Starting phenix.real_space_refine
on Tue Mar 11 20:09:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jf0_36205/03_2025/8jf0_36205.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jf0_36205/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jf0_36205/03_2025/8jf0_36205.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jf0_36205/03_2025/8jf0_36205.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jf0_36205/03_2025/8jf0_36205.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jf0_36205/03_2025/8jf0_36205.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
-------------------------------------------------------------------------------
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.49, per 1000 atoms: 0.83
  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: 1.54
  Conformation dependent library (CDL) restraints added in 982.4 milliseconds
  

  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: 0.62
  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: 1.81

  Time building geometry restraints manager: 1.85 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: 0.03
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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.730
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.340
-------------------------------------------------------------------------------
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= 1.002
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.030   0.007   TRP B 127 
 HIS   0.011   0.004   HIS A 210 
 PHE   0.051   0.006   PHE A 466 
 TYR   0.039   0.007   TYR A 340 
 ARG   0.032   0.004   ARG A 154 

*********************** 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  : 0.802 
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: 0.8544 (t70)
REVERT: A  186 LEU cc_start: 0.8793 (mt) cc_final: 0.8420 (mp)
REVERT: A  295 ASP cc_start: 0.8215 (t70) cc_final: 0.7565 (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: 0.8545 (t70)
REVERT: B  186 LEU cc_start: 0.8793 (mt) cc_final: 0.8419 (mp)
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: 0.8181 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 260
  average time/residue: 0.1676
  time to fit residues: 58.8788
Evaluate side-chains
  172 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 65 optimal weight:    8.9990
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:    8.9990
   chunk 43 optimal weight:   20.0000
   chunk 34 optimal weight:    5.9990
   chunk 67 optimal weight:    9.9990
   chunk 26 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   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
A 230 ASN
A 478 ASN
B  50 GLN
B  77 HIS
B 147 HIS
B 230 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.129214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.102810 restraints weight = 15262.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.106240 restraints weight = 8931.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.108519 restraints weight = 6366.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.3999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6728  Z= 0.287
  Angle     :  0.735   8.528   9178  Z= 0.380
  Chirality :  0.045   0.166   1110
  Planarity :  0.005   0.026   1140
  Dihedral  :  3.764  12.405    916
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 14.51 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.27), residues: 856
  helix:  0.25 (0.19), residues: 618
  sheet:  None (None), residues: 0
  loop : -1.05 (0.39), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 149 
 HIS   0.009   0.002   HIS B 147 
 PHE   0.011   0.002   PHE B 502 
 TYR   0.018   0.002   TYR A 340 
 ARG   0.003   0.001   ARG A 522 

*********************** 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
  196 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 174
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 PHE cc_start: 0.8222 (t80) cc_final: 0.7884 (t80)
REVERT: A   97 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7712 (mm-40)
REVERT: A  255 PHE cc_start: 0.6622 (t80) cc_final: 0.6161 (m-80)
REVERT: A  363 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7843 (mm-30)
REVERT: A  407 MET cc_start: 0.8565 (mmm) cc_final: 0.8289 (mmm)
REVERT: B   56 PHE cc_start: 0.8228 (t80) cc_final: 0.7895 (t80)
REVERT: B   97 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7712 (mm-40)
REVERT: B  255 PHE cc_start: 0.6623 (t80) cc_final: 0.6161 (m-80)
REVERT: B  363 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7842 (mm-30)
REVERT: B  407 MET cc_start: 0.8561 (mmm) cc_final: 0.8284 (mmm)
  outliers start: 22
  outliers final: 10
  residues processed: 180
  average time/residue: 0.1577
  time to fit residues: 38.9904
Evaluate side-chains
  148 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 138
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 ILE
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  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 79 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 52 optimal weight:    8.9990
   chunk 43 optimal weight:   20.0000
   chunk 84 optimal weight:   10.0000
   chunk 2 optimal weight:    0.0000
   chunk 14 optimal weight:    9.9990
   chunk 60 optimal weight:    5.9990
   chunk 27 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    2.9992

