues: 65.4206
Evaluate side-chains
  80 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  337 LYS
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  337 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 76 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 93 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 77 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.116653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.104015 restraints weight = 8433.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 1.18
r_work: 0.2914 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.2823 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7324  Z= 0.133
  Angle     :  0.566   9.548  10022  Z= 0.281
  Chirality :  0.042   0.157   1178
  Planarity :  0.004   0.031   1204
  Dihedral  :  4.735  22.502    980
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 11.29 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.28), residues: 936
  helix:  1.44 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop :  0.21 (0.47), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 228 
 TYR   0.012   0.001   TYR A 421 
 PHE   0.021   0.002   PHE B 233 
 TRP   0.017   0.002   TRP A 411 
 HIS   0.002   0.001   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7324)
  covalent geometry    : angle       0.56644 (10022)
  hydrogen bonds       : bond        0.04059 (  510)
  hydrogen bonds       : angle       4.36188 ( 1518)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  261 MET cc_start: 0.9027 (mmt) cc_final: 0.8363 (mmt)
REVERT: A  320 LEU cc_start: 0.8128 (mt) cc_final: 0.7695 (tp)
REVERT: A  337 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7458 (mmmm)
REVERT: A  342 LYS cc_start: 0.8023 (mtmt) cc_final: 0.7392 (mmpt)
REVERT: A  345 LYS cc_start: 0.7362 (mmpt) cc_final: 0.6766 (tttp)
REVERT: B  261 MET cc_start: 0.9019 (mmt) cc_final: 0.8400 (mmt)
REVERT: B  320 LEU cc_start: 0.8129 (mt) cc_final: 0.7702 (tp)
REVERT: B  337 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7415 (mmmm)
  outliers start: 8
  outliers final: 6
  residues processed: 82
  average time/residue: 0.7599
  time to fit residues: 65.0738
Evaluate side-chains
  82 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  337 LYS
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  337 LYS
Chi-restraints excluded: chain B residue  403 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 37 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 49 optimal weight:    0.4980
   chunk 78 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.110931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.097703 restraints weight = 8561.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 1.21
r_work: 0.2994 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.2103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7324  Z= 0.125
  Angle     :  0.554   9.345  10022  Z= 0.275
  Chirality :  0.042   0.152   1178
  Planarity :  0.004   0.031   1204
  Dihedral  :  4.660  22.020    980
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 11.16 %
    Favored  : 87.47 %
  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 are not related in a simple way.
  whole:  1.88 (0.28), residues: 936
  helix:  1.55 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop :  0.27 (0.47), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 191 
 TYR   0.011   0.001   TYR B 421 
 PHE   0.020   0.002   PHE B 233 
 TRP   0.018   0.002   TRP A 411 
 HIS   0.002   0.001   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 7324)
  covalent geometry    : angle       0.55444 (10022)
  hydrogen bonds       : bond        0.03926 (  510)
  hydrogen bonds       : angle       4.28130 ( 1518)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.261 
Fit side-chains
REVERT: A  215 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7455 (tm-30)
REVERT: A  320 LEU cc_start: 0.8078 (mt) cc_final: 0.7677 (tp)
REVERT: A  337 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7500 (mmmm)
REVERT: A  342 LYS cc_start: 0.8058 (mtmt) cc_final: 0.7458 (mmpt)
REVERT: A  345 LYS cc_start: 0.7365 (mmpt) cc_final: 0.6842 (tttp)
REVERT: B  215 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7404 (tm-30)
REVERT: B  320 LEU cc_start: 0.8076 (mt) cc_final: 0.7683 (tp)
REVERT: B  337 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7486 (mmmm)
REVERT: B  342 LYS cc_start: 0.8042 (mtmt) cc_final: 0.7436 (mmpt)
  outliers start: 10
  outliers final: 6
  residues processed: 86
  average time/residue: 0.7247
  time to fit residues: 65.1029
Evaluate side-chains
  86 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  337 LYS
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  337 LYS
Chi-restraints excluded: chain B residue  403 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.115647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.102891 restraints weight = 8453.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 1.17
r_work: 0.2908 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.2023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7324  Z= 0.156
  Angle     :  0.590  10.070  10022  Z= 0.293
  Chirality :  0.044   0.164   1178
  Planarity :  0.004   0.030   1204
  Dihedral  :  4.845  23.775    980
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 11.02 %
    Favored  : 87.74 %
  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 are not related in a simple way.
  whole:  1.76 (0.28), residues: 936
  helix:  1.44 (0.19), residues: 750
  sheet:  None (None), residues: 0
  loop :  0.31 (0.48), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 228 
 TYR   0.014   0.002   TYR A 459 
 PHE   0.021   0.002   PHE B 233 
 TRP   0.016   0.002   TRP A 411 
 HIS   0.003   0.001   HIS B 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 7324)
  covalent geometry    : angle       0.58996 (10022)
  hydrogen bonds       : bond        0.04336 (  510)
  hydrogen bonds       : angle       4.39240 ( 1518)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  337 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7520 (mmmm)
REVERT: A  342 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7376 (mmpt)
REVERT: A  345 LYS cc_start: 0.7440 (mmpt) cc_final: 0.6802 (mtmp)
REVERT: B  320 LEU cc_start: 0.8163 (mt) cc_final: 0.7759 (tp)
REVERT: B  337 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7507 (mmmm)
REVERT: B  342 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7379 (mmpt)
  outliers start: 9
  outliers final: 4
  residues processed: 83
  average time/residue: 0.7524
  time to fit residues: 65.1849
Evaluate side-chains
  84 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 LEU
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  337 LYS
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  337 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 73 optimal weight:    0.3980
   chunk 43 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0060
   chunk 62 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
B 135 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.111635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.098408 restraints weight = 8536.157|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 1.21
r_work: 0.3019 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 2.82 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7324  Z= 0.120
  Angle     :  0.550   9.481  10022  Z= 0.272
  Chirality :  0.041   0.150   1178
  Planarity :  0.004   0.028   1204
  Dihedral  :  4.625  21.599    980
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.50 %
    Favored  : 98.50 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 11.16 %
    Favored  : 87.74 %
  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 are not related in a simple way.
  whole:  1.92 (0.28), residues: 936
  helix:  1.58 (0.19), residues: 750
  sheet:  None (None), residues: 0
  loop :  0.23 (0.47), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 228 
 TYR   0.011   0.001   TYR B 421 
 PHE   0.020   0.002   PHE B 233 
 TRP   0.018   0.001   TRP A 411 
 HIS   0.002   0.001   HIS B 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 7324)
  covalent geometry    : angle       0.55002 (10022)
  hydrogen bonds       : bond        0.03837 (  510)
  hydrogen bonds       : angle       4.26768 ( 1518)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A  215 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7368 (tm-30)
REVERT: A  320 LEU cc_start: 0.8091 (mt) cc_final: 0.7707 (tp)
REVERT: A  337 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7535 (mmmm)
REVERT: A  342 LYS cc_start: 0.8002 (mtmt) cc_final: 0.7402 (mmpt)
REVERT: A  345 LYS cc_start: 0.7363 (mmpt) cc_final: 0.6769 (mtmp)
REVERT: B  320 LEU cc_start: 0.8099 (mt) cc_final: 0.7723 (tp)
REVERT: B  337 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7536 (mmmm)
REVERT: B  342 LYS cc_start: 0.8045 (mtmt) cc_final: 0.7457 (mmpt)
REVERT: B  345 LYS cc_start: 0.7376 (mmpt) cc_final: 0.6839 (mtmp)
  outliers start: 8
  outliers final: 5
  residues processed: 90
  average time/residue: 0.7156
  time to fit residues: 67.3815
Evaluate side-chains
  90 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  337 LYS
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  337 LYS
Chi-restraints excluded: chain B residue  403 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 53 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 87 optimal weight:    0.8980
   chunk 90 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 86 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 55 optimal weight:    0.0020
   chunk 65 optimal weight:    5.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
B 135 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.113051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.099939 restraints weight = 7802.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 1.15
r_work: 0.2995 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7324  Z= 0.113
  Angle     :  0.540   9.155  10022  Z= 0.267
  Chirality :  0.041   0.148   1178
  Planarity :  0.004   0.028   1204
  Dihedral  :  4.528  20.782    980
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 11.29 %
    Favored  : 87.74 %
  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 are not related in a simple way.
  whole:  2.07 (0.28), residues: 936
  helix:  1.68 (0.19), residues: 750
  sheet:  None (None), residues: 0
  loop :  0.30 (0.47), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 191 
 TYR   0.011   0.001   TYR A 421 
 PHE   0.019   0.001   PHE B 233 
 TRP   0.019   0.001   TRP A 411 
 HIS   0.002   0.001   HIS B 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 7324)
  covalent geometry    : angle       0.54039 (10022)
  hydrogen bonds       : bond        0.03678 (  510)
  hydrogen bonds       : angle       4.17378 ( 1518)

