Starting phenix.real_space_refine
on Fri Aug 22 17:53:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jf0_36205/08_2025/8jf0_36205.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jf0_36205/08_2025/8jf0_36205.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jf0_36205/08_2025/8jf0_36205.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jf0_36205/08_2025/8jf0_36205.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jf0_36205/08_2025/8jf0_36205.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jf0_36205/08_2025/8jf0_36205.map"
  }
  resolution = 3.5
  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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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    4304      2.51       5
     N    1064      2.21       5
     O    1160      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 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: 6578
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3289
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 436, 3289
          Classifications: {'peptide': 436}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 412}
          Chain breaks: 3
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.45, per 1000 atoms: 0.37
  Number of scatterers: 6578
  At special positions: 0
  Unit cell: (83.0003, 98.4936, 77.4669, 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    1160      8.00
     N    1064      7.00
     C    4304      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: 0.56
  Conformation dependent library (CDL) restraints added in 383.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1568

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 0 sheets defined
      74.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 59
      removed outlier: 3.645A  pdb=" N   GLY A  58 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 70
      removed outlier: 3.792A  pdb=" N   PHE A  64 " --> pdb=" O   ILE A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 100
      removed outlier: 4.073A  pdb=" N   VAL A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   THR A  85 " --> pdb=" O   GLN A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 122
      removed outlier: 3.534A  pdb=" N   ALA A 120 " --> pdb=" O   VAL A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 136
    Processing helix  chain 'A' and resid 145 through 174
      Proline residue:  A 151  - end of helix
      removed outlier: 3.827A  pdb=" N   GLU A 155 " --> pdb=" O   PRO A 151 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL A 166 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLU A 167 " --> pdb=" O   SER A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 183
      removed outlier: 3.809A  pdb=" N   ALA A 178 " --> pdb=" O   GLY A 174 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU A 180 " --> pdb=" O   PRO A 176 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   ASN A 181 " --> pdb=" O   GLY A 177 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   TYR A 182 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 199
      removed outlier: 3.705A  pdb=" N   THR A 189 " --> pdb=" O   PRO A 185 " (cutoff:3.500A)
      Proline residue:  A 190  - end of helix
      removed outlier: 3.608A  pdb=" N   GLY A 196 " --> pdb=" O   VAL A 192 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   VAL A 199 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 209
    Processing helix  chain 'A' and resid 210 through 226
      removed outlier: 3.738A  pdb=" N   CYS A 216 " --> pdb=" O   GLY A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 274
    Processing helix  chain 'A' and resid 317 through 345
      removed outlier: 3.962A  pdb=" N   ALA A 327 " --> pdb=" O   GLY A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 374
    Processing helix  chain 'A' and resid 396 through 413
      removed outlier: 3.643A  pdb=" N   THR A 412 " --> pdb=" O   LEU A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 421
      removed outlier: 3.553A  pdb=" N   THR A 417 " --> pdb=" O   ILE A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 444
      removed outlier: 3.921A  pdb=" N   CYS A 433 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   THR A 434 " --> pdb=" O   GLY A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 478
      removed outlier: 3.840A  pdb=" N   PHE A 459 " --> pdb=" O   SER A 455 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   SER A 464 " --> pdb=" O   VAL A 460 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   MET A 465 " --> pdb=" O   LEU A 461 " (cutoff:3.500A)
      Proline residue:  A 472  - end of helix
    Processing helix  chain 'A' and resid 479 through 482
      removed outlier: 3.994A  pdb=" N   ILE A 482 " --> pdb=" O   PRO A 479 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 479 through 482'
    Processing helix  chain 'A' and resid 486 through 498
    Processing helix  chain 'A' and resid 499 through 515
    Processing helix  chain 'A' and resid 518 through 523
    Processing helix  chain 'B' and resid 46 through 59
      removed outlier: 3.645A  pdb=" N   GLY B  58 " --> pdb=" O   THR B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 70
      removed outlier: 3.792A  pdb=" N   PHE B  64 " --> pdb=" O   ILE B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 100
      removed outlier: 4.073A  pdb=" N   VAL B  79 " --> pdb=" O   ASP B  75 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   THR B  85 " --> pdb=" O   GLN B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 122
      removed outlier: 3.534A  pdb=" N   ALA B 120 " --> pdb=" O   VAL B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 136
    Processing helix  chain 'B' and resid 145 through 174
      Proline residue:  B 151  - end of helix
      removed outlier: 3.827A  pdb=" N   GLU B 155 " --> pdb=" O   PRO B 151 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   VAL B 166 " --> pdb=" O   VAL B 162 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLU B 167 " --> pdb=" O   SER B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 183
