Starting phenix.real_space_refine
on Fri Aug 22 16:55:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uyh_42806/08_2025/8uyh_42806.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uyh_42806/08_2025/8uyh_42806.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uyh_42806/08_2025/8uyh_42806.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uyh_42806/08_2025/8uyh_42806.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uyh_42806/08_2025/8uyh_42806.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uyh_42806/08_2025/8uyh_42806.cif"
  }
  resolution = 2.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.025
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: 6
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     Mg      3      5.21       5
     S      40      5.16       5
     C    3840      2.51       5
     N    1013      2.21       5
     O    1132      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 6036
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3003
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 3003
          Classifications: {'peptide': 375}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 17, 'TRANS': 357}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'TPO:plan-1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 2968
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 370, 2968
          Classifications: {'peptide': 370}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 17, 'TRANS': 352}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2, 'TPO:plan-1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ANP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 2, 'ANP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.83, per 1000 atoms: 0.30
  Number of scatterers: 6036
  At special positions: 0
  Unit cell: (116.352, 81.608, 72.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      40     16.00
     P       8     15.00
     Mg      3     11.99
     O    1132      8.00
     N    1013      7.00
     C    3840      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: 0.48
  Conformation dependent library (CDL) restraints added in 334.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1444

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 6 sheets defined
      46.2% alpha, 12.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 119 through 136
    Processing helix  chain 'A' and resid 155 through 159
      removed outlier: 3.577A  pdb=" N   GLU A 158 " --> pdb=" O   ASN A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 215
      removed outlier: 3.559A  pdb=" N   THR A 215 " --> pdb=" O   MET A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 304
    Processing helix  chain 'A' and resid 307 through 328
      removed outlier: 3.659A  pdb=" N   HIS A 328 " --> pdb=" O   HIS A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 338
      No H-bonds generated for 'chain 'A' and resid 336 through 338'
    Processing helix  chain 'A' and resid 357 through 361
      removed outlier: 4.681A  pdb=" N   CYS A 360 " --> pdb=" O   ASP A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 393
    Processing helix  chain 'A' and resid 406 through 420
      removed outlier: 3.590A  pdb=" N   GLY A 413 " --> pdb=" O   LEU A 409 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA A 414 " --> pdb=" O   TRP A 410 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   TYR A 417 " --> pdb=" O   GLY A 413 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   GLU A 418 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 462
    Processing helix  chain 'A' and resid 471 through 485
    Processing helix  chain 'A' and resid 486 through 490
    Processing helix  chain 'A' and resid 498 through 515
    Processing helix  chain 'A' and resid 542 through 554
    Processing helix  chain 'A' and resid 557 through 574
      removed outlier: 3.580A  pdb=" N   LEU A 571 " --> pdb=" O   TRP A 567 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   HIS A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 137
    Processing helix  chain 'B' and resid 155 through 157
      No H-bonds generated for 'chain 'B' and resid 155 through 157'
    Processing helix  chain 'B' and resid 203 through 215
      removed outlier: 3.609A  pdb=" N   THR B 215 " --> pdb=" O   MET B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 304
    Processing helix  chain 'B' and resid 307 through 328
      removed outlier: 3.710A  pdb=" N   HIS B 328 " --> pdb=" O   HIS B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 361
      removed outlier: 4.562A  pdb=" N   CYS B 360 " --> pdb=" O   ASP B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 393
    Processing helix  chain 'B' and resid 406 through 420
      removed outlier: 3.519A  pdb=" N   GLY B 413 " --> pdb=" O   LEU B 409 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ALA B 414 " --> pdb=" O   TRP B 410 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   TYR B 417 " --> pdb=" O   GLY B 413 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLU B 418 " --> pdb=" O   ALA B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 462
    Processing helix  chain 'B' and resid 471 through 485
    Processing helix  chain 'B' and resid 486 through 491
    Processing helix  chain 'B' and resid 498 through 515
    Processing helix  chain 'B' and resid 542 through 554
    Processing helix  chain 'B' and resid 557 through 574
      removed outlier: 3.703A  pdb=" N   HIS B 572 " --> pdb=" O   ILE B 568 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 164 through 167
      removed outlier: 6.587A  pdb=" N   VAL A 173 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   LYS A 167 " --> pdb=" O   ALA A 171 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   ALA A 171 " --> pdb=" O   LYS A 167 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   SER A 251 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   LYS A 291 " --> pdb=" O   MET A 249 " (cutoff:3.500A)
      removed outlier: 7.005A  pdb=" N   MET A 249 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA A 254 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 295 through 296
    Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 372
    Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 167
      removed outlier: 7.454A  pdb=" N   GLY B 162 " --> pdb=" O   LYS B 177 " (cutoff:3.500A)
      removed outlier: 8.926A  pdb=" N   LYS B 177 " --> pdb=" O   GLY B 162 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   SER B 175 " --> pdb=" O   PRO B 164 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   SER B 285 " --> pdb=" O   ASP B 255 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   SER B 251 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   LYS B 291 " --> pdb=" O   MET B 249 " (cutoff:3.500A)
      removed outlier: 7.129A  pdb=" N   MET B 249 " --> pdb=" O   LYS B 291 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   TYR B 250 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ALA B 254 " --> pdb=" O   PHE B 222 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 295 through 296
      removed outlier: 3.708A  pdb=" N   CYS B 295 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 370 through 372

    276 hydrogen bonds defined for protein.
