Starting phenix.real_space_refine
on Thu Jun  5 02:01:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zb0_39893/06_2025/8zb0_39893.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zb0_39893/06_2025/8zb0_39893.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zb0_39893/06_2025/8zb0_39893.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zb0_39893/06_2025/8zb0_39893.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zb0_39893/06_2025/8zb0_39893.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zb0_39893/06_2025/8zb0_39893.cif"
  }
  resolution = 3.7
  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=  -0.000 sd=   0.006
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
     Zn      8      6.06       5
     S      46      5.16       5
     C    3136      2.51       5
     N     822      2.21       5
     O     868      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 4880
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2436
          Classifications: {'peptide': 329}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 12, 'TRANS': 316}
          Chain breaks: 1
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 152
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 61
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' ZN': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2381  SG  CYS A 433      25.072  34.918  24.201  1.00 44.13           S

  Restraints were copied for chains:
    B
  Time building chain proxies: 4.16, per 1000 atoms: 0.85
  Number of scatterers: 4880
  At special positions: 0
  Unit cell: (69.966, 57.798, 125.736, 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)
     Zn      8     29.99
     S      46     16.00
     O     868      8.00
     N     822      7.00
     C    3136      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 286 " - pdb=" SG  CYS A 311 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS B 291 " distance=2.08
    Simple disulfide: pdb=" SG  CYS B 286 " - pdb=" SG  CYS B 311 " distance=2.02

  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: 1.26
  Conformation dependent library (CDL) restraints added in 614.9 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 603 "
        pdb="ZN    ZN A 603 " - pdb=" ND1 HIS A 408 "
        pdb="ZN    ZN A 603 " - pdb=" SG  CYS B 437 "
        pdb="ZN    ZN A 603 " - pdb=" ND1 HIS A 413 "
      pdb="  ZN A 604 "
        pdb="ZN    ZN A 604 " - pdb=" SG  CYS A 433 "
        pdb="ZN    ZN A 604 " - pdb=" ND1 HIS A 387 "
      pdb="  ZN B 603 "
        pdb="ZN    ZN B 603 " - pdb=" ND1 HIS B 408 "
        pdb="ZN    ZN B 603 " - pdb=" SG  CYS A 437 "
        pdb="ZN    ZN B 603 " - pdb=" ND1 HIS B 413 "
      pdb="  ZN B 604 "
        pdb="ZN    ZN B 604 " - pdb=" SG  CYS B 433 "
        pdb="ZN    ZN B 604 " - pdb=" ND1 HIS B 387 "


  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1240

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 2 sheets defined
      55.8% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 4.089A  pdb=" N   LEU A  11 " --> pdb=" O   ASN A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 47
      removed outlier: 3.621A  pdb=" N   SER A  46 " --> pdb=" O   HIS A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 57
      removed outlier: 3.694A  pdb=" N   ALA A  54 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 106
      removed outlier: 3.642A  pdb=" N   GLY A  81 " --> pdb=" O   ALA A  77 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   LEU A  83 " --> pdb=" O   VAL A  79 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   THR A  90 " --> pdb=" O   ALA A  86 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLU A 102 " --> pdb=" O   LEU A  98 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ARG A 103 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   PHE A 104 " --> pdb=" O   ALA A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 133
    Processing helix  chain 'A' and resid 243 through 268
      removed outlier: 4.138A  pdb=" N   HIS A 251 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ASP A 255 " --> pdb=" O   HIS A 251 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL A 268 " --> pdb=" O   VAL A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 299
    Processing helix  chain 'A' and resid 317 through 344
      removed outlier: 3.877A  pdb=" N   TYR A 330 " --> pdb=" O   CYS A 326 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   TYR A 333 " --> pdb=" O   LEU A 329 " (cutoff:3.500A)
      Proline residue:  A 334  - end of helix
    Processing helix  chain 'A' and resid 352 through 363
      removed outlier: 3.543A  pdb=" N   VAL A 363 " --> pdb=" O   GLU A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 395 through 409
      removed outlier: 3.737A  pdb=" N   VAL A 399 " --> pdb=" O   SER A 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 32
    Processing helix  chain 'B' and resid 43 through 47
      removed outlier: 3.622A  pdb=" N   SER B  46 " --> pdb=" O   HIS B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 57
      removed outlier: 3.694A  pdb=" N   ALA B  54 " --> pdb=" O   ALA B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 106
      removed outlier: 3.642A  pdb=" N   GLY B  81 " --> pdb=" O   ALA B  77 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   LEU B  83 " --> pdb=" O   VAL B  79 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   THR B  90 " --> pdb=" O   ALA B  86 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLU B 102 " --> pdb=" O   LEU B  98 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ARG B 103 " --> pdb=" O   GLU B  99 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   PHE B 104 " --> pdb=" O   ALA B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 133
    Processing helix  chain 'B' and resid 243 through 268
      removed outlier: 4.138A  pdb=" N   HIS B 251 " --> pdb=" O   GLY B 247 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ASP B 255 " --> pdb=" O   HIS B 251 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL B 268 " --> pdb=" O   VAL B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 299
    Processing helix  chain 'B' and resid 317 through 344
      removed outlier: 3.877A  pdb=" N   TYR B 330 " --> pdb=" O   CYS B 326 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   TYR B 333 " --> pdb=" O   LEU B 329 " (cutoff:3.500A)
      Proline residue:  B 334  - end of helix
    Processing helix  chain 'B' and resid 352 through 363
      removed outlier: 3.542A  pdb=" N   VAL B 363 " --> pdb=" O   GLU B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 409
      removed outlier: 3.737A  pdb=" N   VAL B 399 " --> pdb=" O   SER B 395 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 374 through 376
      removed outlier: 3.632A  pdb=" N   TRP A 375 " --> pdb=" O   ILE A 383 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ILE A 383 " --> pdb=" O   TRP A 375 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA A 414 " --> pdb=" O   ILE A 382 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 374 through 376
      removed outlier: 3.632A  pdb=" N   TRP B 375 " --> pdb=" O   ILE B 383 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ILE B 383 " --> pdb=" O   TRP B 375 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA B 414 " --> pdb=" O   ILE B 382 " (cutoff:3.500A)

