Starting phenix.real_space_refine
on Tue Feb  3 15:41:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kvx_62603/02_2026/9kvx_62603.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kvx_62603/02_2026/9kvx_62603.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kvx_62603/02_2026/9kvx_62603.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kvx_62603/02_2026/9kvx_62603.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kvx_62603/02_2026/9kvx_62603.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kvx_62603/02_2026/9kvx_62603.cif"
  }
  resolution = 2.79
  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=  -0.000 sd=   0.010
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: 5
    Type Number    sf(0)   Gaussians
     Mn      2      7.51       5
     S      32      5.16       5
     C    2892      2.51       5
     N     720      2.21       5
     O     790      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4436
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2213
          Classifications: {'peptide': 290}
          Link IDs: {'PTRANS': 13, 'TRANS': 276}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
  Restraints were copied for chains:
    A
  Time building chain proxies: 1.17, per 1000 atoms: 0.26
  Number of scatterers: 4436
  At special positions: 0
  Unit cell: (75.492, 60.58, 111.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Mn      2     24.99
     S      32     16.00
     O     790      8.00
     N     720      7.00
     C    2892      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 273 " - pdb=" SG  CYS B 277 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 404 " - pdb=" SG  CYS B 409 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 273 " - pdb=" SG  CYS A 277 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 404 " - pdb=" SG  CYS A 409 " distance=2.03

  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: 0.29
  Conformation dependent library (CDL) restraints added in 129.2 milliseconds
  

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1088

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 2 sheets defined
      59.7% alpha, 9.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'B' and resid 14 through 32
      removed outlier: 3.592A  pdb=" N   ALA B  20 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 61
    Processing helix  chain 'B' and resid 76 through 106
      removed outlier: 3.651A  pdb=" N   ALA B  82 " --> pdb=" O   GLU B  78 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ARG B 103 " --> pdb=" O   GLU B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 122
    Processing helix  chain 'B' and resid 244 through 262
      removed outlier: 3.845A  pdb=" N   ALA B 249 " --> pdb=" O   VAL B 245 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   LEU B 250 " --> pdb=" O   MET B 246 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   GLY B 251 " --> pdb=" O   GLY B 247 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   VAL B 255 " --> pdb=" O   GLY B 251 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL B 256 " --> pdb=" O   SER B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 307
      removed outlier: 3.691A  pdb=" N   ILE B 279 " --> pdb=" O   TRP B 275 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   ASP B 280 " --> pdb=" O   GLN B 276 " (cutoff:3.500A)
      Proline residue:  B 281  - end of helix
      removed outlier: 3.675A  pdb=" N   SER B 294 " --> pdb=" O   ILE B 290 " (cutoff:3.500A)
      Proline residue:  B 297  - end of helix
      removed outlier: 3.955A  pdb=" N   ILE B 305 " --> pdb=" O   GLU B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 324
      removed outlier: 3.511A  pdb=" N   SER B 324 " --> pdb=" O   MET B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 373
    Processing helix  chain 'B' and resid 406 through 412
      removed outlier: 3.861A  pdb=" N   LYS B 411 " --> pdb=" O   GLY B 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 32
      removed outlier: 3.593A  pdb=" N   ALA A  20 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 61
    Processing helix  chain 'A' and resid 76 through 106
      removed outlier: 3.651A  pdb=" N   ALA A  82 " --> pdb=" O   GLU A  78 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG A 103 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 122
    Processing helix  chain 'A' and resid 244 through 262
      removed outlier: 3.845A  pdb=" N   ALA A 249 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   LEU A 250 " --> pdb=" O   MET A 246 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   GLY A 251 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   VAL A 255 " --> pdb=" O   GLY A 251 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   VAL A 256 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 307
      removed outlier: 3.691A  pdb=" N   ILE A 279 " --> pdb=" O   TRP A 275 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   ASP A 280 " --> pdb=" O   GLN A 276 " (cutoff:3.500A)
      Proline residue:  A 281  - end of helix
      removed outlier: 3.675A  pdb=" N   SER A 294 " --> pdb=" O   ILE A 290 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
      removed outlier: 3.955A  pdb=" N   ILE A 305 " --> pdb=" O   GLU A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 324
      removed outlier: 3.511A  pdb=" N   SER A 324 " --> pdb=" O   MET A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 373
    Processing helix  chain 'A' and resid 406 through 412
      removed outlier: 3.861A  pdb=" N   LYS A 411 " --> pdb=" O   GLY A 408 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 331 through 341
      removed outlier: 3.686A  pdb=" N   SER B 331 " --> pdb=" O   LYS B 352 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   VAL B 335 " --> pdb=" O   THR B 348 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   THR B 348 " --> pdb=" O   VAL B 335 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   ILE B 337 " --> pdb=" O   ILE B 346 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   ILE B 346 " --> pdb=" O   ILE B 337 " (cutoff:3.500A)
      removed outlier: 4.866A  pdb=" N   GLU B 339 " --> pdb=" O   LYS B 344 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   LYS B 344 " --> pdb=" O   GLU B 339 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 331 through 341
      removed outlier: 5.785A  pdb=" N   VAL A 332 " --> pdb=" O   LYS A 352 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   LYS A 352 " --> pdb=" O   VAL A 332 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   GLU A 334 " --> pdb=" O   HIS A 350 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   HIS A 350 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   LYS A 344 " --> pdb=" O   LEU A 340 " (cutoff:3.500A)

    262 hydrogen bonds defined for protein.