-------------------------------------------------------------------------------
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  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3993 r_free = 0.3993 target = 0.129701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.103289 restraints weight = 15751.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.106787 restraints weight = 9212.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.109165 restraints weight = 6562.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.4840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6728  Z= 0.240
  Angle     :  0.668   7.402   9178  Z= 0.337
  Chirality :  0.044   0.145   1110
  Planarity :  0.004   0.033   1140
  Dihedral  :  3.738  12.882    916
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 15.92 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.28), residues: 856
  helix:  0.99 (0.20), residues: 618
  sheet:  None (None), residues: 0
  loop : -0.50 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 149 
 HIS   0.008   0.001   HIS B 147 
 PHE   0.013   0.002   PHE B 466 
 TYR   0.014   0.002   TYR B 340 
 ARG   0.003   0.001   ARG A 126 

*********************** 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
  196 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 162
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 PHE cc_start: 0.6245 (t80) cc_final: 0.5963 (m-80)
REVERT: A  328 THR cc_start: 0.8545 (m) cc_final: 0.8235 (m)
REVERT: A  407 MET cc_start: 0.8641 (mmm) cc_final: 0.8440 (mmm)
REVERT: A  410 LEU cc_start: 0.9311 (mp) cc_final: 0.9066 (mp)
REVERT: A  451 ASP cc_start: 0.8207 (t70) cc_final: 0.7983 (t0)
REVERT: B  255 PHE cc_start: 0.6230 (t80) cc_final: 0.5963 (m-80)
REVERT: B  328 THR cc_start: 0.8539 (m) cc_final: 0.8232 (m)
REVERT: B  407 MET cc_start: 0.8646 (mmm) cc_final: 0.8440 (mmm)
REVERT: B  410 LEU cc_start: 0.9311 (mp) cc_final: 0.9065 (mp)
REVERT: B  451 ASP cc_start: 0.8210 (t70) cc_final: 0.7986 (t0)
  outliers start: 34
  outliers final: 18
  residues processed: 174
  average time/residue: 0.1517
  time to fit residues: 36.5301
Evaluate side-chains
  144 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
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  115 LEU
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  476 GLU
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  115 LEU
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  194 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  425 ASP
Chi-restraints excluded: chain B residue  476 GLU
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 1 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 81 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 66 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 13 optimal weight:   20.0000
   chunk 48 optimal weight:   20.0000
   chunk 75 optimal weight:    5.9990
   overall best weight:    2.6986

-------------------------------------------------------------------------------
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 = 0.3994 r_free = 0.3994 target = 0.128999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.102366 restraints weight = 15736.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.105739 restraints weight = 9266.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.107895 restraints weight = 6634.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.5384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6728  Z= 0.218
  Angle     :  0.651   7.155   9178  Z= 0.325
  Chirality :  0.043   0.136   1110
  Planarity :  0.004   0.034   1140
  Dihedral  :  3.705  12.836    916
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 17.89 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.28), residues: 856
  helix:  1.25 (0.20), residues: 624
  sheet:  None (None), residues: 0
  loop : -0.18 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 149 
 HIS   0.007   0.001   HIS A 147 
 PHE   0.010   0.001   PHE A 466 
 TYR   0.012   0.002   TYR A 340 
 ARG   0.002   0.000   ARG B 289 