      removed outlier: 3.809A  pdb=" N   ALA B 178 " --> pdb=" O   GLY B 174 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU B 180 " --> pdb=" O   PRO B 176 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   ASN B 181 " --> pdb=" O   GLY B 177 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   TYR B 182 " --> pdb=" O   ALA B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 184 through 199
      removed outlier: 3.705A  pdb=" N   THR B 189 " --> pdb=" O   PRO B 185 " (cutoff:3.500A)
      Proline residue:  B 190  - end of helix
      removed outlier: 3.608A  pdb=" N   GLY B 196 " --> pdb=" O   VAL B 192 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   VAL B 199 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 209
    Processing helix  chain 'B' and resid 210 through 226
      removed outlier: 3.738A  pdb=" N   CYS B 216 " --> pdb=" O   GLY B 212 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 274
    Processing helix  chain 'B' and resid 317 through 345
      removed outlier: 3.962A  pdb=" N   ALA B 327 " --> pdb=" O   GLY B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 374
    Processing helix  chain 'B' and resid 396 through 413
      removed outlier: 3.643A  pdb=" N   THR B 412 " --> pdb=" O   LEU B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 413 through 421
      removed outlier: 3.553A  pdb=" N   THR B 417 " --> pdb=" O   ILE B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 424 through 444
      removed outlier: 3.921A  pdb=" N   CYS B 433 " --> pdb=" O   GLY B 429 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   THR B 434 " --> pdb=" O   GLY B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 478
      removed outlier: 3.840A  pdb=" N   PHE B 459 " --> pdb=" O   SER B 455 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   SER B 464 " --> pdb=" O   VAL B 460 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   MET B 465 " --> pdb=" O   LEU B 461 " (cutoff:3.500A)
      Proline residue:  B 472  - end of helix
    Processing helix  chain 'B' and resid 479 through 482
      removed outlier: 3.994A  pdb=" N   ILE B 482 " --> pdb=" O   PRO B 479 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 479 through 482'
    Processing helix  chain 'B' and resid 486 through 498
    Processing helix  chain 'B' and resid 499 through 515
    Processing helix  chain 'B' and resid 518 through 523

    418 hydrogen bonds defined for protein.
    1254 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: 1.06

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1112
        1.32 -     1.45: 1686
        1.45 -     1.57: 3850
        1.57 -     1.70: 4
        1.70 -     1.82: 76
  Bond restraints: 6728
  Sorted by residual:
  bond pdb=" C   ASP A 205 "
       pdb=" N   ARG A 206 "
    ideal  model  delta    sigma   weight residual
    1.335  1.404 -0.069 1.31e-02 5.83e+03 2.81e+01
  bond pdb=" C   ASP B 205 "
       pdb=" N   ARG B 206 "
    ideal  model  delta    sigma   weight residual
    1.335  1.404 -0.069 1.31e-02 5.83e+03 2.81e+01
  bond pdb=" C   ILE B 222 "
       pdb=" O   ILE B 222 "
    ideal  model  delta    sigma   weight residual
    1.237  1.295 -0.059 1.13e-02 7.83e+03 2.69e+01
  bond pdb=" C   ILE A 222 "
       pdb=" O   ILE A 222 "
    ideal  model  delta    sigma   weight residual
    1.237  1.295 -0.059 1.13e-02 7.83e+03 2.69e+01
  bond pdb=" C   ARG B 456 "
       pdb=" O   ARG B 456 "
    ideal  model  delta    sigma   weight residual
    1.236  1.285 -0.049 1.16e-02 7.43e+03 1.75e+01
  ... (remaining 6723 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 5204
        1.43 -     2.87: 2928
        2.87 -     4.30: 920
        4.30 -     5.74: 110
        5.74 -     7.17: 16
  Bond angle restraints: 9178
  Sorted by residual:
  angle pdb=" O   ASP A 205 "
        pdb=" C   ASP A 205 "
        pdb=" N   ARG A 206 "
      ideal   model   delta    sigma   weight residual
     122.07  128.06   -5.99 1.03e+00 9.43e-01 3.38e+01
  angle pdb=" O   ASP B 205 "
        pdb=" C   ASP B 205 "
        pdb=" N   ARG B 206 "
      ideal   model   delta    sigma   weight residual
     122.07  128.06   -5.99 1.03e+00 9.43e-01 3.38e+01
  angle pdb=" N   GLN B 287 "
        pdb=" CA  GLN B 287 "
        pdb=" C   GLN B 287 "
      ideal   model   delta    sigma   weight residual
     114.04  107.87    6.17 1.24e+00 6.50e-01 2.47e+01
  angle pdb=" N   GLN A 287 "
        pdb=" CA  GLN A 287 "
        pdb=" C   GLN A 287 "
      ideal   model   delta    sigma   weight residual
     114.04  107.87    6.17 1.24e+00 6.50e-01 2.47e+01
  angle pdb=" CA  PHE A 200 "
        pdb=" CB  PHE A 200 "
        pdb=" CG  PHE A 200 "
      ideal   model   delta    sigma   weight residual
     113.80  118.63   -4.83 1.00e+00 1.00e+00 2.34e+01
  ... (remaining 9173 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    14.06: 3598
       14.06 -    28.12: 220
       28.12 -    42.17: 44
       42.17 -    56.23: 20
       56.23 -    70.29: 24
  Dihedral angle restraints: 3906
    sinusoidal: 1452
      harmonic: 2454
  Sorted by residual:
  dihedral pdb=" N   LYS A 128 "
           pdb=" CA  LYS A 128 "
           pdb=" CB  LYS A 128 "
           pdb=" CG  LYS A 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.07  -58.93     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" N   LYS B 128 "
           pdb=" CA  LYS B 128 "
           pdb=" CB  LYS B 128 "
           pdb=" CG  LYS B 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.07  -58.93     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" CA  ILE B 369 "
           pdb=" CB  ILE B 369 "
           pdb=" CG1 ILE B 369 "
           pdb=" CD1 ILE B 369 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.31   57.69     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 3903 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 544
       0.050 -    0.100: 350
       0.100 -    0.150: 152
