Starting phenix.real_space_refine
on Tue Jan 14 07:49:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uyh_42806/01_2025/8uyh_42806.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uyh_42806/01_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_42806/01_2025/8uyh_42806.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uyh_42806/01_2025/8uyh_42806.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uyh_42806/01_2025/8uyh_42806.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uyh_42806/01_2025/8uyh_42806.cif"
  }
  resolution = 2.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'TYR:plan': 1, 'TPO:plan-1': 1, 'ARG:plan': 1, 'HIS: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: {'TYR:plan': 1, 'TPO:plan-1': 1, 'ARG:plan': 2, 'HIS: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: 4.43, per 1000 atoms: 0.73
  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: 1.55
  Conformation dependent library (CDL) restraints added in 960.9 milliseconds
  

  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: 0.60
  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: 1.61

  Time building geometry restraints manager: 1.78 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 574 o \ 
r resid 601 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 574 or resid 601 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:             1.360
  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:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     18.010
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.060
  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:16.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.140
-------------------------------------------------------------------------------
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= 0.305
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (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
 TRP   0.006   0.001   TRP B 484 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.010   0.001   PHE B 253 
 TYR   0.011   0.001   TYR A 494 
 ARG   0.002   0.000   ARG B 384 

*********************** 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  : 0.571 
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: 1.1629
  time to fit residues: 221.3190
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  : 0.691 
-------------------------------------------------------------------------------
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 62 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   chunk 37 optimal weight:    9.9990
   chunk 29 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0970
   chunk 35 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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
A 569 GLN
B 197 ASN
B 572 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.179919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.153855 restraints weight = 6845.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 1.89
r_work: 0.3617 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3483 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6152  Z= 0.165
  Angle     :  0.512   5.781   8342  Z= 0.261
  Chirality :  0.041   0.159    943
  Planarity :  0.004   0.044   1038
  Dihedral  : 10.821  92.825    867
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 12.12 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.30), residues: 711
  helix:  1.26 (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
 TRP   0.014   0.001   TRP B 129 
 HIS   0.003   0.001   HIS B 324 
 PHE   0.012   0.001   PHE A 196 
 TYR   0.014   0.001   TYR A 482 
 ARG   0.007   0.001   ARG A 557 

*********************** 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
  165 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 0.751 
Fit side-chains
REVERT: A  167 LYS cc_start: 0.7306 (mttt) cc_final: 0.6744 (mttp)
REVERT: A  177 LYS cc_start: 0.7285 (tttt) cc_final: 0.7052 (tttp)
REVERT: A  248 ARG cc_start: 0.7964 (ttt90) cc_final: 0.7687 (tpp-160)
REVERT: A  300 TYR cc_start: 0.8199 (t80) cc_final: 0.7792 (t80)
REVERT: A  376 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7722 (mt-10)
REVERT: A  379 ASP cc_start: 0.7694 (p0) cc_final: 0.7434 (p0)
REVERT: A  554 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7542 (mtp-110)
REVERT: A  566 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7410 (mtpt)
REVERT: B  189 GLN cc_start: 0.8141 (mt0) cc_final: 0.7386 (mm110)
REVERT: B  201 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7587 (mp0)
REVERT: B  212 TYR cc_start: 0.8214 (t80) cc_final: 0.6952 (m-10)
REVERT: B  423 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7719 (t70)
REVERT: B  436 LYS cc_start: 0.7742 (tttt) cc_final: 0.7464 (tttp)
REVERT: B  510 SER cc_start: 0.8861 (p) cc_final: 0.8521 (m)
  outliers start: 24
  outliers final: 4
  residues processed: 153
  average time/residue: 1.1533
  time to fit residues: 185.0084
Evaluate side-chains
  135 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 128
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
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  285 SER
Chi-restraints excluded: chain B residue  423 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 41 optimal weight:    9.9990
   chunk 24 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:    0.3980
   chunk 7 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 52 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3996 r_free = 0.3996 target = 0.178955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.152947 restraints weight = 6928.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 1.88
r_work: 0.3604 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3470 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.2241