*********************** 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
  178 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 150
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 THR cc_start: 0.8469 (p) cc_final: 0.8194 (p)
REVERT: A  258 MET cc_start: 0.7077 (mtm) cc_final: 0.6482 (mtm)
REVERT: A  407 MET cc_start: 0.8618 (mmm) cc_final: 0.8403 (mmm)
REVERT: A  408 LEU cc_start: 0.9208 (pp) cc_final: 0.9005 (pp)
REVERT: B   94 THR cc_start: 0.8472 (p) cc_final: 0.8197 (p)
REVERT: B  258 MET cc_start: 0.7088 (mtm) cc_final: 0.6490 (mtm)
REVERT: B  407 MET cc_start: 0.8630 (mmm) cc_final: 0.8406 (mmm)
REVERT: B  408 LEU cc_start: 0.9210 (pp) cc_final: 0.9006 (pp)
  outliers start: 28
  outliers final: 18
  residues processed: 166
  average time/residue: 0.1440
  time to fit residues: 33.7047
Evaluate side-chains
  158 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
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  147 HIS
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 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  147 HIS
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  425 ASP
Chi-restraints excluded: chain B residue  493 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 73 optimal weight:   40.0000
   chunk 60 optimal weight:    6.9990
   chunk 51 optimal weight:    0.0470
   chunk 26 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 23 optimal weight:    0.2980
   chunk 77 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9980
   overall best weight:    1.2682

-------------------------------------------------------------------------------
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 = 0.4027 r_free = 0.4027 target = 0.131762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.104607 restraints weight = 15456.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.108003 restraints weight = 9132.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.110273 restraints weight = 6595.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.5669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6728  Z= 0.182
  Angle     :  0.632   7.780   9178  Z= 0.310
  Chirality :  0.044   0.201   1110
  Planarity :  0.004   0.033   1140
  Dihedral  :  3.686  13.826    916
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 17.61 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.28), residues: 856
  helix:  1.45 (0.20), residues: 622
  sheet:  None (None), residues: 0
  loop : -0.09 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 149 
 HIS   0.007   0.001   HIS B 147 
 PHE   0.009   0.001   PHE A 420 
 TYR   0.011   0.001   TYR A 340 
 ARG   0.002   0.000   ARG B 206 

*********************** 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
  178 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 150
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 THR cc_start: 0.8342 (p) cc_final: 0.8122 (p)
REVERT: A  336 ILE cc_start: 0.8685 (mt) cc_final: 0.8484 (tp)
REVERT: A  407 MET cc_start: 0.8553 (mmm) cc_final: 0.8174 (mmm)
REVERT: A  451 ASP cc_start: 0.8251 (t0) cc_final: 0.8043 (t0)
REVERT: B   94 THR cc_start: 0.8344 (p) cc_final: 0.8124 (p)
REVERT: B  336 ILE cc_start: 0.8683 (mt) cc_final: 0.8482 (tp)
REVERT: B  407 MET cc_start: 0.8561 (mmm) cc_final: 0.8178 (mmm)
REVERT: B  451 ASP cc_start: 0.8256 (t0) cc_final: 0.8049 (t0)
  outliers start: 28
  outliers final: 22
  residues processed: 164
  average time/residue: 0.1321
  time to fit residues: 31.3417
Evaluate side-chains
  164 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
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  197 LEU
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 A residue  484 THR
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  197 LEU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  425 ASP
Chi-restraints excluded: chain B residue  484 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 19 optimal weight:    7.9990
   chunk 39 optimal weight:    3.9990
   chunk 10 optimal weight:    0.4980
   chunk 41 optimal weight:    9.9990
   chunk 75 optimal weight:    6.9990
   chunk 62 optimal weight:    9.9990
   chunk 78 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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 = 0.4026 r_free = 0.4026 target = 0.131833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.104985 restraints weight = 15214.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.108294 restraints weight = 9046.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.110530 restraints weight = 6540.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.5964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6728  Z= 0.190
  Angle     :  0.660  10.262   9178  Z= 0.320
  Chirality :  0.043   0.140   1110
  Planarity :  0.004   0.032   1140
  Dihedral  :  3.758  12.694    916
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 18.87 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.28), residues: 856
  helix:  1.36 (0.20), residues: 620
  sheet:  None (None), residues: 0
  loop : -0.11 (0.39), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 149 
 HIS   0.013   0.002   HIS A 147 
 PHE   0.015   0.001   PHE B 255 
 TYR   0.012   0.002   TYR A 339 
 ARG   0.001   0.000   ARG A 289 