       0.150 -    0.200: 58
       0.200 -    0.250: 6
  Chirality restraints: 1110
  Sorted by residual:
  chirality pdb=" CA  VAL A 450 "
            pdb=" N   VAL A 450 "
            pdb=" C   VAL A 450 "
            pdb=" CB  VAL A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.69   -0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" CA  VAL B 450 "
            pdb=" N   VAL B 450 "
            pdb=" C   VAL B 450 "
            pdb=" CB  VAL B 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.69   -0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" CA  PRO B 151 "
            pdb=" N   PRO B 151 "
            pdb=" C   PRO B 151 "
            pdb=" CB  PRO B 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 1107 not shown)

  Planarity restraints: 1140
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 466 "   -0.035 2.00e-02 2.50e+03   2.82e-02 1.39e+01
        pdb=" CG  PHE B 466 "    0.007 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 466 "    0.051 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 466 "    0.024 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 466 "   -0.032 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 466 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 466 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 466 "    0.035 2.00e-02 2.50e+03   2.82e-02 1.39e+01
        pdb=" CG  PHE A 466 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 466 "   -0.051 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 466 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 466 "    0.032 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 466 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 466 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 340 "    0.039 2.00e-02 2.50e+03   2.10e-02 8.82e+00
        pdb=" CG  TYR A 340 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 340 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 340 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 340 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 340 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 340 "    0.023 2.00e-02 2.50e+03
        pdb=" OH  TYR A 340 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1137 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 488
        2.77 -     3.30: 7642
        3.30 -     3.83: 11118
        3.83 -     4.37: 14817
        4.37 -     4.90: 23097
  Nonbonded interactions: 57162
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 325 "
            pdb=" OG1 THR A 328 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   PHE B 325 "
            pdb=" OG1 THR B 328 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OH  TYR A 340 "
            pdb=" NH1 ARG A 344 "
     model   vdw
     2.338 3.120
  nonbonded pdb=" OH  TYR B 340 "
            pdb=" NH1 ARG B 344 "
     model   vdw
     2.338 3.120
  nonbonded pdb=" O   VAL A 460 "
            pdb=" OG  SER A 464 "
     model   vdw
     2.378 3.040
  ... (remaining 57157 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 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:             0.070
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.770
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
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      :  0.015   0.082   6728  Z= 1.134
  Angle     :  1.804   7.172   9178  Z= 1.397
  Chirality :  0.077   0.250   1110
  Planarity :  0.010   0.094   1140
  Dihedral  : 12.099  70.286   2338
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  4.79 %
    Favored  : 94.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -2.70 (0.25), residues: 856
  helix: -1.51 (0.18), residues: 572
  sheet:  None (None), residues: 0
  loop : -2.08 (0.35), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.032   0.004   ARG A 154 
 TYR   0.039   0.007   TYR A 340 
 PHE   0.051   0.006   PHE A 466 
 TRP   0.030   0.007   TRP B 127 
 HIS   0.011   0.004   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.01520 ( 6728)
  covalent geometry    : angle       1.80408 ( 9178)
  hydrogen bonds       : bond        0.23971 (  418)
  hydrogen bonds       : angle       7.70625 ( 1254)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 258
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 HIS cc_start: 0.8949 (t-90) cc_final: 0.8545 (t70)
REVERT: A  186 LEU cc_start: 0.8793 (mt) cc_final: 0.8419 (mp)
REVERT: A  199 VAL cc_start: 0.9173 (t) cc_final: 0.8908 (p)
REVERT: A  295 ASP cc_start: 0.8215 (t70) cc_final: 0.7564 (t0)
REVERT: A  363 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8331 (mm-30)
REVERT: A  451 ASP cc_start: 0.8389 (t70) cc_final: 0.8180 (t0)
REVERT: B   77 HIS cc_start: 0.8949 (t-90) cc_final: 0.8546 (t70)
REVERT: B  186 LEU cc_start: 0.8793 (mt) cc_final: 0.8419 (mp)
REVERT: B  199 VAL cc_start: 0.9172 (t) cc_final: 0.8907 (p)
REVERT: B  295 ASP cc_start: 0.8212 (t70) cc_final: 0.7561 (t0)
REVERT: B  363 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8330 (mm-30)
REVERT: B  451 ASP cc_start: 0.8391 (t70) cc_final: 0.8182 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 260
  average time/residue: 0.0752
  time to fit residues: 26.7367
Evaluate side-chains
  174 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:   20.0000
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:   20.0000
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
A  77 HIS
A 147 HIS
B  50 GLN
B  77 HIS
B 147 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.129882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.103747 restraints weight = 15591.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.107321 restraints weight = 8890.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.109639 restraints weight = 6281.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.111046 restraints weight = 5015.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.112119 restraints weight = 4360.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.4130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6728  Z= 0.198