    762 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: 0.58

  Time building geometry restraints manager: 0.39 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 738
        1.32 -     1.45: 1128
        1.45 -     1.59: 2596
        1.59 -     1.72: 0
        1.72 -     1.85: 46
  Bond restraints: 4508
  Sorted by residual:
  bond pdb=" CA  SER B  39 "
       pdb=" CB  SER B  39 "
    ideal  model  delta    sigma   weight residual
    1.529  1.466  0.063 1.55e-02 4.16e+03 1.65e+01
  bond pdb=" CA  SER A  39 "
       pdb=" CB  SER A  39 "
    ideal  model  delta    sigma   weight residual
    1.529  1.466  0.063 1.55e-02 4.16e+03 1.63e+01
  bond pdb=" C   SER A  39 "
       pdb=" O   SER A  39 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.044 1.15e-02 7.56e+03 1.44e+01
  bond pdb=" C   MET A  44 "
       pdb=" O   MET A  44 "
    ideal  model  delta    sigma   weight residual
    1.236  1.189  0.048 1.26e-02 6.30e+03 1.43e+01
  bond pdb=" C   SER B  39 "
       pdb=" O   SER B  39 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.043 1.15e-02 7.56e+03 1.42e+01
  ... (remaining 4503 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.78: 5962
        1.78 -     3.55: 122
        3.55 -     5.33: 38
        5.33 -     7.11: 10
        7.11 -     8.89: 2
  Bond angle restraints: 6134
  Sorted by residual:
  angle pdb=" CA  SER B  39 "
        pdb=" C   SER B  39 "
        pdb=" O   SER B  39 "
      ideal   model   delta    sigma   weight residual
     120.82  116.06    4.76 1.05e+00 9.07e-01 2.05e+01
  angle pdb=" CA  SER A  39 "
        pdb=" C   SER A  39 "
        pdb=" O   SER A  39 "
      ideal   model   delta    sigma   weight residual
     120.82  116.07    4.75 1.05e+00 9.07e-01 2.05e+01
  angle pdb=" N   VAL A 264 "
        pdb=" CA  VAL A 264 "
        pdb=" C   VAL A 264 "
      ideal   model   delta    sigma   weight residual
     112.80  108.36    4.44 1.15e+00 7.56e-01 1.49e+01
  angle pdb=" N   VAL B 264 "
        pdb=" CA  VAL B 264 "
        pdb=" C   VAL B 264 "
      ideal   model   delta    sigma   weight residual
     112.80  108.37    4.43 1.15e+00 7.56e-01 1.49e+01
  angle pdb=" N   GLU A  25 "
        pdb=" CA  GLU A  25 "
        pdb=" CB  GLU A  25 "
      ideal   model   delta    sigma   weight residual
     110.28  104.57    5.71 1.55e+00 4.16e-01 1.36e+01
  ... (remaining 6129 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 2342
       17.56 -    35.12: 252
       35.12 -    52.68: 76
       52.68 -    70.24: 38
       70.24 -    87.81: 6
  Dihedral angle restraints: 2714
    sinusoidal: 1036
      harmonic: 1678
  Sorted by residual:
  dihedral pdb=" CB  CYS A 404 "
           pdb=" SG  CYS A 404 "
           pdb=" SG  CYS A 409 "
           pdb=" CB  CYS A 409 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -14.18  -71.82     1      1.00e+01 1.00e-02 6.60e+01
  dihedral pdb=" CB  CYS B 404 "
           pdb=" SG  CYS B 404 "
           pdb=" SG  CYS B 409 "
           pdb=" CB  CYS B 409 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -14.20  -71.80     1      1.00e+01 1.00e-02 6.60e+01
  dihedral pdb=" CA  GLY A 123 "
           pdb=" C   GLY A 123 "
           pdb=" N   LEU A 124 "
           pdb=" CA  LEU A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.93   19.07     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 2711 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 457
       0.033 -    0.065: 236
       0.065 -    0.097: 47
       0.097 -    0.130: 26
       0.130 -    0.162: 2
  Chirality restraints: 768
  Sorted by residual:
  chirality pdb=" CA  MET A  44 "
            pdb=" N   MET A  44 "
            pdb=" C   MET A  44 "
            pdb=" CB  MET A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.57e-01
  chirality pdb=" CA  MET B  44 "
            pdb=" N   MET B  44 "
            pdb=" C   MET B  44 "
            pdb=" CB  MET B  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.35e-01
  chirality pdb=" CA  VAL B 332 "
            pdb=" N   VAL B 332 "
            pdb=" C   VAL B 332 "
            pdb=" CB  VAL B 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.18e-01
  ... (remaining 765 not shown)

  Planarity restraints: 752
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A  39 "    0.008 2.00e-02 2.50e+03   1.74e-02 3.03e+00
        pdb=" C   SER A  39 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   SER A  39 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ASP A  40 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B  39 "   -0.008 2.00e-02 2.50e+03   1.72e-02 2.97e+00
        pdb=" C   SER B  39 "    0.030 2.00e-02 2.50e+03
        pdb=" O   SER B  39 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ASP B  40 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B  44 "    0.008 2.00e-02 2.50e+03   1.69e-02 2.84e+00