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= 0.167
  Angle     :  0.476   4.875   8342  Z= 0.244
  Chirality :  0.040   0.144    943
  Planarity :  0.004   0.044   1038
  Dihedral  :  8.962  88.570    865
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 14.39 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.32), residues: 711
  helix:  2.01 (0.29), residues: 310
  sheet: -0.57 (0.48), residues: 96
  loop : -0.38 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.010   0.001   PHE A 253 
 TYR   0.011   0.001   TYR B 174 
 ARG   0.005   0.000   ARG A 557 

*********************** 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
  156 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 129
  time to evaluate  : 0.893 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7379 (mt)
REVERT: A  167 LYS cc_start: 0.7345 (mttt) cc_final: 0.6756 (mttp)
REVERT: A  177 LYS cc_start: 0.7388 (tttt) cc_final: 0.7021 (tttp)
REVERT: A  248 ARG cc_start: 0.7978 (ttt90) cc_final: 0.7733 (tpp-160)
REVERT: A  300 TYR cc_start: 0.8203 (t80) cc_final: 0.7879 (t80)
REVERT: A  302 ARG cc_start: 0.7342 (ttp80) cc_final: 0.6880 (ttp-110)
REVERT: A  376 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7732 (mt-10)
REVERT: A  379 ASP cc_start: 0.7725 (p0) cc_final: 0.7427 (p0)
REVERT: A  554 ARG cc_start: 0.8194 (mtt90) cc_final: 0.7528 (mtp-110)
REVERT: A  566 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7297 (mmtt)
REVERT: B  189 GLN cc_start: 0.8169 (mt0) cc_final: 0.7353 (mm110)
REVERT: B  196 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.6888 (p90)
REVERT: B  212 TYR cc_start: 0.8225 (t80) cc_final: 0.6965 (m-10)
REVERT: B  239 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.6968 (mtp85)
REVERT: B  423 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7718 (t70)
REVERT: B  436 LYS cc_start: 0.7731 (tttt) cc_final: 0.7454 (tttp)
REVERT: B  510 SER cc_start: 0.8915 (p) cc_final: 0.8601 (m)
  outliers start: 27
  outliers final: 6
  residues processed: 142
  average time/residue: 1.1297
  time to fit residues: 168.5896
Evaluate side-chains
  134 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 57 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    9.9990
   chunk 68 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9980
   overall best weight:    1.6984

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

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

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 = 0.174278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.149421 restraints weight = 7025.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 1.69
r_work: 0.3570 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3442 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6152  Z= 0.249
  Angle     :  0.508   5.364   8342  Z= 0.262
  Chirality :  0.042   0.145    943
  Planarity :  0.005   0.045   1038
  Dihedral  :  8.734  88.614    865
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 13.94 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.32), residues: 711
  helix:  2.11 (0.29), residues: 310
  sheet: -0.50 (0.49), residues: 96
  loop : -0.46 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.015   0.002   PHE B 452 
 TYR   0.012   0.001   TYR B 221 
 ARG   0.004   0.000   ARG A 557 