  Angle     :  0.750   8.761   9178  Z= 0.383
  Chirality :  0.046   0.173   1110
  Planarity :  0.005   0.027   1140
  Dihedral  :  3.872  12.965    916
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 13.80 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -0.16 (0.27), residues: 856
  helix:  0.31 (0.19), residues: 622
  sheet:  None (None), residues: 0
  loop : -0.98 (0.40), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 522 
 TYR   0.018   0.002   TYR B 340 
 PHE   0.012   0.002   PHE B 432 
 TRP   0.011   0.001   TRP B 149 
 HIS   0.009   0.002   HIS B 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 6728)
  covalent geometry    : angle       0.74957 ( 9178)
  hydrogen bonds       : bond        0.06307 (  418)
  hydrogen bonds       : angle       5.08143 ( 1254)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 174
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6634 (mm-30)
REVERT: A  255 PHE cc_start: 0.6472 (t80) cc_final: 0.6149 (m-80)
REVERT: A  407 MET cc_start: 0.8610 (mmm) cc_final: 0.8331 (mmm)
REVERT: B  155 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6635 (mm-30)
REVERT: B  255 PHE cc_start: 0.6466 (t80) cc_final: 0.6149 (m-80)
REVERT: B  407 MET cc_start: 0.8612 (mmm) cc_final: 0.8333 (mmm)
  outliers start: 24
  outliers final: 10
  residues processed: 182
  average time/residue: 0.0712
  time to fit residues: 18.0957
Evaluate side-chains
  154 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 142
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  425 ASP
Chi-restraints excluded: chain B residue  493 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 43 optimal weight:   20.0000
   chunk 53 optimal weight:    0.7980
   chunk 27 optimal weight:    8.9990
   chunk 68 optimal weight:    0.9990
   chunk 32 optimal weight:   10.0000
   chunk 45 optimal weight:    9.9990
   chunk 80 optimal weight:    3.9990
   chunk 64 optimal weight:   30.0000
   chunk 1 optimal weight:    8.9990
   chunk 66 optimal weight:    8.9990
   chunk 8 optimal weight:    0.0270
   overall best weight:    2.9644

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

Flipped N/Q/H residues before XYZ refinement:
A 147 HIS
A 473 ASN
B 147 HIS
B 473 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.130014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.103408 restraints weight = 15466.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.106782 restraints weight = 9206.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.109097 restraints weight = 6574.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.110675 restraints weight = 5274.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.111375 restraints weight = 4547.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.4965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6728  Z= 0.161
  Angle     :  0.671   7.306   9178  Z= 0.338
  Chirality :  0.044   0.144   1110
  Planarity :  0.004   0.033   1140
  Dihedral  :  3.755  11.897    916
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 17.18 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  0.86 (0.28), residues: 856
  helix:  1.01 (0.20), residues: 622
  sheet:  None (None), residues: 0
  loop : -0.44 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 126 
 TYR   0.013   0.002   TYR B 340 
 PHE   0.011   0.001   PHE B 466 
 TRP   0.011   0.001   TRP B 149 
 HIS   0.008   0.001   HIS A 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6728)
  covalent geometry    : angle       0.67145 ( 9178)
  hydrogen bonds       : bond        0.05716 (  418)
  hydrogen bonds       : angle       4.55854 ( 1254)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 164
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7704 (mp10)
REVERT: A  155 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6654 (mm-30)
REVERT: A  255 PHE cc_start: 0.6190 (t80) cc_final: 0.5945 (m-80)
REVERT: A  293 ARG cc_start: 0.5695 (mtm180) cc_final: 0.5426 (mtm180)
REVERT: A  451 ASP cc_start: 0.8208 (t70) cc_final: 0.7990 (t0)
REVERT: B   81 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7702 (mp10)
REVERT: B  155 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6653 (mm-30)
REVERT: B  255 PHE cc_start: 0.6182 (t80) cc_final: 0.5945 (m-80)
REVERT: B  293 ARG cc_start: 0.5696 (mtm180) cc_final: 0.5427 (mtm180)
REVERT: B  451 ASP cc_start: 0.8207 (t70) cc_final: 0.7991 (t0)
  outliers start: 38
  outliers final: 20
  residues processed: 180
  average time/residue: 0.0700
  time to fit residues: 17.7715
Evaluate side-chains
  158 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 134
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 TYR
Chi-restraints excluded: chain A residue   56 PHE
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain B residue   52 TYR
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  425 ASP
Chi-restraints excluded: chain B residue  493 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 35 optimal weight:    9.9990
   chunk 34 optimal weight:    2.9990
   chunk 55 optimal weight:    9.9990
   chunk 73 optimal weight:   40.0000
   chunk 61 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0970
   chunk 78 optimal weight:    0.9980
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
A 147 HIS
B 147 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.131872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.104987 restraints weight = 15437.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.108395 restraints weight = 9282.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.110754 restraints weight = 6681.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.112298 restraints weight = 5383.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.113438 restraints weight = 4656.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.5400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6728  Z= 0.134
  Angle     :  0.641   7.862   9178  Z= 0.318