    789 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.95

  Time building geometry restraints manager: 0.66 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1920
        1.34 -     1.46: 1237
        1.46 -     1.58: 2917
        1.58 -     1.69: 16
        1.69 -     1.81: 62
  Bond restraints: 6152
  Sorted by residual:
  bond pdb=" O3A ANP A 601 "
       pdb=" PB  ANP A 601 "
    ideal  model  delta    sigma   weight residual
    1.700  1.558  0.142 2.00e-02 2.50e+03 5.04e+01
  bond pdb=" O3A ANP B 601 "
       pdb=" PB  ANP B 601 "
    ideal  model  delta    sigma   weight residual
    1.700  1.558  0.142 2.00e-02 2.50e+03 5.02e+01
  bond pdb=" OG1 TPO A 305 "
       pdb=" P   TPO A 305 "
    ideal  model  delta    sigma   weight residual
    1.717  1.610  0.107 2.00e-02 2.50e+03 2.87e+01
  bond pdb=" OG1 TPO B 305 "
       pdb=" P   TPO B 305 "
    ideal  model  delta    sigma   weight residual
    1.717  1.610  0.107 2.00e-02 2.50e+03 2.84e+01
  bond pdb=" N3B ANP B 601 "
       pdb=" PG  ANP B 601 "
    ideal  model  delta    sigma   weight residual
    1.795  1.693  0.102 2.00e-02 2.50e+03 2.62e+01
  ... (remaining 6147 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.57: 8287
        3.57 -     7.15: 44
        7.15 -    10.72: 6
       10.72 -    14.30: 3
       14.30 -    17.87: 2
  Bond angle restraints: 8342
  Sorted by residual:
  angle pdb=" PB  ANP B 601 "
        pdb=" N3B ANP B 601 "
        pdb=" PG  ANP B 601 "
      ideal   model   delta    sigma   weight residual
     126.95  109.08   17.87 3.00e+00 1.11e-01 3.55e+01
  angle pdb=" PB  ANP A 601 "
        pdb=" N3B ANP A 601 "
        pdb=" PG  ANP A 601 "
      ideal   model   delta    sigma   weight residual
     126.95  109.87   17.08 3.00e+00 1.11e-01 3.24e+01
  angle pdb=" CB  TPO A 305 "
        pdb=" OG1 TPO A 305 "
        pdb=" P   TPO A 305 "
      ideal   model   delta    sigma   weight residual
     119.31  107.60   11.71 3.00e+00 1.11e-01 1.52e+01
  angle pdb=" CB  TPO B 305 "
        pdb=" OG1 TPO B 305 "
        pdb=" P   TPO B 305 "
      ideal   model   delta    sigma   weight residual
     119.31  107.87   11.44 3.00e+00 1.11e-01 1.46e+01
  angle pdb=" O1B ANP A 601 "
        pdb=" PB  ANP A 601 "
        pdb=" O2B ANP A 601 "
      ideal   model   delta    sigma   weight residual
     120.08  109.30   10.78 3.00e+00 1.11e-01 1.29e+01
  ... (remaining 8337 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.93: 3605
       21.93 -    43.87: 118
       43.87 -    65.80: 30
       65.80 -    87.73: 23
       87.73 -   109.66: 1
  Dihedral angle restraints: 3777
    sinusoidal: 1570
      harmonic: 2207
  Sorted by residual:
  dihedral pdb=" O1B ANP B 601 "
           pdb=" N3B ANP B 601 "
           pdb=" PB  ANP B 601 "
           pdb=" PG  ANP B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      35.15  -74.51  109.66     1      3.00e+01 1.11e-03 1.43e+01
  dihedral pdb=" CA  LEU A 483 "
           pdb=" C   LEU A 483 "
           pdb=" N   TRP A 484 "
           pdb=" CA  TRP A 484 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.28  -15.72     0      5.00e+00 4.00e-02 9.89e+00
  dihedral pdb=" N   GLU B 376 "
           pdb=" CA  GLU B 376 "
           pdb=" CB  GLU B 376 "
           pdb=" CG  GLU B 376 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.43  -59.57     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 3774 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 801
       0.055 -    0.111: 123
       0.111 -    0.166: 17
       0.166 -    0.221: 0
       0.221 -    0.277: 2
  Chirality restraints: 943
  Sorted by residual:
  chirality pdb=" C3' ANP B 601 "
            pdb=" C2' ANP B 601 "
            pdb=" C4' ANP B 601 "
            pdb=" O3' ANP B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.63    0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" C3' ANP A 601 "
            pdb=" C2' ANP A 601 "
            pdb=" C4' ANP A 601 "
            pdb=" O3' ANP A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.63    0.27 2.00e-01 2.50e+01 1.85e+00
  chirality pdb=" CA  ILE A 450 "
            pdb=" N   ILE A 450 "
            pdb=" C   ILE A 450 "
            pdb=" CB  ILE A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.64e-01
  ... (remaining 940 not shown)

  Planarity restraints: 1038
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 450 "   -0.033 5.00e-02 4.00e+02   4.96e-02 3.93e+00
        pdb=" N   PRO B 451 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO B 451 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 451 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 450 "    0.032 5.00e-02 4.00e+02   4.92e-02 3.88e+00
        pdb=" N   PRO A 451 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 451 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 451 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 243 "    0.030 5.00e-02 4.00e+02   4.46e-02 3.19e+00
        pdb=" N   PRO B 244 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 244 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 244 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1035 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 68
        2.64 -     3.20: 4957
        3.20 -     3.77: 9004
        3.77 -     4.33: 13307
        4.33 -     4.90: 21614
  Nonbonded interactions: 48950
  Sorted by model distance:
  nonbonded pdb=" O2B ANP B 601 "
            pdb="MG    MG B 602 "
     model   vdw
     2.074 2.170