*********************** 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
  161 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 129
  time to evaluate  : 0.632 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7328 (mt)
REVERT: A  167 LYS cc_start: 0.7477 (mttt) cc_final: 0.6826 (mttp)
REVERT: A  177 LYS cc_start: 0.7447 (tttt) cc_final: 0.7092 (tttp)
REVERT: A  248 ARG cc_start: 0.7880 (ttt90) cc_final: 0.7593 (tpp-160)
REVERT: A  300 TYR cc_start: 0.8123 (t80) cc_final: 0.7783 (t80)
REVERT: A  376 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7689 (mt-10)
REVERT: A  554 ARG cc_start: 0.8240 (mtt90) cc_final: 0.7532 (mtp-110)
REVERT: A  566 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7153 (mtpt)
REVERT: B  189 GLN cc_start: 0.8220 (mt0) cc_final: 0.7382 (mm110)
REVERT: B  196 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.6819 (p90)
REVERT: B  212 TYR cc_start: 0.8163 (t80) cc_final: 0.6778 (m-10)
REVERT: B  239 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7031 (mtp85)
REVERT: B  395 LYS cc_start: 0.6877 (mttt) cc_final: 0.6483 (mmtt)
REVERT: B  423 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7772 (t70)
REVERT: B  436 LYS cc_start: 0.7775 (tttt) cc_final: 0.7333 (tttp)
REVERT: B  439 LYS cc_start: 0.8232 (mttt) cc_final: 0.8006 (mtpp)
REVERT: B  510 SER cc_start: 0.8935 (p) cc_final: 0.8595 (m)
REVERT: B  570 GLU cc_start: 0.7382 (pp20) cc_final: 0.6934 (tm-30)
  outliers start: 32
  outliers final: 9
  residues processed: 145
  average time/residue: 1.1728
  time to fit residues: 178.2193
Evaluate side-chains
  141 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
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  423 ASP
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   chunk 28 optimal weight:    6.9990
   chunk 25 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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 = 0.3901 r_free = 0.3901 target = 0.171298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.146352 restraints weight = 6964.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 1.70
r_work: 0.3504 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3374 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   6152  Z= 0.405
  Angle     :  0.605   6.046   8342  Z= 0.310
  Chirality :  0.046   0.154    943
  Planarity :  0.005   0.054   1038
  Dihedral  :  9.113  89.077    865
  Min Nonbonded Distance : 1.823

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 14.39 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.31), residues: 711
  helix:  1.92 (0.29), residues: 308
  sheet: -0.27 (0.51), residues: 88
  loop : -0.58 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 129 
 HIS   0.005   0.001   HIS A 559 
 PHE   0.017   0.002   PHE A 253 
 TYR   0.016   0.002   TYR A 494 
 ARG   0.003   0.001   ARG A 302 

*********************** 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
  169 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 131
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 LYS cc_start: 0.7446 (mttt) cc_final: 0.6730 (mttp)
REVERT: A  177 LYS cc_start: 0.7538 (tttt) cc_final: 0.7187 (ttpp)
REVERT: A  248 ARG cc_start: 0.7894 (ttt90) cc_final: 0.7576 (tpp-160)
REVERT: A  300 TYR cc_start: 0.8128 (t80) cc_final: 0.7791 (t80)
REVERT: A  302 ARG cc_start: 0.7288 (ttp80) cc_final: 0.6763 (ttp-110)
REVERT: A  376 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7762 (mt-10)
REVERT: A  554 ARG cc_start: 0.8303 (mtt90) cc_final: 0.7944 (mtt180)
REVERT: A  566 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7250 (mtpt)
REVERT: B  196 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.6919 (p90)
REVERT: B  212 TYR cc_start: 0.8103 (t80) cc_final: 0.6682 (m-10)
REVERT: B  239 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7089 (mtp85)
REVERT: B  395 LYS cc_start: 0.6961 (mttt) cc_final: 0.6545 (mmtt)
REVERT: B  423 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7837 (t70)
REVERT: B  439 LYS cc_start: 0.8263 (mttt) cc_final: 0.8045 (mtpp)
REVERT: B  510 SER cc_start: 0.8960 (p) cc_final: 0.8552 (m)
REVERT: B  541 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6799 (mpt-90)
  outliers start: 38
  outliers final: 13
  residues processed: 146
  average time/residue: 1.1887
  time to fit residues: 182.0303
Evaluate side-chains
  147 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
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  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  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  374 ARG
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  541 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 170 ASN
A 189 GLN
B 155 ASN
B 504 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.174525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.149929 restraints weight = 6806.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3657 rms_B_bonded: 1.67
r_work: 0.3558 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3431 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6152  Z= 0.193
  Angle     :  0.481   5.221   8342  Z= 0.249
  Chirality :  0.040   0.143    943
  Planarity :  0.004   0.049   1038
  Dihedral  :  8.728  91.248    865
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 16.82 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.32), residues: 711
  helix:  2.14 (0.29), residues: 310
  sheet: -0.09 (0.51), residues: 88
  loop : -0.42 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.016   0.001   PHE A 253 
 TYR   0.009   0.001   TYR B 174 
 ARG   0.003   0.000   ARG B 309 