*********************** 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
  176 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 146
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  258 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7032 (mtt)
REVERT: A  407 MET cc_start: 0.8473 (mmm) cc_final: 0.8200 (mmm)
REVERT: A  451 ASP cc_start: 0.8335 (t0) cc_final: 0.8075 (t0)
REVERT: B  258 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7033 (mtt)
REVERT: B  407 MET cc_start: 0.8480 (mmm) cc_final: 0.8203 (mmm)
REVERT: B  451 ASP cc_start: 0.8337 (t0) cc_final: 0.8076 (t0)
  outliers start: 30
  outliers final: 22
  residues processed: 160
  average time/residue: 0.1294
  time to fit residues: 30.0030
Evaluate side-chains
  166 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 142
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
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  147 HIS
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  258 MET
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 A residue  484 THR
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  147 HIS
Chi-restraints excluded: chain B residue  197 LEU
Chi-restraints excluded: chain B residue  258 MET
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  425 ASP
Chi-restraints excluded: chain B residue  484 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 0 optimal weight:   30.0000
   chunk 70 optimal weight:    0.0670
   chunk 9 optimal weight:    0.0000
   chunk 64 optimal weight:    6.9990
   chunk 51 optimal weight:   20.0000
   chunk 74 optimal weight:    8.9990
   chunk 32 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   overall best weight:    2.2128

-------------------------------------------------------------------------------
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 = 0.4022 r_free = 0.4022 target = 0.130935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.104665 restraints weight = 15188.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.108070 restraints weight = 8906.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.110421 restraints weight = 6336.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.6194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6728  Z= 0.203
  Angle     :  0.678  12.343   9178  Z= 0.332
  Chirality :  0.045   0.296   1110
  Planarity :  0.004   0.028   1140
  Dihedral  :  4.008  21.662    916
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 21.55 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.28), residues: 856
  helix:  1.39 (0.20), residues: 616
  sheet:  None (None), residues: 0
  loop : -0.18 (0.39), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 149 
 HIS   0.018   0.002   HIS A 147 
 PHE   0.010   0.002   PHE A 224 
 TYR   0.012   0.002   TYR B 136 
 ARG   0.002   0.000   ARG A 152 

*********************** 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
  174 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 152
  time to evaluate  : 0.677 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.9220 (tp) cc_final: 0.8949 (tt)
REVERT: A  407 MET cc_start: 0.8454 (mmm) cc_final: 0.8228 (mmm)
REVERT: A  451 ASP cc_start: 0.8387 (t0) cc_final: 0.8089 (t0)
REVERT: A  476 GLU cc_start: 0.7823 (pp20) cc_final: 0.7528 (pp20)
REVERT: B   95 LEU cc_start: 0.9235 (tp) cc_final: 0.8972 (tt)
REVERT: B  407 MET cc_start: 0.8465 (mmm) cc_final: 0.8234 (mmm)
REVERT: B  451 ASP cc_start: 0.8385 (t0) cc_final: 0.8088 (t0)
REVERT: B  476 GLU cc_start: 0.7832 (pp20) cc_final: 0.7533 (pp20)
  outliers start: 22
  outliers final: 18
  residues processed: 166
  average time/residue: 0.1429
  time to fit residues: 33.3825
Evaluate side-chains
  152 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
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  345 LEU
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   89 CYS
Chi-restraints excluded: chain B residue  115 LEU
Chi-restraints excluded: chain B residue  145 THR
Chi-restraints excluded: chain B residue  345 LEU
Chi-restraints excluded: chain B residue  425 ASP
Chi-restraints excluded: chain B residue  493 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 53 optimal weight:    7.9990
   chunk 33 optimal weight:    0.6980
   chunk 54 optimal weight:    5.9990
   chunk 9 optimal weight:    8.9990
   chunk 52 optimal weight:    9.9990
   chunk 44 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0370
   overall best weight:    0.7058