  nonbonded pdb=" OD2 ASP B 357 "
            pdb="MG    MG B 603 "
     model   vdw
     2.131 2.170
  nonbonded pdb=" N3B ANP A 601 "
            pdb="MG    MG A 602 "
     model   vdw
     2.238 2.250
  nonbonded pdb=" O   THR A 215 "
            pdb=" OH  TYR A 221 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O2B ANP A 601 "
            pdb="MG    MG A 602 "
     model   vdw
     2.321 2.170
  ... (remaining 48945 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 121 through 223 or resid 238 through 515 or (resid 541 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 542 through 602)) \ 

  selection = (chain 'B' and (resid 121 through 136 or resid 148 through 427 or (resid 432 and \ 
 (name N or name CA or name C or name O or name CB )) or resid 433 through 540 o \ 
r resid 542 through 602))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.850
  Find NCS groups from input model:        0.110
  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:6.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
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      :  0.006   0.142   6152  Z= 0.280
  Angle     :  0.763  17.873   8342  Z= 0.361
  Chirality :  0.042   0.277    943
  Planarity :  0.005   0.050   1038
  Dihedral  : 13.962 109.665   2333
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  4.55 %
    Favored  : 93.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.53 (0.27), residues: 711
  helix: -1.14 (0.21), residues: 307
  sheet: -1.13 (0.49), residues: 103
  loop : -0.58 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 384 
 TYR   0.011   0.001   TYR A 494 
 PHE   0.010   0.001   PHE B 253 
 TRP   0.006   0.001   TRP B 484 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00564 ( 6152)
  covalent geometry    : angle       0.76326 ( 8342)
  hydrogen bonds       : bond        0.26222 (  276)
  hydrogen bonds       : angle       7.24179 (  789)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 174
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A  167 LYS cc_start: 0.7289 (mttt) cc_final: 0.6642 (mttp)
REVERT: A  177 LYS cc_start: 0.6773 (tttt) cc_final: 0.6474 (ttpp)
REVERT: A  189 GLN cc_start: 0.7291 (mt0) cc_final: 0.7081 (mm110)
REVERT: A  211 MET cc_start: 0.8201 (mtt) cc_final: 0.7979 (mtt)
REVERT: A  248 ARG cc_start: 0.7539 (ttt90) cc_final: 0.7211 (ttm170)
REVERT: A  300 TYR cc_start: 0.7999 (t80) cc_final: 0.7729 (t80)
REVERT: A  343 ASP cc_start: 0.7352 (t0) cc_final: 0.7140 (t0)
REVERT: A  346 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6164 (mp0)
REVERT: A  350 TYR cc_start: 0.7705 (m-80) cc_final: 0.7345 (m-80)
REVERT: A  545 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6534 (mt-10)
REVERT: A  554 ARG cc_start: 0.7979 (mtt90) cc_final: 0.7658 (mtt-85)
REVERT: B  133 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7430 (mm-30)
REVERT: B  167 LYS cc_start: 0.7724 (mtpt) cc_final: 0.7524 (mppt)
REVERT: B  177 LYS cc_start: 0.7401 (pttt) cc_final: 0.7129 (mtmm)
REVERT: B  189 GLN cc_start: 0.7820 (mt0) cc_final: 0.7124 (mm110)
REVERT: B  201 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6981 (mp0)
REVERT: B  212 TYR cc_start: 0.7892 (t80) cc_final: 0.6540 (m-10)
REVERT: B  290 MET cc_start: 0.8586 (mtm) cc_final: 0.8360 (mtp)
REVERT: B  510 SER cc_start: 0.8833 (p) cc_final: 0.8418 (m)
  outliers start: 10
  outliers final: 1
  residues processed: 182
  average time/residue: 0.5672
  time to fit residues: 107.9833
Evaluate side-chains
  139 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  471 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0970
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0870
   overall best weight:    0.8360

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 500 ASN
A 569 GLN
B 197 ASN
B 572 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.179723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.153478 restraints weight = 6938.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 1.91
r_work: 0.3611 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3479 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6152  Z= 0.119
  Angle     :  0.513   5.633   8342  Z= 0.262
  Chirality :  0.041   0.150    943
  Planarity :  0.005   0.044   1038
  Dihedral  : 10.709  92.679    867
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 11.36 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.30), residues: 711
  helix:  1.16 (0.27), residues: 308
  sheet: -0.71 (0.50), residues: 96
  loop : -0.45 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 557 
 TYR   0.013   0.001   TYR A 482 
 PHE   0.013   0.001   PHE A 196 
 TRP   0.014   0.001   TRP B 129 
 HIS   0.003   0.001   HIS B 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 6152)
  covalent geometry    : angle       0.51276 ( 8342)
  hydrogen bonds       : bond        0.04949 (  276)
  hydrogen bonds       : angle       4.74807 (  789)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 139
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  167 LYS cc_start: 0.7317 (mttt) cc_final: 0.6743 (mttp)
REVERT: A  177 LYS cc_start: 0.7286 (tttt) cc_final: 0.7042 (tttp)
REVERT: A  248 ARG cc_start: 0.7986 (ttt90) cc_final: 0.7695 (tpp-160)
REVERT: A  300 TYR cc_start: 0.8195 (t80) cc_final: 0.7790 (t80)
REVERT: A  376 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7725 (mt-10)
REVERT: A  379 ASP cc_start: 0.7709 (p0) cc_final: 0.7450 (p0)