        pdb=" C   MET B  44 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   MET B  44 "    0.011 2.00e-02 2.50e+03
        pdb=" N   LEU B  45 "    0.010 2.00e-02 2.50e+03
  ... (remaining 749 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 107
        2.69 -     3.24: 4279
        3.24 -     3.80: 6956
        3.80 -     4.35: 9503
        4.35 -     4.90: 15186
  Nonbonded interactions: 36031
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 248 "
            pdb="MN    MN B 501 "
     model   vdw
     2.139 2.320
  nonbonded pdb=" OD1 ASP A 248 "
            pdb="MN    MN A 501 "
     model   vdw
     2.151 2.320
  nonbonded pdb=" OG  SER A 252 "
            pdb="MN    MN A 501 "
     model   vdw
     2.152 2.320
  nonbonded pdb=" OG  SER B 252 "
            pdb="MN    MN B 501 "
     model   vdw
     2.183 2.320
  nonbonded pdb=" OD1 ASP B  40 "
            pdb="MN    MN B 501 "
     model   vdw
     2.204 2.320
  ... (remaining 36026 not shown)

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

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:             1.720
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.630
  Find NCS groups from input model:        0.030
  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:6.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
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      :  0.005   0.083   4512  Z= 0.248
  Angle     :  0.707   8.887   6142  Z= 0.379
  Chirality :  0.042   0.162    768
  Planarity :  0.004   0.029    752
  Dihedral  : 18.068  87.806   1614
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 32.13 %
    Favored  : 65.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.73 (0.35), residues: 568
  helix: -1.59 (0.26), residues: 328
  sheet: -0.76 (0.79), residues: 50
  loop :  0.08 (0.47), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 109 
 TYR   0.015   0.001   TYR A 263 
 PHE   0.008   0.001   PHE B 382 
 TRP   0.007   0.002   TRP B 338 
 HIS   0.004   0.002   HIS B 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 4508)
  covalent geometry    : angle       0.69983 ( 6134)
  SS BOND              : bond        0.00686 (    4)
  SS BOND              : angle       2.82483 (    8)
  hydrogen bonds       : bond        0.23689 (  262)
  hydrogen bonds       : angle       9.34546 (  762)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 169
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 4
  residues processed: 177
  average time/residue: 0.4892
  time to fit residues: 89.5957
Evaluate side-chains
  130 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 126
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 SER
Chi-restraints excluded: chain B residue  415 CYS
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue  415 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 56 optimal weight:    0.1980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0670
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
B  43 ASN
B 308 GLN
B 336 HIS
B 401 ASN
A 308 GLN
A 384 ASN
A 401 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.110878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.086181 restraints weight = 7081.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 3.03
r_work: 0.2923 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.2478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4512  Z= 0.154
  Angle     :  0.680   9.463   6142  Z= 0.333
  Chirality :  0.042   0.146    768
  Planarity :  0.004   0.022    752
  Dihedral  :  5.273  39.205    614
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 35.94 %
    Favored  : 59.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.36), residues: 568
  helix: -0.06 (0.28), residues: 348
  sheet: -0.49 (0.77), residues: 50
  loop :  0.24 (0.50), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 103 
 TYR   0.010   0.001   TYR B 263 
 PHE   0.009   0.001   PHE B  88 
 TRP   0.007   0.001   TRP A 338 
 HIS   0.004   0.001   HIS A 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 4508)
  covalent geometry    : angle       0.67966 ( 6134)
  SS BOND              : bond        0.00400 (    4)
  SS BOND              : angle       1.13256 (    8)
  hydrogen bonds       : bond        0.04904 (  262)
  hydrogen bonds       : angle       4.93503 (  762)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   10 ARG cc_start: 0.4138 (pmt-80) cc_final: 0.3888 (pmt-80)
REVERT: B   14 MET cc_start: 0.8139 (mmt) cc_final: 0.7917 (mmt)
REVERT: B  103 ARG cc_start: 0.8819 (ttm-80) cc_final: 0.8574 (mtt180)
REVERT: B  263 TYR cc_start: 0.8681 (t80) cc_final: 0.8401 (t80)
REVERT: A   10 ARG cc_start: 0.4169 (pmt-80) cc_final: 0.3959 (pmt-80)
REVERT: A   43 ASN cc_start: 0.8721 (t0) cc_final: 0.8446 (t160)