*********************** 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
  159 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 129
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7343 (mt)
REVERT: A  167 LYS cc_start: 0.7459 (mttt) cc_final: 0.6758 (mttp)
REVERT: A  177 LYS cc_start: 0.7527 (tttt) cc_final: 0.7214 (tttp)
REVERT: A  248 ARG cc_start: 0.7824 (ttt90) cc_final: 0.7519 (tpp-160)
REVERT: A  300 TYR cc_start: 0.8107 (t80) cc_final: 0.7906 (t80)
REVERT: A  302 ARG cc_start: 0.7326 (ttp80) cc_final: 0.6786 (ttp-110)
REVERT: A  308 MET cc_start: 0.7078 (tpt) cc_final: 0.6848 (tpp)
REVERT: A  376 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7720 (mt-10)
REVERT: A  379 ASP cc_start: 0.7753 (p0) cc_final: 0.7472 (p0)
REVERT: A  554 ARG cc_start: 0.8246 (mtt90) cc_final: 0.7910 (mtt180)
REVERT: A  566 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7223 (mtpt)
REVERT: B  189 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7487 (mm-40)
REVERT: B  196 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.6901 (p90)
REVERT: B  212 TYR cc_start: 0.8084 (t80) cc_final: 0.6667 (m-10)
REVERT: B  239 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7114 (mtp85)
REVERT: B  423 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7759 (t70)
REVERT: B  510 SER cc_start: 0.8924 (p) cc_final: 0.8568 (m)
  outliers start: 30
  outliers final: 11
  residues processed: 146
  average time/residue: 1.1761
  time to fit residues: 180.1096
Evaluate side-chains
  145 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
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  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 11 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 39 optimal weight:    0.3980
   chunk 60 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 45 optimal weight:    0.4980
   chunk 35 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
A 500 ASN
B 155 ASN
B 504 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.175862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.151518 restraints weight = 6872.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 1.66
r_work: 0.3571 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3445 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6152  Z= 0.154
  Angle     :  0.450   5.039   8342  Z= 0.232
  Chirality :  0.039   0.147    943
  Planarity :  0.004   0.048   1038
  Dihedral  :  8.422  93.526    865
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 18.18 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.32), residues: 711
  helix:  2.34 (0.29), residues: 311
  sheet: -0.02 (0.51), residues: 88
  loop : -0.23 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.015   0.001   PHE A 253 
 TYR   0.008   0.001   TYR A 482 
 ARG   0.003   0.000   ARG B 309 

*********************** 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
  163 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 134
  time to evaluate  : 0.672 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7306 (mt)
REVERT: A  167 LYS cc_start: 0.7500 (mttt) cc_final: 0.6802 (mttp)
REVERT: A  177 LYS cc_start: 0.7532 (tttt) cc_final: 0.7196 (tttp)
REVERT: A  248 ARG cc_start: 0.7793 (ttt90) cc_final: 0.7513 (tpp-160)
REVERT: A  302 ARG cc_start: 0.7316 (ttp80) cc_final: 0.6775 (ttp-110)
REVERT: A  308 MET cc_start: 0.6940 (tpt) cc_final: 0.6663 (tpp)
REVERT: A  376 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7689 (mt-10)
REVERT: A  379 ASP cc_start: 0.7719 (p0) cc_final: 0.7494 (p0)
REVERT: A  554 ARG cc_start: 0.8195 (mtt90) cc_final: 0.7882 (mtt180)
REVERT: A  566 LYS cc_start: 0.7973 (mtpt) cc_final: 0.7166 (mtpt)
REVERT: B  196 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.6855 (p90)
REVERT: B  212 TYR cc_start: 0.8094 (t80) cc_final: 0.6690 (m-10)
REVERT: B  239 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7062 (mtp85)
REVERT: B  423 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7742 (t70)
REVERT: B  510 SER cc_start: 0.8888 (p) cc_final: 0.8541 (m)
  outliers start: 29
  outliers final: 11
  residues processed: 151
  average time/residue: 1.1145
  time to fit residues: 176.8200
Evaluate side-chains
  138 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
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  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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 59 optimal weight:    0.1980
   chunk 37 optimal weight:    8.9990
   chunk 35 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0980
   chunk 46 optimal weight:    0.3980
   chunk 11 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
A 559 HIS
B 155 ASN
B 378 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.175886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.151525 restraints weight = 6766.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 1.66
r_work: 0.3577 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3452 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6152  Z= 0.176
  Angle     :  0.477   4.820   8342  Z= 0.248
  Chirality :  0.039   0.143    943
  Planarity :  0.004   0.048   1038
  Dihedral  :  8.305  93.461    865
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 20.00 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.32), residues: 711
  helix:  2.36 (0.29), residues: 311
  sheet: -0.04 (0.51), residues: 88
  loop : -0.23 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.014   0.001   PHE A 253 
 TYR   0.012   0.001   TYR B 494 
 ARG   0.003   0.000   ARG A 557 