  Chirality :  0.042   0.133   1110
  Planarity :  0.004   0.034   1140
  Dihedral  :  3.644  12.118    916
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 15.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 19.72 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.44 (0.28), residues: 856
  helix:  1.42 (0.20), residues: 622
  sheet:  None (None), residues: 0
  loop : -0.16 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 206 
 TYR   0.012   0.001   TYR B 340 
 PHE   0.009   0.001   PHE A 466 
 TRP   0.009   0.001   TRP B 149 
 HIS   0.007   0.001   HIS A 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6728)
  covalent geometry    : angle       0.64136 ( 9178)
  hydrogen bonds       : bond        0.04906 (  418)
  hydrogen bonds       : angle       4.27354 ( 1254)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 154
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  254 MET cc_start: 0.5057 (ttp) cc_final: 0.4824 (tpp)
REVERT: A  255 PHE cc_start: 0.6179 (t80) cc_final: 0.5881 (m-80)
REVERT: A  407 MET cc_start: 0.8422 (mmm) cc_final: 0.8099 (mmm)
REVERT: A  408 LEU cc_start: 0.9171 (pp) cc_final: 0.8936 (pp)
REVERT: B  254 MET cc_start: 0.5054 (ttp) cc_final: 0.4819 (tpp)
REVERT: B  255 PHE cc_start: 0.6173 (t80) cc_final: 0.5879 (m-80)
REVERT: B  407 MET cc_start: 0.8419 (mmm) cc_final: 0.8096 (mmm)
REVERT: B  408 LEU cc_start: 0.9169 (pp) cc_final: 0.8934 (pp)
  outliers start: 26
  outliers final: 16
  residues processed: 166
  average time/residue: 0.0590
  time to fit residues: 14.5029
Evaluate side-chains
  156 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 TYR
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue   89 CYS
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  147 HIS
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain B residue   52 TYR
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue   89 CYS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  147 HIS
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  425 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 30 optimal weight:   40.0000
   chunk 55 optimal weight:   10.0000
   chunk 75 optimal weight:    0.0370
   chunk 80 optimal weight:    9.9990
   chunk 52 optimal weight:    2.9990
   chunk 73 optimal weight:   40.0000
   chunk 6 optimal weight:    7.9990
   chunk 49 optimal weight:    7.9990
   chunk 81 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 8 optimal weight:   20.0000
   overall best weight:    3.1864

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

Flipped N/Q/H residues before XYZ refinement:
A 147 HIS
B 147 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.129301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.102044 restraints weight = 15855.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.105412 restraints weight = 9422.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.107641 restraints weight = 6772.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.109097 restraints weight = 5490.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.109816 restraints weight = 4785.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.5663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6728  Z= 0.154
  Angle     :  0.646   6.675   9178  Z= 0.320
  Chirality :  0.044   0.194   1110
  Planarity :  0.004   0.033   1140
  Dihedral  :  3.642  13.929    916
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 21.41 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.38 (0.28), residues: 856
  helix:  1.37 (0.20), residues: 624
  sheet:  None (None), residues: 0
  loop : -0.18 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 522 
 TYR   0.011   0.002   TYR B 340 
 PHE   0.013   0.001   PHE A 420 
 TRP   0.010   0.001   TRP A 149 
 HIS   0.013   0.002   HIS B 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6728)
  covalent geometry    : angle       0.64623 ( 9178)
  hydrogen bonds       : bond        0.05142 (  418)
  hydrogen bonds       : angle       4.28544 ( 1254)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6825 (mm-30)
REVERT: A  254 MET cc_start: 0.5189 (ttp) cc_final: 0.4905 (tpp)
REVERT: A  258 MET cc_start: 0.7111 (mtm) cc_final: 0.5731 (mtm)
REVERT: A  407 MET cc_start: 0.8587 (mmm) cc_final: 0.8095 (mmm)
REVERT: A  408 LEU cc_start: 0.9219 (pp) cc_final: 0.8998 (pp)
REVERT: B  155 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6827 (mm-30)
REVERT: B  254 MET cc_start: 0.5183 (ttp) cc_final: 0.4893 (tpp)
REVERT: B  258 MET cc_start: 0.7120 (mtm) cc_final: 0.5744 (mtm)
REVERT: B  407 MET cc_start: 0.8592 (mmm) cc_final: 0.8096 (mmm)
REVERT: B  408 LEU cc_start: 0.9218 (pp) cc_final: 0.8997 (pp)
  outliers start: 28
  outliers final: 18
  residues processed: 164
  average time/residue: 0.0686
  time to fit residues: 15.9676
Evaluate side-chains
  158 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 TYR
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue   89 CYS
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain B residue   52 TYR
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue   89 CYS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  425 ASP
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain B residue  493 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 1 optimal weight:    0.5980
   chunk 15 optimal weight:    9.9990
   chunk 64 optimal weight:    0.1980
   chunk 57 optimal weight:    0.5980
   chunk 58 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9990
   chunk 72 optimal weight:    6.9990
   chunk 18 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 67 optimal weight:    9.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A 147 HIS
B 147 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.132811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.105919 restraints weight = 15619.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.109385 restraints weight = 9168.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.111646 restraints weight = 6539.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.113117 restraints weight = 5274.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.113789 restraints weight = 4586.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.5975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6728  Z= 0.127