REVERT: A  263 TYR cc_start: 0.8651 (t80) cc_final: 0.8418 (t80)
  outliers start: 24
  outliers final: 11
  residues processed: 153
  average time/residue: 0.4957
  time to fit residues: 78.3870
Evaluate side-chains
  146 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 135
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   46 SER
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  293 SER
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  397 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 46 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 384 ASN
B 401 ASN
A 384 ASN
A 401 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.109312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.084354 restraints weight = 6997.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 3.03
r_work: 0.2924 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4512  Z= 0.149
  Angle     :  0.620   8.741   6142  Z= 0.299
  Chirality :  0.042   0.135    768
  Planarity :  0.003   0.021    752
  Dihedral  :  4.698  21.938    612
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  5.62 %
    Allowed  : 33.94 %
    Favored  : 60.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.37), residues: 568
  helix:  0.80 (0.28), residues: 348
  sheet: -0.03 (0.78), residues: 50
  loop :  0.20 (0.52), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 357 
 TYR   0.014   0.002   TYR B 359 
 PHE   0.008   0.001   PHE B  88 
 TRP   0.007   0.001   TRP A 338 
 HIS   0.003   0.001   HIS B 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 4508)
  covalent geometry    : angle       0.61800 ( 6134)
  SS BOND              : bond        0.00308 (    4)
  SS BOND              : angle       1.41117 (    8)
  hydrogen bonds       : bond        0.04260 (  262)
  hydrogen bonds       : angle       4.34116 (  762)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 138
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   99 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8113 (mm-30)
REVERT: B  280 ASP cc_start: 0.8627 (t0) cc_final: 0.8417 (t0)
REVERT: A   43 ASN cc_start: 0.8712 (t0) cc_final: 0.8415 (t160)
REVERT: A  103 ARG cc_start: 0.8706 (ttm170) cc_final: 0.8420 (mtt-85)
REVERT: A  280 ASP cc_start: 0.8633 (t0) cc_final: 0.8406 (t0)
  outliers start: 28
  outliers final: 12
  residues processed: 149
  average time/residue: 0.4290
  time to fit residues: 66.0652
Evaluate side-chains
  139 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  293 SER
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  316 MET
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0470
   chunk 38 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0170
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.4716

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

Flipped N/Q/H residues before XYZ refinement:
B 333 HIS
B 401 ASN
A 401 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.109311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.084833 restraints weight = 6909.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 3.00
r_work: 0.2918 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.3230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4512  Z= 0.129
  Angle     :  0.596   6.100   6142  Z= 0.292
  Chirality :  0.042   0.140    768
  Planarity :  0.003   0.025    752
  Dihedral  :  4.467  19.024    610
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 33.53 %
    Favored  : 62.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.29 (0.37), residues: 568
  helix:  1.29 (0.29), residues: 350
  sheet:  0.18 (0.75), residues: 50
  loop :  0.37 (0.53), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 367 
 TYR   0.013   0.001   TYR A 359 
 PHE   0.007   0.001   PHE B  88 
 TRP   0.007   0.001   TRP A 338 
 HIS   0.002   0.001   HIS A 244 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 4508)
  covalent geometry    : angle       0.59371 ( 6134)
  SS BOND              : bond        0.00449 (    4)
  SS BOND              : angle       1.48415 (    8)
  hydrogen bonds       : bond        0.03860 (  262)
  hydrogen bonds       : angle       3.99476 (  762)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  103 ARG cc_start: 0.8495 (ttm170) cc_final: 0.8278 (mtt-85)
REVERT: B  108 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7777 (pt0)
REVERT: B  263 TYR cc_start: 0.8630 (t80) cc_final: 0.8017 (t80)
REVERT: B  315 ASN cc_start: 0.8679 (t0) cc_final: 0.8164 (t0)
REVERT: B  355 LYS cc_start: 0.9037 (tppp) cc_final: 0.8379 (tppp)
REVERT: A   43 ASN cc_start: 0.8683 (t0) cc_final: 0.8364 (t0)
REVERT: A   99 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8056 (mm-30)
REVERT: A  263 TYR cc_start: 0.8666 (t80) cc_final: 0.7925 (t80)
REVERT: A  280 ASP cc_start: 0.8561 (t0) cc_final: 0.8357 (t0)