REVERT: A  554 ARG cc_start: 0.8178 (mtt90) cc_final: 0.7531 (mtp-110)
REVERT: A  566 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7411 (mtpt)
REVERT: B  189 GLN cc_start: 0.8155 (mt0) cc_final: 0.7387 (mm110)
REVERT: B  201 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7574 (mp0)
REVERT: B  212 TYR cc_start: 0.8223 (t80) cc_final: 0.6937 (m-10)
REVERT: B  239 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.6977 (mtp85)
REVERT: B  423 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7722 (t70)
REVERT: B  436 LYS cc_start: 0.7743 (tttt) cc_final: 0.7458 (tttp)
REVERT: B  510 SER cc_start: 0.8890 (p) cc_final: 0.8563 (m)
  outliers start: 28
  outliers final: 5
  residues processed: 153
  average time/residue: 0.5795
  time to fit residues: 92.8335
Evaluate side-chains
  136 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 127
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  343 ASP
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  566 LYS
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  472 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 13 optimal weight:    8.9990
   chunk 39 optimal weight:   10.0000
   chunk 34 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 16 optimal weight:    0.1980
   chunk 44 optimal weight:    0.3980
   chunk 73 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 500 ASN
B 393 ASN
B 504 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.178172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.152060 restraints weight = 6892.180|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 1.89
r_work: 0.3606 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3473 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6152  Z= 0.122
  Angle     :  0.482   4.927   8342  Z= 0.247
  Chirality :  0.041   0.144    943
  Planarity :  0.004   0.045   1038
  Dihedral  :  8.857  88.581    865
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 13.94 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.31), residues: 711
  helix:  1.95 (0.29), residues: 310
  sheet: -0.61 (0.48), residues: 96
  loop : -0.38 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 557 
 TYR   0.011   0.001   TYR B 174 
 PHE   0.011   0.001   PHE B 452 
 TRP   0.017   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6152)
  covalent geometry    : angle       0.48240 ( 8342)
  hydrogen bonds       : bond        0.04335 (  276)
  hydrogen bonds       : angle       4.49036 (  789)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 136
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7383 (mt)
REVERT: A  167 LYS cc_start: 0.7360 (mttt) cc_final: 0.6779 (mttp)
REVERT: A  177 LYS cc_start: 0.7367 (tttt) cc_final: 0.6999 (tttp)
REVERT: A  248 ARG cc_start: 0.7973 (ttt90) cc_final: 0.7740 (tpp-160)
REVERT: A  300 TYR cc_start: 0.8222 (t80) cc_final: 0.7875 (t80)
REVERT: A  376 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7716 (mt-10)
REVERT: A  379 ASP cc_start: 0.7728 (p0) cc_final: 0.7413 (p0)
REVERT: A  554 ARG cc_start: 0.8218 (mtt90) cc_final: 0.7554 (mtp-110)
REVERT: A  566 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7334 (mmtt)
REVERT: B  189 GLN cc_start: 0.8187 (mt0) cc_final: 0.7361 (mm110)
REVERT: B  196 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.6902 (p90)
REVERT: B  201 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7656 (mm-30)
REVERT: B  212 TYR cc_start: 0.8214 (t80) cc_final: 0.6908 (m-10)
REVERT: B  239 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7068 (mtp85)
REVERT: B  395 LYS cc_start: 0.6920 (mttt) cc_final: 0.6517 (mmtt)
REVERT: B  423 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7739 (t70)
REVERT: B  436 LYS cc_start: 0.7739 (tttt) cc_final: 0.7336 (tttp)
REVERT: B  439 LYS cc_start: 0.8187 (mttt) cc_final: 0.7945 (mtpp)
REVERT: B  510 SER cc_start: 0.8924 (p) cc_final: 0.8610 (m)
  outliers start: 30
  outliers final: 8
  residues processed: 150
  average time/residue: 0.5738
  time to fit residues: 90.0402
Evaluate side-chains
  141 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  566 LYS
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  472 CYS
Chi-restraints excluded: chain B residue  508 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 50 optimal weight:    3.9990
   chunk 37 optimal weight:    8.9990
   chunk 47 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0970
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
A 421 ASN
A 500 ASN
B 504 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.176098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.151323 restraints weight = 6863.815|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 1.68
r_work: 0.3591 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3465 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6152  Z= 0.123
  Angle     :  0.473   4.958   8342  Z= 0.245
  Chirality :  0.040   0.141    943
  Planarity :  0.004   0.045   1038
  Dihedral  :  8.597  89.258    865
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 14.39 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.32), residues: 711
  helix:  2.19 (0.29), residues: 310
  sheet: -0.48 (0.48), residues: 96
  loop : -0.37 (0.37), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 557 
 TYR   0.010   0.001   TYR A 482 
 PHE   0.012   0.001   PHE B 452 
 TRP   0.018   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6152)
  covalent geometry    : angle       0.47281 ( 8342)
  hydrogen bonds       : bond        0.03928 (  276)