  Angle     :  0.641   7.141   9178  Z= 0.314
  Chirality :  0.042   0.134   1110
  Planarity :  0.004   0.032   1140
  Dihedral  :  3.637  13.968    916
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 18.31 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.66 (0.28), residues: 856
  helix:  1.61 (0.21), residues: 622
  sheet:  None (None), residues: 0
  loop : -0.15 (0.40), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 126 
 TYR   0.011   0.002   TYR A 339 
 PHE   0.008   0.001   PHE B 255 
 TRP   0.007   0.001   TRP B 311 
 HIS   0.012   0.002   HIS B 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6728)
  covalent geometry    : angle       0.64083 ( 9178)
  hydrogen bonds       : bond        0.04272 (  418)
  hydrogen bonds       : angle       4.09356 ( 1254)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 150
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  254 MET cc_start: 0.5536 (ttp) cc_final: 0.5274 (tpp)
REVERT: A  407 MET cc_start: 0.8467 (mmm) cc_final: 0.8160 (mmm)
REVERT: A  408 LEU cc_start: 0.9175 (pp) cc_final: 0.8947 (pp)
REVERT: B  254 MET cc_start: 0.5538 (ttp) cc_final: 0.5272 (tpp)
REVERT: B  407 MET cc_start: 0.8476 (mmm) cc_final: 0.8163 (mmm)
REVERT: B  408 LEU cc_start: 0.9174 (pp) cc_final: 0.8944 (pp)
  outliers start: 32
  outliers final: 22
  residues processed: 166
  average time/residue: 0.0612
  time to fit residues: 15.1092
Evaluate side-chains
  160 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 TYR
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue   89 CYS
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  147 HIS
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain B residue   52 TYR
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue   89 CYS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  147 HIS
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  484 THR
Chi-restraints excluded: chain B residue  493 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 63 optimal weight:    0.5980
   chunk 55 optimal weight:    8.9990
   chunk 31 optimal weight:   30.0000
   chunk 42 optimal weight:    7.9990
   chunk 51 optimal weight:   20.0000
   chunk 75 optimal weight:    9.9990
   chunk 60 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 21 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    4.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 147 HIS
A 491 GLN
B 147 HIS
** B 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.127303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.100318 restraints weight = 15693.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.103383 restraints weight = 9422.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.105633 restraints weight = 6890.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.106910 restraints weight = 5596.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.107944 restraints weight = 4923.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.6077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6728  Z= 0.187
  Angle     :  0.677   7.239   9178  Z= 0.340
  Chirality :  0.046   0.293   1110
  Planarity :  0.004   0.028   1140
  Dihedral  :  3.692  14.582    916
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 21.27 %
    Favored  : 74.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.44 (0.28), residues: 856
  helix:  1.38 (0.20), residues: 622
  sheet:  None (None), residues: 0
  loop : -0.03 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 522 
 TYR   0.011   0.002   TYR A 340 
 PHE   0.012   0.002   PHE A 200 
 TRP   0.012   0.001   TRP B 149 
 HIS   0.015   0.002   HIS B 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 6728)
  covalent geometry    : angle       0.67725 ( 9178)
  hydrogen bonds       : bond        0.05191 (  418)
  hydrogen bonds       : angle       4.22261 ( 1254)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 146
  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: A  155 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6846 (mm-30)
REVERT: A  254 MET cc_start: 0.5613 (ttp) cc_final: 0.5408 (tpp)
REVERT: A  407 MET cc_start: 0.8551 (mmm) cc_final: 0.8146 (mmm)
REVERT: A  408 LEU cc_start: 0.9240 (pp) cc_final: 0.9032 (pp)
REVERT: A  501 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8041 (ptm)
REVERT: B  155 GLU cc_start: 0.7133 (OUTLIER) cc_final: 0.6853 (mm-30)
REVERT: B  254 MET cc_start: 0.5615 (ttp) cc_final: 0.5403 (tpp)
REVERT: B  407 MET cc_start: 0.8541 (mmm) cc_final: 0.8141 (mmm)
REVERT: B  408 LEU cc_start: 0.9238 (pp) cc_final: 0.9033 (pp)
REVERT: B  501 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8035 (ptm)
  outliers start: 31
  outliers final: 21
  residues processed: 165
  average time/residue: 0.0582
  time to fit residues: 14.2559
Evaluate side-chains
  185 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 160
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 TYR
Chi-restraints excluded: chain A residue   56 PHE
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue   89 CYS
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  484 THR
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  501 MET
Chi-restraints excluded: chain B residue   52 TYR
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue   89 CYS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  425 ASP
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  501 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 20 optimal weight:   10.0000
   chunk 18 optimal weight:    6.9990
   chunk 10 optimal weight:    0.4980
   chunk 15 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 44 optimal weight:    0.0980
   chunk 71 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 77 optimal weight:    6.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 147 HIS