*********************** 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
  151 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.659 
Fit side-chains
REVERT: A  124 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7382 (mt)
REVERT: A  167 LYS cc_start: 0.7498 (mttt) cc_final: 0.6805 (mttp)
REVERT: A  177 LYS cc_start: 0.7549 (tttt) cc_final: 0.7196 (ttpp)
REVERT: A  248 ARG cc_start: 0.7779 (ttt90) cc_final: 0.7500 (tpp-160)
REVERT: A  302 ARG cc_start: 0.7427 (ttp80) cc_final: 0.6884 (ttp-110)
REVERT: A  308 MET cc_start: 0.6930 (tpt) cc_final: 0.6693 (tpp)
REVERT: A  376 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7725 (mt-10)
REVERT: A  554 ARG cc_start: 0.8198 (mtt90) cc_final: 0.7892 (mtt180)
REVERT: A  566 LYS cc_start: 0.7985 (mtpt) cc_final: 0.7177 (mtpt)
REVERT: B  196 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.6849 (p90)
REVERT: B  212 TYR cc_start: 0.8096 (t80) cc_final: 0.6707 (m-10)
REVERT: B  239 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7042 (mtp85)
REVERT: B  423 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7726 (t70)
REVERT: B  510 SER cc_start: 0.8896 (p) cc_final: 0.8546 (m)
  outliers start: 24
  outliers final: 14
  residues processed: 141
  average time/residue: 1.1044
  time to fit residues: 164.0791
Evaluate side-chains
  141 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
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  284 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 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 5 optimal weight:    9.9990
   chunk 48 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0870
   overall best weight:    0.6160

-------------------------------------------------------------------------------
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 = 0.3965 r_free = 0.3965 target = 0.177582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.152679 restraints weight = 6835.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 1.75
r_work: 0.3580 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3452 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.2922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6152  Z= 0.148
  Angle     :  0.459   5.309   8342  Z= 0.237
  Chirality :  0.039   0.145    943
  Planarity :  0.004   0.048   1038
  Dihedral  :  8.138  93.880    865
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 20.30 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.32), residues: 711
  helix:  2.45 (0.29), residues: 311
  sheet:  0.03 (0.51), residues: 88
  loop : -0.20 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.014   0.001   PHE A 253 
 TYR   0.013   0.001   TYR B 494 
 ARG   0.003   0.000   ARG A 557 