-------------------------------------------------------------------------------
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 = 0.4062 r_free = 0.4062 target = 0.133647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.107351 restraints weight = 15423.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.110721 restraints weight = 9172.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.112765 restraints weight = 6597.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.6475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6728  Z= 0.185
  Angle     :  0.702  11.405   9178  Z= 0.342
  Chirality :  0.044   0.284   1110
  Planarity :  0.004   0.028   1140
  Dihedral  :  3.912  21.124    916
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 22.11 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.28), residues: 856
  helix:  1.51 (0.21), residues: 620
  sheet:  None (None), residues: 0
  loop : -0.11 (0.40), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 311 
 HIS   0.013   0.002   HIS B 147 
 PHE   0.009   0.001   PHE A 255 
 TYR   0.017   0.002   TYR A 136 
 ARG   0.002   0.000   ARG B 206 

*********************** 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
  174 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 LEU cc_start: 0.9163 (tp) cc_final: 0.8913 (tt)
REVERT: A  407 MET cc_start: 0.8493 (mmm) cc_final: 0.8276 (mmm)
REVERT: A  428 LEU cc_start: 0.8543 (mm) cc_final: 0.8301 (mm)
REVERT: A  451 ASP cc_start: 0.8412 (t0) cc_final: 0.8100 (t0)
REVERT: B   95 LEU cc_start: 0.9170 (tp) cc_final: 0.8921 (tt)
REVERT: B  407 MET cc_start: 0.8493 (mmm) cc_final: 0.8276 (mmm)
REVERT: B  428 LEU cc_start: 0.8542 (mm) cc_final: 0.8298 (mm)
REVERT: B  451 ASP cc_start: 0.8412 (t0) cc_final: 0.8100 (t0)
  outliers start: 26
  outliers final: 16
  residues processed: 162
  average time/residue: 0.1266
  time to fit residues: 29.6545
Evaluate side-chains
  160 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
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   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  147 HIS
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain B residue   52 TYR
Chi-restraints excluded: chain B residue   56 PHE
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  147 HIS
Chi-restraints excluded: chain B residue  345 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 56 optimal weight:    6.9990
   chunk 10 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9980
   chunk 49 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 60 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 24 optimal weight:    8.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    3.7988

-------------------------------------------------------------------------------
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 491 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.128801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.102059 restraints weight = 15510.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.105047 restraints weight = 9239.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.107341 restraints weight = 6754.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.6523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6728  Z= 0.266
  Angle     :  0.721   9.933   9178  Z= 0.359
  Chirality :  0.046   0.202   1110
  Planarity :  0.004   0.025   1140
  Dihedral  :  3.976  21.747    916
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 22.68 %
    Favored  : 74.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.29), residues: 856
  helix:  1.21 (0.21), residues: 624
  sheet:  None (None), residues: 0
  loop :  0.02 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 149 
 HIS   0.018   0.002   HIS B 147 
 PHE   0.013   0.002   PHE A 224 
 TYR   0.015   0.002   TYR A 136 
 ARG   0.002   0.000   ARG A 522 

*********************** 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
  160 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 140
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 THR cc_start: 0.8841 (p) cc_final: 0.8573 (t)
REVERT: A   95 LEU cc_start: 0.9172 (tp) cc_final: 0.8913 (tt)
REVERT: A  407 MET cc_start: 0.8587 (mmm) cc_final: 0.8334 (mmm)
REVERT: A  451 ASP cc_start: 0.8430 (t0) cc_final: 0.8119 (t0)
REVERT: B   59 THR cc_start: 0.8840 (p) cc_final: 0.8573 (t)
REVERT: B   95 LEU cc_start: 0.9175 (tp) cc_final: 0.8916 (tt)
REVERT: B  407 MET cc_start: 0.8592 (mmm) cc_final: 0.8337 (mmm)
REVERT: B  451 ASP cc_start: 0.8424 (t0) cc_final: 0.8113 (t0)
  outliers start: 20
  outliers final: 16
  residues processed: 150
  average time/residue: 0.1348
  time to fit residues: 29.1551
Evaluate side-chains
  150 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 134
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
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   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  345 LEU
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain B residue   52 TYR
Chi-restraints excluded: chain B residue   56 PHE
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  345 LEU
Chi-restraints excluded: chain B residue  425 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 70 optimal weight:    7.9990
   chunk 67 optimal weight:   10.0000
   chunk 68 optimal weight:    4.9990
   chunk 56 optimal weight:    7.9990
   chunk 20 optimal weight:    0.4980
   chunk 76 optimal weight:    0.4980
   chunk 6 optimal weight:    7.9990
   chunk 60 optimal weight:    6.9990
   chunk 5 optimal weight:    8.9990
   chunk 17 optimal weight:    7.9990
   overall best weight:    2.7984