B 147 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.129557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.102427 restraints weight = 15905.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.105636 restraints weight = 9591.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.107930 restraints weight = 6959.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.109131 restraints weight = 5632.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.110199 restraints weight = 4956.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.6306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6728  Z= 0.140
  Angle     :  0.698  13.541   9178  Z= 0.336
  Chirality :  0.044   0.315   1110
  Planarity :  0.004   0.028   1140
  Dihedral  :  3.663  13.582    916
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 22.82 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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 (0.29), residues: 856
  helix:  1.37 (0.21), residues: 622
  sheet:  None (None), residues: 0
  loop :  0.08 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 152 
 TYR   0.017   0.002   TYR A 136 
 PHE   0.009   0.001   PHE A 502 
 TRP   0.006   0.001   TRP B 311 
 HIS   0.013   0.002   HIS B 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6728)
  covalent geometry    : angle       0.69766 ( 9178)
  hydrogen bonds       : bond        0.04679 (  418)
  hydrogen bonds       : angle       4.11258 ( 1254)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 166
  time to evaluate  : 0.252 
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: A  254 MET cc_start: 0.5620 (ttp) cc_final: 0.5330 (tpp)
REVERT: A  407 MET cc_start: 0.8527 (mmm) cc_final: 0.8215 (mmm)
REVERT: A  408 LEU cc_start: 0.9220 (pp) cc_final: 0.9014 (pp)
REVERT: A  476 GLU cc_start: 0.7784 (pp20) cc_final: 0.7519 (pp20)
REVERT: A  501 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8045 (ptm)
REVERT: B  254 MET cc_start: 0.5615 (ttp) cc_final: 0.5317 (tpp)
REVERT: B  407 MET cc_start: 0.8526 (mmm) cc_final: 0.8214 (mmm)
REVERT: B  408 LEU cc_start: 0.9220 (pp) cc_final: 0.9014 (pp)
REVERT: B  476 GLU cc_start: 0.7799 (pp20) cc_final: 0.7528 (pp20)
REVERT: B  501 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8045 (ptm)
  outliers start: 30
  outliers final: 24
  residues processed: 184
  average time/residue: 0.0619
  time to fit residues: 16.6251
Evaluate side-chains
  172 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 146
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 TYR
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue   77 HIS
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue   89 CYS
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  147 HIS
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  501 MET
Chi-restraints excluded: chain B residue   52 TYR
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue   89 CYS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  147 HIS
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  501 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 65 optimal weight:   30.0000
   chunk 23 optimal weight:    8.9990
   chunk 32 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 26 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 85 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 50 optimal weight:   40.0000
   chunk 73 optimal weight:   20.0000
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 147 HIS
B 147 HIS
B 150 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.129379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.102347 restraints weight = 15950.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.105610 restraints weight = 9363.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.107888 restraints weight = 6680.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.108986 restraints weight = 5352.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.110252 restraints weight = 4729.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.6424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6728  Z= 0.159
  Angle     :  0.751  12.131   9178  Z= 0.367
  Chirality :  0.044   0.228   1110
  Planarity :  0.004   0.027   1140
  Dihedral  :  3.673  12.109    916
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 24.37 %
    Favored  : 71.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.36 (0.29), residues: 856
  helix:  1.24 (0.21), residues: 620
  sheet:  None (None), residues: 0
  loop :  0.20 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 206 
 TYR   0.016   0.002   TYR B 136 
 PHE   0.010   0.001   PHE A 200 
 TRP   0.008   0.001   TRP A 149 
 HIS   0.011   0.002   HIS B 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 6728)
  covalent geometry    : angle       0.75135 ( 9178)
  hydrogen bonds       : bond        0.04719 (  418)
  hydrogen bonds       : angle       4.16284 ( 1254)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 144
  time to evaluate  : 0.265 
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: A  407 MET cc_start: 0.8551 (mmm) cc_final: 0.8236 (mmm)
REVERT: A  408 LEU cc_start: 0.9223 (pp) cc_final: 0.9015 (pp)
REVERT: A  501 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.8043 (ptm)
REVERT: B  407 MET cc_start: 0.8560 (mmm) cc_final: 0.8239 (mmm)
REVERT: B  408 LEU cc_start: 0.9223 (pp) cc_final: 0.9016 (pp)
REVERT: B  501 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.8039 (ptm)
  outliers start: 26
  outliers final: 20
  residues processed: 160
  average time/residue: 0.0604
  time to fit residues: 14.1601
Evaluate side-chains
  166 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 144
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 TYR
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue   89 CYS
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  155 GLU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  501 MET
Chi-restraints excluded: chain B residue   52 TYR