  hydrogen bonds       : angle       4.41509 (  789)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 132
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7302 (mt)
REVERT: A  167 LYS cc_start: 0.7486 (mttt) cc_final: 0.6832 (mttp)
REVERT: A  177 LYS cc_start: 0.7393 (tttt) cc_final: 0.7061 (tttp)
REVERT: A  248 ARG cc_start: 0.7822 (ttt90) cc_final: 0.7556 (tpp-160)
REVERT: A  376 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7610 (mt-10)
REVERT: A  554 ARG cc_start: 0.8199 (mtt90) cc_final: 0.7855 (mtt180)
REVERT: A  566 LYS cc_start: 0.7968 (mtpt) cc_final: 0.7143 (mtpt)
REVERT: B  189 GLN cc_start: 0.8161 (mt0) cc_final: 0.7359 (mm-40)
REVERT: B  196 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.6782 (p90)
REVERT: B  201 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7628 (mm-30)
REVERT: B  212 TYR cc_start: 0.8143 (t80) cc_final: 0.6745 (m-10)
REVERT: B  239 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7053 (mtp85)
REVERT: B  395 LYS cc_start: 0.6848 (mttt) cc_final: 0.6433 (mmtt)
REVERT: B  423 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7732 (t70)
REVERT: B  436 LYS cc_start: 0.7688 (tttt) cc_final: 0.7222 (tttp)
REVERT: B  510 SER cc_start: 0.8907 (p) cc_final: 0.8575 (m)
REVERT: B  570 GLU cc_start: 0.7319 (pp20) cc_final: 0.6914 (tm-30)
  outliers start: 30
  outliers final: 10
  residues processed: 148
  average time/residue: 0.5593
  time to fit residues: 86.6693
Evaluate side-chains
  139 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 124
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  155 ASN
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  343 ASP
Chi-restraints excluded: chain A residue  350 TYR
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  472 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 2 optimal weight:    9.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
B 504 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.173076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.148026 restraints weight = 7023.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 1.69
r_work: 0.3514 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3385 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   6152  Z= 0.209
  Angle     :  0.553   5.513   8342  Z= 0.284
  Chirality :  0.044   0.151    943
  Planarity :  0.005   0.049   1038
  Dihedral  :  8.862  89.859    865
  Min Nonbonded Distance : 1.835

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 14.85 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.32), residues: 711
  helix:  2.07 (0.29), residues: 310
  sheet: -0.54 (0.50), residues: 96
  loop : -0.50 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 557 
 TYR   0.013   0.002   TYR B 221 
 PHE   0.016   0.002   PHE B 452 
 TRP   0.019   0.002   TRP B 129 
 HIS   0.004   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 6152)
  covalent geometry    : angle       0.55339 ( 8342)
  hydrogen bonds       : bond        0.04748 (  276)
  hydrogen bonds       : angle       4.59772 (  789)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 125
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7321 (mt)
REVERT: A  167 LYS cc_start: 0.7421 (mttt) cc_final: 0.6731 (mttp)
REVERT: A  177 LYS cc_start: 0.7500 (tttt) cc_final: 0.7126 (tttp)
REVERT: A  248 ARG cc_start: 0.7857 (ttt90) cc_final: 0.7539 (tpp-160)
REVERT: A  302 ARG cc_start: 0.7263 (ttp80) cc_final: 0.6714 (ttp-110)
REVERT: A  376 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7738 (mt-10)
REVERT: A  379 ASP cc_start: 0.7672 (p0) cc_final: 0.7419 (p0)
REVERT: A  554 ARG cc_start: 0.8257 (mtt90) cc_final: 0.7900 (mtt180)
REVERT: A  566 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7215 (mtpt)
REVERT: B  196 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.6841 (p90)
REVERT: B  212 TYR cc_start: 0.8108 (t80) cc_final: 0.6701 (m-10)
REVERT: B  239 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7049 (mtp85)
REVERT: B  395 LYS cc_start: 0.6922 (mttt) cc_final: 0.6646 (mmmt)
REVERT: B  423 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7789 (t70)
REVERT: B  510 SER cc_start: 0.8950 (p) cc_final: 0.8579 (m)
REVERT: B  570 GLU cc_start: 0.7480 (pp20) cc_final: 0.6976 (tm-30)
  outliers start: 34
  outliers final: 12
  residues processed: 141
  average time/residue: 0.5231
  time to fit residues: 77.1409
Evaluate side-chains
  142 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  423 ASP
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  515 CYS
Chi-restraints excluded: chain A residue  566 LYS
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  472 CYS
Chi-restraints excluded: chain B residue  508 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 37 optimal weight:    7.9990
   chunk 63 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0770
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 40 optimal weight:    9.9990
   overall best weight:    1.1944

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
B 155 ASN
B 504 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.175392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.149245 restraints weight = 6897.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3646 rms_B_bonded: 1.79
r_work: 0.3540 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3409 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6152  Z= 0.124
  Angle     :  0.472   5.200   8342  Z= 0.244
  Chirality :  0.040   0.140    943