REVERT: A  315 ASN cc_start: 0.8666 (t0) cc_final: 0.8138 (t0)
  outliers start: 20
  outliers final: 9
  residues processed: 146
  average time/residue: 0.3933
  time to fit residues: 59.4805
Evaluate side-chains
  136 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 127
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  293 SER
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  398 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 53 optimal weight:    0.6980
   chunk 24 optimal weight:    0.4980
   chunk 12 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 31 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 333 HIS
B 401 ASN
A 401 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.109280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.084654 restraints weight = 6953.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 3.03
r_work: 0.2929 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4512  Z= 0.139
  Angle     :  0.595   6.679   6142  Z= 0.292
  Chirality :  0.042   0.124    768
  Planarity :  0.003   0.036    752
  Dihedral  :  4.458  19.745    610
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 33.13 %
    Favored  : 62.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.37), residues: 568
  helix:  1.69 (0.29), residues: 346
  sheet:  0.56 (0.75), residues: 50
  loop :  0.42 (0.52), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 357 
 TYR   0.013   0.002   TYR B 359 
 PHE   0.007   0.001   PHE B  88 
 TRP   0.007   0.001   TRP A 338 
 HIS   0.002   0.001   HIS B 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 4508)
  covalent geometry    : angle       0.59249 ( 6134)
  SS BOND              : bond        0.00890 (    4)
  SS BOND              : angle       1.59574 (    8)
  hydrogen bonds       : bond        0.03712 (  262)
  hydrogen bonds       : angle       3.87207 (  762)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: B  108 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7705 (pt0)
REVERT: B  315 ASN cc_start: 0.8705 (t0) cc_final: 0.8191 (t0)
REVERT: B  355 LYS cc_start: 0.8920 (tppp) cc_final: 0.8446 (tppp)
REVERT: B  365 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8277 (mttt)
REVERT: A   43 ASN cc_start: 0.8669 (t0) cc_final: 0.8351 (t0)
REVERT: A   59 TYR cc_start: 0.8856 (t80) cc_final: 0.8615 (t80)
REVERT: A   99 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7962 (mm-30)
REVERT: A  280 ASP cc_start: 0.8635 (t0) cc_final: 0.8413 (t0)
REVERT: A  315 ASN cc_start: 0.8679 (t0) cc_final: 0.8149 (t0)
REVERT: A  339 GLU cc_start: 0.8910 (tt0) cc_final: 0.8654 (tt0)
REVERT: A  355 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8802 (mmmm)
REVERT: A  365 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8299 (mttt)
REVERT: A  384 ASN cc_start: 0.8795 (m110) cc_final: 0.8292 (m110)
  outliers start: 20
  outliers final: 9
  residues processed: 138
  average time/residue: 0.4750
  time to fit residues: 67.6559
Evaluate side-chains
  136 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  293 SER
Chi-restraints excluded: chain B residue  365 LYS
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  365 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 37 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0870
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
B 333 HIS
B 401 ASN
A 401 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.108851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.084057 restraints weight = 6994.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 3.08
r_work: 0.2908 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.3655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4512  Z= 0.136
  Angle     :  0.654   9.635   6142  Z= 0.309
  Chirality :  0.042   0.126    768
  Planarity :  0.004   0.042    752
  Dihedral  :  4.419  19.413    610
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 32.73 %
    Favored  : 63.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.90 (0.37), residues: 568
  helix:  1.87 (0.29), residues: 346
  sheet:  0.61 (0.74), residues: 50
  loop :  0.35 (0.51), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 357 
 TYR   0.013   0.001   TYR A 359 
 PHE   0.007   0.001   PHE B  88 
 TRP   0.007   0.001   TRP A 338 
 HIS   0.002   0.000   HIS B 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 4508)
  covalent geometry    : angle       0.65186 ( 6134)
  SS BOND              : bond        0.00544 (    4)
  SS BOND              : angle       1.74199 (    8)
  hydrogen bonds       : bond        0.03558 (  262)
  hydrogen bonds       : angle       3.75930 (  762)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: B   99 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8025 (mm-30)
REVERT: B  315 ASN cc_start: 0.8681 (t0) cc_final: 0.8165 (t0)