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

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

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1872 Ramachandran restraints generated.
    936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  215 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7286 (tm-30)
REVERT: A  262 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7277 (tt)
REVERT: A  320 LEU cc_start: 0.7974 (mt) cc_final: 0.7629 (tp)
REVERT: A  337 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7514 (mmmm)
REVERT: A  342 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7277 (mmpt)
REVERT: A  345 LYS cc_start: 0.7335 (mmpt) cc_final: 0.6757 (mtmp)
REVERT: A  346 MET cc_start: 0.8316 (mtp) cc_final: 0.8112 (mtt)
REVERT: B  215 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7310 (tm-30)
REVERT: B  320 LEU cc_start: 0.7975 (mt) cc_final: 0.7630 (tp)
REVERT: B  337 LYS cc_start: 0.7733 (ttpp) cc_final: 0.7459 (mmmm)
REVERT: B  342 LYS cc_start: 0.7944 (mtmt) cc_final: 0.7329 (mmpt)
REVERT: B  345 LYS cc_start: 0.7372 (mmpt) cc_final: 0.6841 (tttp)
  outliers start: 7
  outliers final: 3
  residues processed: 90
  average time/residue: 0.7174
  time to fit residues: 67.5272
Evaluate side-chains
  90 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  337 LYS
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain B residue  403 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0980
   chunk 90 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 93 optimal weight:    5.9990
   chunk 13 optimal weight:    0.5980
   chunk 52 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 135 GLN
B 135 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.109437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.096073 restraints weight = 7956.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 1.17
r_work: 0.2957 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2864 rms_B_bonded: 2.78 restraints_weight: 0.2500
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7324  Z= 0.130
  Angle     :  0.567   9.422  10022  Z= 0.279
  Chirality :  0.042   0.163   1178
  Planarity :  0.004   0.029   1204
  Dihedral  :  4.636  22.084    980
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 11.57 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.05 (0.28), residues: 936
  helix:  1.65 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop :  0.42 (0.47), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 191 
 TYR   0.012   0.001   TYR A 459 
 PHE   0.020   0.002   PHE B 233 
 TRP   0.018   0.002   TRP A 411 
 HIS   0.002   0.001   HIS B 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7324)
  covalent geometry    : angle       0.56696 (10022)
  hydrogen bonds       : bond        0.03966 (  510)
  hydrogen bonds       : angle       4.23814 ( 1518)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2408.07 seconds
wall clock time: 41 minutes 47.89 seconds (2507.89 seconds total)