  Planarity :  0.004   0.049   1038
  Dihedral  :  8.775  92.206    865
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 16.36 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.32), residues: 711
  helix:  2.27 (0.29), residues: 310
  sheet: -0.11 (0.52), residues: 88
  loop : -0.39 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 309 
 TYR   0.009   0.001   TYR A 482 
 PHE   0.016   0.001   PHE A 253 
 TRP   0.021   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6152)
  covalent geometry    : angle       0.47228 ( 8342)
  hydrogen bonds       : bond        0.03846 (  276)
  hydrogen bonds       : angle       4.37228 (  789)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7309 (mt)
REVERT: A  167 LYS cc_start: 0.7433 (mttt) cc_final: 0.6732 (mttp)
REVERT: A  177 LYS cc_start: 0.7521 (tttt) cc_final: 0.7193 (tttp)
REVERT: A  248 ARG cc_start: 0.7833 (ttt90) cc_final: 0.7560 (tpp-160)
REVERT: A  302 ARG cc_start: 0.7332 (ttp80) cc_final: 0.6786 (ttp-110)
REVERT: A  308 MET cc_start: 0.7062 (tpt) cc_final: 0.6821 (tpp)
REVERT: A  376 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7727 (mt-10)
REVERT: A  379 ASP cc_start: 0.7728 (p0) cc_final: 0.7470 (p0)
REVERT: A  554 ARG cc_start: 0.8230 (mtt90) cc_final: 0.7896 (mtt180)
REVERT: A  566 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7187 (mtpt)
REVERT: B  196 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.6920 (p90)
REVERT: B  212 TYR cc_start: 0.8116 (t80) cc_final: 0.6707 (m-10)
REVERT: B  239 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7088 (mtp85)
REVERT: B  395 LYS cc_start: 0.6947 (mttt) cc_final: 0.6527 (mmtt)
REVERT: B  423 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7770 (t70)
REVERT: B  510 SER cc_start: 0.8910 (p) cc_final: 0.8564 (m)
REVERT: B  570 GLU cc_start: 0.7489 (pp20) cc_final: 0.7032 (tm-30)
  outliers start: 33
  outliers final: 13
  residues processed: 151
  average time/residue: 0.4914
  time to fit residues: 77.8022
Evaluate side-chains
  146 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  566 LYS
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  189 GLN
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  472 CYS
Chi-restraints excluded: chain B residue  513 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 37 optimal weight:    8.9990
   chunk 66 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
B 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.174079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.149236 restraints weight = 6948.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 1.68
r_work: 0.3538 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3410 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6152  Z= 0.154
  Angle     :  0.508   5.384   8342  Z= 0.262
  Chirality :  0.041   0.147    943
  Planarity :  0.005   0.049   1038
  Dihedral  :  8.694  92.430    865
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 17.12 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.32), residues: 711
  helix:  2.26 (0.29), residues: 310
  sheet: -0.12 (0.52), residues: 88
  loop : -0.40 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 374 
 TYR   0.010   0.001   TYR A 482 
 PHE   0.015   0.002   PHE A 253 
 TRP   0.024   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 6152)
  covalent geometry    : angle       0.50823 ( 8342)
  hydrogen bonds       : bond        0.04128 (  276)
  hydrogen bonds       : angle       4.41774 (  789)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 130
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7338 (mt)
REVERT: A  167 LYS cc_start: 0.7421 (mttt) cc_final: 0.6725 (mttp)
REVERT: A  177 LYS cc_start: 0.7520 (tttt) cc_final: 0.7188 (tttp)
REVERT: A  248 ARG cc_start: 0.7822 (ttt90) cc_final: 0.7521 (tpp-160)
REVERT: A  302 ARG cc_start: 0.7313 (ttp80) cc_final: 0.6772 (ttp-110)
REVERT: A  308 MET cc_start: 0.7047 (tpt) cc_final: 0.6755 (tpp)
REVERT: A  376 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7744 (mt-10)
REVERT: A  379 ASP cc_start: 0.7752 (p0) cc_final: 0.7482 (p0)
REVERT: A  554 ARG cc_start: 0.8262 (mtt90) cc_final: 0.7930 (mtt180)
REVERT: A  566 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7188 (mtpt)
REVERT: B  196 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.6939 (p90)
REVERT: B  212 TYR cc_start: 0.8109 (t80) cc_final: 0.6700 (m-10)
REVERT: B  239 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7063 (mtp85)
REVERT: B  395 LYS cc_start: 0.6943 (mttt) cc_final: 0.6548 (mmtt)
REVERT: B  423 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7777 (t70)
REVERT: B  510 SER cc_start: 0.8922 (p) cc_final: 0.8561 (m)
REVERT: B  570 GLU cc_start: 0.7501 (pp20) cc_final: 0.7017 (tm-30)
  outliers start: 34
  outliers final: 16
  residues processed: 147
  average time/residue: 0.5634
  time to fit residues: 86.7656
Evaluate side-chains
  149 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  423 ASP
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  515 CYS
Chi-restraints excluded: chain A residue  566 LYS
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  472 CYS
Chi-restraints excluded: chain B residue  508 CYS
Chi-restraints excluded: chain B residue  513 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 70 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 5 optimal weight:   10.0000
   chunk 64 optimal weight:    7.9990
   chunk 72 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 39 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.4982