-------------------------------------------------------------------------------
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 = 0.4094 r_free = 0.4094 target = 0.132623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.106546 restraints weight = 15199.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.109965 restraints weight = 8926.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.112294 restraints weight = 6330.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.6646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6728  Z= 0.244
  Angle     :  0.739  10.297   9178  Z= 0.365
  Chirality :  0.046   0.214   1110
  Planarity :  0.004   0.030   1140
  Dihedral  :  3.981  22.183    916
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 24.93 %
    Favored  : 72.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.29), residues: 856
  helix:  1.19 (0.21), residues: 620
  sheet:  None (None), residues: 0
  loop : -0.02 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 311 
 HIS   0.015   0.002   HIS B 147 
 PHE   0.014   0.002   PHE B 224 
 TYR   0.019   0.002   TYR B 136 
 ARG   0.001   0.000   ARG A 289 

********************** 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
  152 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.657 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 THR cc_start: 0.8801 (p) cc_final: 0.8436 (t)
REVERT: A   95 LEU cc_start: 0.9072 (tp) cc_final: 0.8816 (tt)
REVERT: A  254 MET cc_start: 0.5295 (ttp) cc_final: 0.3973 (mtt)
REVERT: A  451 ASP cc_start: 0.8405 (t0) cc_final: 0.8087 (t0)
REVERT: B   59 THR cc_start: 0.8797 (p) cc_final: 0.8429 (t)
REVERT: B   95 LEU cc_start: 0.9070 (tp) cc_final: 0.8813 (tt)
REVERT: B  254 MET cc_start: 0.5294 (ttp) cc_final: 0.3961 (mtt)
REVERT: B  451 ASP cc_start: 0.8398 (t0) cc_final: 0.8083 (t0)
  outliers start: 18
  outliers final: 18
  residues processed: 144
  average time/residue: 0.1358
  time to fit residues: 28.1806
Evaluate side-chains
  154 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 136
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
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   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  147 HIS
Chi-restraints excluded: chain A residue  183 ILE
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain B residue   52 TYR
Chi-restraints excluded: chain B residue   56 PHE
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  147 HIS
Chi-restraints excluded: chain B residue  183 ILE
Chi-restraints excluded: chain B residue  345 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 53 optimal weight:    0.5980
   chunk 76 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   chunk 9 optimal weight:    9.9990
   chunk 59 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   overall best weight:    2.1184

-------------------------------------------------------------------------------
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 = 0.4026 r_free = 0.4026 target = 0.129536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.103378 restraints weight = 15561.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.106555 restraints weight = 9133.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.108803 restraints weight = 6503.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.6834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6728  Z= 0.236
  Angle     :  0.777  13.440   9178  Z= 0.372
  Chirality :  0.045   0.190   1110
  Planarity :  0.004   0.031   1140
  Dihedral  :  4.017  22.645    916
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 25.77 %
    Favored  : 71.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.29), residues: 856
  helix:  1.11 (0.21), residues: 620
  sheet:  None (None), residues: 0
  loop :  0.08 (0.41), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 265 
 HIS   0.011   0.002   HIS B 147 
 PHE   0.014   0.002   PHE B  56 
 TYR   0.015   0.002   TYR B 136 
 ARG   0.001   0.000   ARG B 522 

===============================================================================
Job complete
usr+sys time: 2283.51 seconds
wall clock time: 40 minutes 15.78 seconds (2415.78 seconds total)