*********************** 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
  144 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 0.747 
Fit side-chains
REVERT: A  167 LYS cc_start: 0.7494 (mttt) cc_final: 0.6805 (mttp)
REVERT: A  177 LYS cc_start: 0.7547 (tttt) cc_final: 0.7158 (ttpp)
REVERT: A  248 ARG cc_start: 0.7824 (ttt90) cc_final: 0.7506 (tpp-160)
REVERT: A  302 ARG cc_start: 0.7398 (ttp80) cc_final: 0.6856 (ttp-110)
REVERT: A  308 MET cc_start: 0.6902 (tpt) cc_final: 0.6668 (tpp)
REVERT: A  376 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7709 (mt-10)
REVERT: A  554 ARG cc_start: 0.8204 (mtt90) cc_final: 0.7902 (mtt180)
REVERT: A  566 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7142 (mtpt)
REVERT: B  196 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.6866 (p90)
REVERT: B  212 TYR cc_start: 0.8122 (t80) cc_final: 0.6706 (m-10)
REVERT: B  239 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7064 (mtp85)
REVERT: B  423 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7723 (t70)
REVERT: B  510 SER cc_start: 0.8882 (p) cc_final: 0.8537 (m)
  outliers start: 23
  outliers final: 13
  residues processed: 133
  average time/residue: 1.0463
  time to fit residues: 146.6902
Evaluate side-chains
  136 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  284 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 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  325 MET
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  423 ASP
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 20 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 45 optimal weight:    0.2980
   chunk 14 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 58 optimal weight:    0.4980
   chunk 4 optimal weight:   10.0000
   chunk 72 optimal weight:    0.7980
   overall best weight:    0.6180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.177235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.152832 restraints weight = 6941.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3691 rms_B_bonded: 1.68
r_work: 0.3594 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3470 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6152  Z= 0.149
  Angle     :  0.459   5.080   8342  Z= 0.236
  Chirality :  0.039   0.145    943
  Planarity :  0.004   0.049   1038
  Dihedral  :  8.033  94.063    865
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 21.52 %
    Favored  : 75.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.32), residues: 711
  helix:  2.49 (0.29), residues: 311
  sheet:  0.04 (0.51), residues: 88
  loop : -0.17 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.014   0.001   PHE A 253 
 TYR   0.012   0.001   TYR B 494 
 ARG   0.002   0.000   ARG A 557 

********************** 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
  140 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.666 
Fit side-chains
REVERT: A  167 LYS cc_start: 0.7476 (mttt) cc_final: 0.6839 (mttp)
REVERT: A  177 LYS cc_start: 0.7553 (tttt) cc_final: 0.7264 (ttpp)
REVERT: A  248 ARG cc_start: 0.7787 (ttt90) cc_final: 0.7490 (tpp-160)
REVERT: A  302 ARG cc_start: 0.7420 (ttp80) cc_final: 0.6888 (ttp-110)
REVERT: A  308 MET cc_start: 0.6870 (tpt) cc_final: 0.6642 (tpp)
REVERT: A  376 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7667 (mt-10)
REVERT: A  566 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7234 (mmtt)
REVERT: B  196 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.6866 (p90)
REVERT: B  212 TYR cc_start: 0.8092 (t80) cc_final: 0.6701 (m-10)
REVERT: B  239 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7028 (mtp85)
REVERT: B  423 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7722 (t70)
REVERT: B  510 SER cc_start: 0.8890 (p) cc_final: 0.8536 (m)
  outliers start: 18
  outliers final: 10
  residues processed: 132
  average time/residue: 1.0121
  time to fit residues: 140.9254
Evaluate side-chains
  135 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  284 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 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  325 MET
Chi-restraints excluded: chain B residue  366 GLN
Chi-restraints excluded: chain B residue  423 ASP
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 49 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 39 optimal weight:    8.9990
   chunk 66 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 68 optimal weight:    0.8980
   chunk 27 optimal weight:    0.8980
   chunk 2 optimal weight:    6.9990
   chunk 56 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.9184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.176312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.151835 restraints weight = 6950.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3671 rms_B_bonded: 1.69
r_work: 0.3574 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3447 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6152  Z= 0.175
  Angle     :  0.474   5.272   8342  Z= 0.246
  Chirality :  0.039   0.150    943
  Planarity :  0.004   0.049   1038
  Dihedral  :  8.031  93.247    865
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 21.82 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.50 (0.32), residues: 711
  helix:  2.45 (0.29), residues: 311
  sheet:  0.07 (0.51), residues: 88
  loop : -0.19 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP B 129 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.015   0.001   PHE A 253 
 TYR   0.013   0.001   TYR B 494 
 ARG   0.002   0.000   ARG A 557 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4827.29 seconds
wall clock time: 86 minutes 33.50 seconds (5193.50 seconds total)