REVERT: B  365 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8284 (mttt)
REVERT: A   43 ASN cc_start: 0.8690 (t0) cc_final: 0.8350 (t0)
REVERT: A   99 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7978 (mm-30)
REVERT: A  315 ASN cc_start: 0.8638 (t0) cc_final: 0.8098 (t0)
REVERT: A  339 GLU cc_start: 0.8937 (tt0) cc_final: 0.8668 (tt0)
REVERT: A  355 LYS cc_start: 0.9147 (ttmt) cc_final: 0.8607 (mmmm)
REVERT: A  365 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8270 (mttt)
REVERT: A  384 ASN cc_start: 0.8816 (m110) cc_final: 0.8479 (t0)
  outliers start: 21
  outliers final: 13
  residues processed: 134
  average time/residue: 0.4325
  time to fit residues: 59.9611
Evaluate side-chains
  138 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  293 SER
Chi-restraints excluded: chain B residue  322 LYS
Chi-restraints excluded: chain B residue  365 LYS
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  322 LYS
Chi-restraints excluded: chain A residue  365 LYS
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0870
   chunk 44 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 57 optimal weight:    0.1980
   chunk 50 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
B 333 HIS
B 401 ASN
A 401 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.110303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.085516 restraints weight = 7021.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 3.11
r_work: 0.2921 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.3717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4512  Z= 0.124
  Angle     :  0.647   8.336   6142  Z= 0.306
  Chirality :  0.042   0.123    768
  Planarity :  0.003   0.021    752
  Dihedral  :  4.443  19.061    610
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 33.73 %
    Favored  : 62.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.37), residues: 568
  helix:  2.03 (0.29), residues: 346
  sheet:  0.65 (0.74), residues: 50
  loop :  0.33 (0.51), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 103 
 TYR   0.024   0.002   TYR A  59 
 PHE   0.006   0.001   PHE A  68 
 TRP   0.007   0.001   TRP A 338 
 HIS   0.004   0.001   HIS B 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4508)
  covalent geometry    : angle       0.64218 ( 6134)
  SS BOND              : bond        0.00422 (    4)
  SS BOND              : angle       2.18426 (    8)
  hydrogen bonds       : bond        0.03418 (  262)
  hydrogen bonds       : angle       3.71059 (  762)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: B   66 ARG cc_start: 0.7691 (mmm160) cc_final: 0.7369 (mmm160)
REVERT: B   99 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8089 (mm-30)
REVERT: B  315 ASN cc_start: 0.8692 (t0) cc_final: 0.8159 (t0)
REVERT: B  365 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8302 (mttt)
REVERT: A   43 ASN cc_start: 0.8707 (t0) cc_final: 0.8392 (t0)
REVERT: A   66 ARG cc_start: 0.7639 (mmm160) cc_final: 0.7248 (mmm160)
REVERT: A   99 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8001 (mm-30)
REVERT: A  108 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7695 (pt0)
REVERT: A  315 ASN cc_start: 0.8690 (t0) cc_final: 0.8151 (t0)
REVERT: A  339 GLU cc_start: 0.8948 (tt0) cc_final: 0.8687 (tt0)
REVERT: A  355 LYS cc_start: 0.9126 (ttmt) cc_final: 0.8833 (mmmm)
REVERT: A  365 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8290 (mttt)
REVERT: A  384 ASN cc_start: 0.8838 (m110) cc_final: 0.8353 (m110)
  outliers start: 18
  outliers final: 12
  residues processed: 139
  average time/residue: 0.4882
  time to fit residues: 69.9813
Evaluate side-chains
  139 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  293 SER
Chi-restraints excluded: chain B residue  322 LYS
Chi-restraints excluded: chain B residue  365 LYS
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  322 LYS
Chi-restraints excluded: chain A residue  365 LYS
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 22 optimal weight:    0.0050
   chunk 0 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.5794

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

Flipped N/Q/H residues before XYZ refinement:
B 333 HIS
B 401 ASN
A 401 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.109612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.084909 restraints weight = 6999.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 3.11
r_work: 0.2917 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.3911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4512  Z= 0.141
  Angle     :  0.685   9.316   6142  Z= 0.328
  Chirality :  0.042   0.124    768
  Planarity :  0.005   0.090    752
  Dihedral  :  4.527  22.138    610
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 33.53 %
    Favored  : 62.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.14 (0.37), residues: 568