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
B 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.174356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.148589 restraints weight = 6922.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 1.80
r_work: 0.3547 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3414 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6152  Z= 0.146
  Angle     :  0.498   5.120   8342  Z= 0.258
  Chirality :  0.041   0.140    943
  Planarity :  0.005   0.049   1038
  Dihedral  :  8.534  92.222    865
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 18.48 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.32), residues: 711
  helix:  2.26 (0.29), residues: 311
  sheet: -0.08 (0.52), residues: 88
  loop : -0.35 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 557 
 TYR   0.010   0.001   TYR A 482 
 PHE   0.015   0.002   PHE A 253 
 TRP   0.027   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 6152)
  covalent geometry    : angle       0.49845 ( 8342)
  hydrogen bonds       : bond        0.04022 (  276)
  hydrogen bonds       : angle       4.38011 (  789)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7347 (mt)
REVERT: A  167 LYS cc_start: 0.7457 (mttt) cc_final: 0.6738 (mttp)
REVERT: A  177 LYS cc_start: 0.7538 (tttt) cc_final: 0.7220 (ttpp)
REVERT: A  248 ARG cc_start: 0.7815 (ttt90) cc_final: 0.7514 (tpp-160)
REVERT: A  302 ARG cc_start: 0.7339 (ttp80) cc_final: 0.6794 (ttp-110)
REVERT: A  308 MET cc_start: 0.7055 (tpt) cc_final: 0.6777 (tpp)
REVERT: A  376 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7761 (mt-10)
REVERT: A  379 ASP cc_start: 0.7786 (p0) cc_final: 0.7544 (p0)
REVERT: A  554 ARG cc_start: 0.8249 (mtt90) cc_final: 0.7918 (mtt180)
REVERT: A  566 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7188 (mtpt)
REVERT: B  189 GLN cc_start: 0.8272 (mt0) cc_final: 0.7471 (mm-40)
REVERT: B  196 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.6893 (p90)
REVERT: B  212 TYR cc_start: 0.8112 (t80) cc_final: 0.6684 (m-10)
REVERT: B  239 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7085 (mtp85)
REVERT: B  395 LYS cc_start: 0.6950 (mttt) cc_final: 0.6535 (mmtt)
REVERT: B  423 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7805 (t70)
REVERT: B  510 SER cc_start: 0.8934 (p) cc_final: 0.8561 (m)
REVERT: B  570 GLU cc_start: 0.7496 (pp20) cc_final: 0.6959 (tm-30)
  outliers start: 28
  outliers final: 14
  residues processed: 146
  average time/residue: 0.5539
  time to fit residues: 84.7445
Evaluate side-chains
  145 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  515 CYS
Chi-restraints excluded: chain A residue  566 LYS
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  472 CYS
Chi-restraints excluded: chain B residue  508 CYS
Chi-restraints excluded: chain B residue  513 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 5 optimal weight:    9.9990
   chunk 64 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 47 optimal weight:    0.1980
   chunk 54 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 39 optimal weight:    5.9990
   chunk 57 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
B 155 ASN
B 378 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.174909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.149222 restraints weight = 6933.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 1.78
r_work: 0.3531 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3399 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6152  Z= 0.119
  Angle     :  0.487   5.411   8342  Z= 0.252
  Chirality :  0.040   0.143    943
  Planarity :  0.004   0.049   1038
  Dihedral  :  8.374  91.971    865
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 19.39 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.36 (0.32), residues: 711
  helix:  2.36 (0.29), residues: 311
  sheet: -0.08 (0.52), residues: 88
  loop : -0.27 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 557 
 TYR   0.009   0.001   TYR A 482 
 PHE   0.015   0.001   PHE A 253 
 TRP   0.030   0.001   TRP B 129 
 HIS   0.002   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6152)
  covalent geometry    : angle       0.48736 ( 8342)
  hydrogen bonds       : bond        0.03705 (  276)
  hydrogen bonds       : angle       4.29484 (  789)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7291 (mt)
REVERT: A  167 LYS cc_start: 0.7499 (mttt) cc_final: 0.6796 (mttp)
REVERT: A  177 LYS cc_start: 0.7571 (tttt) cc_final: 0.7222 (ttpp)
REVERT: A  248 ARG cc_start: 0.7829 (ttt90) cc_final: 0.7543 (tpp-160)
REVERT: A  300 TYR cc_start: 0.8012 (t80) cc_final: 0.7758 (t80)
REVERT: A  302 ARG cc_start: 0.7350 (ttp80) cc_final: 0.6807 (ttp-110)
REVERT: A  308 MET cc_start: 0.7015 (tpt) cc_final: 0.6782 (tpp)
REVERT: A  376 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7730 (mt-10)
REVERT: A  379 ASP cc_start: 0.7742 (p0) cc_final: 0.7515 (p0)
REVERT: A  554 ARG cc_start: 0.8222 (mtt90) cc_final: 0.7904 (mtt180)
REVERT: A  566 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7185 (mtpt)
REVERT: B  196 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.6889 (p90)
REVERT: B  212 TYR cc_start: 0.8142 (t80) cc_final: 0.6709 (m-10)
REVERT: B  239 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7059 (mtp85)
REVERT: B  395 LYS cc_start: 0.6952 (mttt) cc_final: 0.6546 (mmtt)
REVERT: B  423 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7770 (t70)