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue   89 CYS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  155 GLU
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  501 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 66 optimal weight:   10.0000
   chunk 43 optimal weight:   30.0000
   chunk 72 optimal weight:    8.9990
   chunk 63 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 20 optimal weight:    9.9990
   chunk 85 optimal weight:    0.0370
   chunk 55 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 64 optimal weight:    9.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    4.8066

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

Flipped N/Q/H residues before XYZ refinement:
A 147 HIS
A 150 HIS
B 147 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.126548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.099320 restraints weight = 15680.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.102337 restraints weight = 9534.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.104541 restraints weight = 6959.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.105516 restraints weight = 5650.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.106680 restraints weight = 5043.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.6555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   6728  Z= 0.214
  Angle     :  0.814  11.729   9178  Z= 0.403
  Chirality :  0.046   0.186   1110
  Planarity :  0.005   0.033   1140
  Dihedral  :  3.966  15.003    916
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 24.23 %
    Favored  : 71.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  0.95 (0.28), residues: 856
  helix:  0.94 (0.20), residues: 618
  sheet:  None (None), residues: 0
  loop :  0.09 (0.42), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 522 
 TYR   0.021   0.002   TYR A 136 
 PHE   0.021   0.002   PHE A 255 
 TRP   0.003   0.001   TRP A 265 
 HIS   0.016   0.002   HIS B 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 6728)
  covalent geometry    : angle       0.81388 ( 9178)
  hydrogen bonds       : bond        0.05648 (  418)
  hydrogen bonds       : angle       4.42861 ( 1254)

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

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

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1712 Ramachandran restraints generated.
    856 Oldfield, 0 Emsley, 856 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 142
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 PHE cc_start: 0.8753 (m-80) cc_final: 0.8390 (m-80)
REVERT: A  407 MET cc_start: 0.8596 (mmm) cc_final: 0.8132 (mmm)
REVERT: A  408 LEU cc_start: 0.9252 (pp) cc_final: 0.9039 (pp)
REVERT: A  501 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8058 (ptm)
REVERT: B   87 PHE cc_start: 0.8758 (m-80) cc_final: 0.8392 (m-80)
REVERT: B  407 MET cc_start: 0.8599 (mmm) cc_final: 0.8132 (mmm)
REVERT: B  408 LEU cc_start: 0.9251 (pp) cc_final: 0.9039 (pp)
REVERT: B  501 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8048 (ptm)
  outliers start: 32
  outliers final: 24
  residues processed: 158
  average time/residue: 0.0602
  time to fit residues: 14.0606
Evaluate side-chains
  156 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 130
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 TYR
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue   81 GLN
Chi-restraints excluded: chain A residue   89 CYS
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  147 HIS
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  501 MET
Chi-restraints excluded: chain A residue  506 CYS
Chi-restraints excluded: chain B residue   52 TYR
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   81 GLN
Chi-restraints excluded: chain B residue   89 CYS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  147 HIS
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  425 ASP
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  501 MET
Chi-restraints excluded: chain B residue  506 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 29 optimal weight:    9.9990
   chunk 68 optimal weight:    3.9990
   chunk 15 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 82 optimal weight:    8.9990
   chunk 73 optimal weight:    5.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 147 HIS
A 226 GLN
B 147 HIS
B 226 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.129037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.102407 restraints weight = 15770.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.105479 restraints weight = 9373.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.107685 restraints weight = 6771.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.108732 restraints weight = 5471.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.109719 restraints weight = 4865.358|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.6760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   6728  Z= 0.163
  Angle     :  0.794  11.763   9178  Z= 0.385
  Chirality :  0.044   0.197   1110
  Planarity :  0.004   0.032   1140
  Dihedral  :  3.925  14.984    916
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 26.76 %
    Favored  : 69.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  1.08 (0.29), residues: 856
  helix:  1.01 (0.21), residues: 622
  sheet:  None (None), residues: 0
  loop :  0.19 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 206 
 TYR   0.016   0.002   TYR A 136 
 PHE   0.020   0.002   PHE B 255 
 TRP   0.005   0.001   TRP B 149 
 HIS   0.012   0.002   HIS B 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 6728)
  covalent geometry    : angle       0.79440 ( 9178)
  hydrogen bonds       : bond        0.04937 (  418)
  hydrogen bonds       : angle       4.27077 ( 1254)

===============================================================================
Job complete
usr+sys time: 1303.38 seconds
wall clock time: 23 minutes 16.06 seconds (1396.06 seconds total)