  helix:  2.11 (0.29), residues: 346
  sheet:  0.68 (0.74), residues: 50
  loop :  0.31 (0.51), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  63 
 TYR   0.025   0.002   TYR A  59 
 PHE   0.007   0.001   PHE B  88 
 TRP   0.007   0.001   TRP A 338 
 HIS   0.004   0.001   HIS B 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 4508)
  covalent geometry    : angle       0.67910 ( 6134)
  SS BOND              : bond        0.00498 (    4)
  SS BOND              : angle       2.52972 (    8)
  hydrogen bonds       : bond        0.03448 (  262)
  hydrogen bonds       : angle       3.68059 (  762)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 127
  time to evaluate  : 0.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   66 ARG cc_start: 0.7682 (mmm160) cc_final: 0.7357 (mmm160)
REVERT: B   99 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8036 (mm-30)
REVERT: B  315 ASN cc_start: 0.8654 (t0) cc_final: 0.8088 (t0)
REVERT: B  365 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8301 (mttt)
REVERT: A   43 ASN cc_start: 0.8680 (t0) cc_final: 0.8347 (t0)
REVERT: A   66 ARG cc_start: 0.7638 (mmm160) cc_final: 0.7244 (mmm160)
REVERT: A   99 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8043 (mm-30)
REVERT: A  108 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7682 (pt0)
REVERT: A  315 ASN cc_start: 0.8632 (t0) cc_final: 0.8056 (t0)
REVERT: A  339 GLU cc_start: 0.8943 (tt0) cc_final: 0.8674 (tt0)
REVERT: A  355 LYS cc_start: 0.9134 (ttmt) cc_final: 0.8599 (mmmm)
REVERT: A  365 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8255 (mttt)
REVERT: A  384 ASN cc_start: 0.8834 (m110) cc_final: 0.8499 (t0)
  outliers start: 18
  outliers final: 14
  residues processed: 137
  average time/residue: 0.5123
  time to fit residues: 72.4844
Evaluate side-chains
  139 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  293 SER
Chi-restraints excluded: chain B residue  322 LYS
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  365 LYS
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  322 LYS
Chi-restraints excluded: chain A residue  365 LYS
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 401 ASN
A 401 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.108921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.084210 restraints weight = 6998.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 3.11
r_work: 0.2919 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.3973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4512  Z= 0.153
  Angle     :  0.696   9.301   6142  Z= 0.334
  Chirality :  0.043   0.125    768
  Planarity :  0.004   0.056    752
  Dihedral  :  4.606  25.669    610
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 34.74 %
    Favored  : 62.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.03 (0.37), residues: 568
  helix:  2.08 (0.29), residues: 346
  sheet:  0.70 (0.75), residues: 50
  loop :  0.12 (0.52), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  63 
 TYR   0.025   0.002   TYR A  59 
 PHE   0.008   0.001   PHE B  88 
 TRP   0.006   0.001   TRP A 338 
 HIS   0.007   0.001   HIS A 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 4508)
  covalent geometry    : angle       0.68682 ( 6134)
  SS BOND              : bond        0.00240 (    4)
  SS BOND              : angle       3.14144 (    8)
  hydrogen bonds       : bond        0.03476 (  262)
  hydrogen bonds       : angle       3.67100 (  762)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   66 ARG cc_start: 0.7644 (mmm160) cc_final: 0.7300 (mmm160)
REVERT: B   99 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8032 (mm-30)
REVERT: B  271 ASP cc_start: 0.8123 (m-30) cc_final: 0.7873 (m-30)
REVERT: B  315 ASN cc_start: 0.8663 (t0) cc_final: 0.8095 (t0)
REVERT: B  365 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8302 (mttt)
REVERT: A   43 ASN cc_start: 0.8734 (t0) cc_final: 0.8398 (t0)
REVERT: A   66 ARG cc_start: 0.7666 (mmm160) cc_final: 0.7265 (mmm160)
REVERT: A   99 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8004 (mm-30)
REVERT: A  263 TYR cc_start: 0.8586 (t80) cc_final: 0.7855 (t80)
REVERT: A  315 ASN cc_start: 0.8660 (t0) cc_final: 0.8113 (t0)
REVERT: A  339 GLU cc_start: 0.8894 (tt0) cc_final: 0.8627 (tt0)
REVERT: A  355 LYS cc_start: 0.9144 (ttmt) cc_final: 0.8581 (mmmm)
REVERT: A  365 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8289 (mttt)
REVERT: A  384 ASN cc_start: 0.8831 (m110) cc_final: 0.8478 (t0)
  outliers start: 15
  outliers final: 13
  residues processed: 136
  average time/residue: 0.6121
  time to fit residues: 85.7895
Evaluate side-chains
  140 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  293 SER
Chi-restraints excluded: chain B residue  322 LYS
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  365 LYS