REVERT: B  510 SER cc_start: 0.8919 (p) cc_final: 0.8552 (m)
REVERT: B  570 GLU cc_start: 0.7474 (pp20) cc_final: 0.6955 (tm-30)
  outliers start: 24
  outliers final: 14
  residues processed: 143
  average time/residue: 0.5365
  time to fit residues: 80.6150
Evaluate side-chains
  143 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  350 TYR
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  566 LYS
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  472 CYS
Chi-restraints excluded: chain B residue  508 CYS
Chi-restraints excluded: chain B residue  513 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   chunk 73 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 17 optimal weight:    6.9990
   chunk 38 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
A 559 HIS
B 155 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.175408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.149565 restraints weight = 6911.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 1.81
r_work: 0.3553 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3423 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6152  Z= 0.123
  Angle     :  0.492   5.230   8342  Z= 0.254
  Chirality :  0.040   0.144    943
  Planarity :  0.004   0.049   1038
  Dihedral  :  8.274  90.773    865
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 19.39 %
    Favored  : 77.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.32), residues: 711
  helix:  2.34 (0.29), residues: 311
  sheet: -0.05 (0.52), residues: 88
  loop : -0.24 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 292 
 TYR   0.012   0.001   TYR B 494 
 PHE   0.014   0.001   PHE A 253 
 TRP   0.033   0.001   TRP B 129 
 HIS   0.002   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6152)
  covalent geometry    : angle       0.49242 ( 8342)
  hydrogen bonds       : bond        0.03689 (  276)
  hydrogen bonds       : angle       4.29161 (  789)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7338 (mt)
REVERT: A  167 LYS cc_start: 0.7484 (mttt) cc_final: 0.6828 (mttp)
REVERT: A  177 LYS cc_start: 0.7604 (tttt) cc_final: 0.7225 (ttpp)
REVERT: A  248 ARG cc_start: 0.7828 (ttt90) cc_final: 0.7517 (tpp-160)
REVERT: A  300 TYR cc_start: 0.7991 (t80) cc_final: 0.7752 (t80)
REVERT: A  302 ARG cc_start: 0.7343 (ttp80) cc_final: 0.6803 (ttp-110)
REVERT: A  308 MET cc_start: 0.6988 (tpt) cc_final: 0.6754 (tpp)
REVERT: A  376 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7742 (mt-10)
REVERT: A  379 ASP cc_start: 0.7771 (p0) cc_final: 0.7567 (p0)
REVERT: A  566 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7158 (mtpt)
REVERT: B  196 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.6898 (p90)
REVERT: B  212 TYR cc_start: 0.8141 (t80) cc_final: 0.6692 (m-10)
REVERT: B  239 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7037 (mtp85)
REVERT: B  344 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8274 (mm)
REVERT: B  395 LYS cc_start: 0.6938 (mttt) cc_final: 0.6650 (mmmt)
REVERT: B  423 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7766 (t70)
REVERT: B  510 SER cc_start: 0.8909 (p) cc_final: 0.8528 (m)
REVERT: B  570 GLU cc_start: 0.7440 (pp20) cc_final: 0.6922 (tm-30)
  outliers start: 22
  outliers final: 12
  residues processed: 137
  average time/residue: 0.4757
  time to fit residues: 68.7008
Evaluate side-chains
  143 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  343 ASP
Chi-restraints excluded: chain A residue  376 GLU
Chi-restraints excluded: chain A residue  477 THR
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain A residue  566 LYS
Chi-restraints excluded: chain B residue  122 ASP
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  239 ARG
Chi-restraints excluded: chain B residue  285 SER
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  472 CYS
Chi-restraints excluded: chain B residue  508 CYS
Chi-restraints excluded: chain B residue  513 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    8.9990
   chunk 8 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0370
   overall best weight:    1.5262

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
B 155 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.174495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.148882 restraints weight = 6920.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 1.77
r_work: 0.3541 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3409 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6152  Z= 0.152
  Angle     :  0.513   5.044   8342  Z= 0.266
  Chirality :  0.041   0.142    943
  Planarity :  0.005   0.049   1038
  Dihedral  :  8.289  89.039    865
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 19.39 %
    Favored  : 76.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.29 (0.32), residues: 711
  helix:  2.29 (0.29), residues: 311
  sheet: -0.07 (0.52), residues: 88
  loop : -0.32 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 557 
 TYR   0.015   0.001   TYR B 494 
 PHE   0.014   0.001   PHE A 253 
 TRP   0.033   0.002   TRP B 129 
 HIS   0.003   0.001   HIS A 559 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 6152)
  covalent geometry    : angle       0.51305 ( 8342)
  hydrogen bonds       : bond        0.03947 (  276)
  hydrogen bonds       : angle       4.36932 (  789)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2439.73 seconds
wall clock time: 42 minutes 13.77 seconds (2533.77 seconds total)