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  322 LYS
Chi-restraints excluded: chain A residue  365 LYS
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 43 optimal weight:    0.1980
   chunk 25 optimal weight:    0.0970
   chunk 23 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
B 401 ASN
A 401 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.110138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.085186 restraints weight = 6950.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 3.13
r_work: 0.2936 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.2936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.4142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4512  Z= 0.138
  Angle     :  0.707   9.579   6142  Z= 0.341
  Chirality :  0.043   0.125    768
  Planarity :  0.004   0.045    752
  Dihedral  :  4.676  27.865    610
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 34.54 %
    Favored  : 62.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.05 (0.38), residues: 568
  helix:  2.13 (0.29), residues: 346
  sheet:  0.77 (0.76), residues: 50
  loop :  0.01 (0.52), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  63 
 TYR   0.023   0.002   TYR A  59 
 PHE   0.007   0.001   PHE B  88 
 TRP   0.007   0.001   TRP A 338 
 HIS   0.006   0.001   HIS B 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4508)
  covalent geometry    : angle       0.69543 ( 6134)
  SS BOND              : bond        0.00102 (    4)
  SS BOND              : angle       3.58939 (    8)
  hydrogen bonds       : bond        0.03373 (  262)
  hydrogen bonds       : angle       3.60780 (  762)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   66 ARG cc_start: 0.7618 (mmm160) cc_final: 0.7291 (mmm160)
REVERT: B   99 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7872 (mm-30)
REVERT: B  263 TYR cc_start: 0.8549 (t80) cc_final: 0.7841 (t80)
REVERT: B  315 ASN cc_start: 0.8651 (t0) cc_final: 0.8095 (t0)
REVERT: B  365 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8278 (mttt)
REVERT: A   43 ASN cc_start: 0.8681 (t0) cc_final: 0.8334 (t0)
REVERT: A   66 ARG cc_start: 0.7638 (mmm160) cc_final: 0.7253 (mmm160)
REVERT: A  108 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7590 (pt0)
REVERT: A  315 ASN cc_start: 0.8657 (t0) cc_final: 0.8208 (t0)
REVERT: A  318 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8782 (tp30)
REVERT: A  339 GLU cc_start: 0.8902 (tt0) cc_final: 0.8636 (tt0)
REVERT: A  355 LYS cc_start: 0.9145 (ttmt) cc_final: 0.8579 (mmmm)
REVERT: A  365 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8275 (mttt)
REVERT: A  384 ASN cc_start: 0.8866 (m110) cc_final: 0.8495 (m-40)
  outliers start: 16
  outliers final: 12
  residues processed: 136
  average time/residue: 0.6256
  time to fit residues: 87.8457
Evaluate side-chains
  135 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue  293 SER
Chi-restraints excluded: chain B residue  322 LYS
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  365 LYS
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  322 LYS
Chi-restraints excluded: chain A residue  365 LYS
Chi-restraints excluded: chain A residue  385 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0970
   chunk 52 optimal weight:    0.4980
   chunk 39 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0980
   chunk 53 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
B 401 ASN
A 401 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.111403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.086788 restraints weight = 6946.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3090 rms_B_bonded: 3.11
r_work: 0.2925 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.4186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   4512  Z= 0.140
  Angle     :  0.742   9.499   6142  Z= 0.360
  Chirality :  0.044   0.137    768
  Planarity :  0.004   0.043    752
  Dihedral  :  4.728  29.114    610
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 35.94 %
    Favored  : 61.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.38), residues: 568
  helix:  2.08 (0.29), residues: 346
  sheet:  0.91 (0.76), residues: 50
  loop : -0.04 (0.53), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B  63 
 TYR   0.023   0.002   TYR A  59 
 PHE   0.007   0.001   PHE B 262 
 TRP   0.007   0.001   TRP B 275 
 HIS   0.006   0.001   HIS B 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 4508)
  covalent geometry    : angle       0.73005 ( 6134)
  SS BOND              : bond        0.00176 (    4)
  SS BOND              : angle       3.82035 (    8)
  hydrogen bonds       : bond        0.03426 (  262)
  hydrogen bonds       : angle       3.66459 (  762)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1752.92 seconds
wall clock time: 30 minutes 33.96 seconds (1833.96 seconds total)