    262 hydrogen bonds defined for protein.
    780 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: 1.20

  Time building geometry restraints manager: 1.49 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1447
        1.33 -     1.45: 722
        1.45 -     1.57: 2721
        1.57 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 4956
  Sorted by residual:
  bond pdb=" N   VAL A 313 "
       pdb=" CA  VAL A 313 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.07e-02 8.73e+03 1.14e+01
  bond pdb=" N   VAL B 313 "
       pdb=" CA  VAL B 313 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.07e-02 8.73e+03 1.13e+01
  bond pdb=" N   HIS B  65 "
       pdb=" CA  HIS B  65 "
    ideal  model  delta    sigma   weight residual
    1.455  1.489 -0.033 1.25e-02 6.40e+03 7.16e+00
  bond pdb=" N   GLN B 440 "
       pdb=" CA  GLN B 440 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.036 1.34e-02 5.57e+03 7.14e+00
  bond pdb=" N   GLN A 440 "
       pdb=" CA  GLN A 440 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.036 1.34e-02 5.57e+03 7.03e+00
  ... (remaining 4951 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 6269
        2.08 -     4.17: 413
        4.17 -     6.25: 47
        6.25 -     8.33: 15
        8.33 -    10.42: 4
  Bond angle restraints: 6748
  Sorted by residual:
  angle pdb=" C   ASP B 289 "
        pdb=" N   PRO B 290 "
        pdb=" CA  PRO B 290 "
      ideal   model   delta    sigma   weight residual
     119.05  127.32   -8.27 1.11e+00 8.12e-01 5.55e+01
  angle pdb=" C   ASP A 289 "
        pdb=" N   PRO A 290 "
        pdb=" CA  PRO A 290 "
      ideal   model   delta    sigma   weight residual
     119.05  127.31   -8.26 1.11e+00 8.12e-01 5.54e+01
  angle pdb=" N   PRO A 290 "
        pdb=" CA  PRO A 290 "
        pdb=" C   PRO A 290 "
      ideal   model   delta    sigma   weight residual
     113.53  120.63   -7.10 1.39e+00 5.18e-01 2.61e+01
  angle pdb=" N   GLU B  58 "
        pdb=" CA  GLU B  58 "
        pdb=" C   GLU B  58 "
      ideal   model   delta    sigma   weight residual
     113.88  107.62    6.26 1.23e+00 6.61e-01 2.59e+01
  angle pdb=" N   PRO B 290 "
        pdb=" CA  PRO B 290 "
        pdb=" C   PRO B 290 "
      ideal   model   delta    sigma   weight residual
     113.53  120.60   -7.07 1.39e+00 5.18e-01 2.59e+01
  ... (remaining 6743 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.49: 2567
       17.49 -    34.99: 292
       34.99 -    52.48: 74
       52.48 -    69.97: 10
       69.97 -    87.47: 4
  Dihedral angle restraints: 2947
    sinusoidal: 1043
      harmonic: 1904
  Sorted by residual:
  dihedral pdb=" CB  CYS A 286 "
           pdb=" SG  CYS A 286 "
           pdb=" SG  CYS A 311 "
           pdb=" CB  CYS A 311 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.58  -80.58     1      1.00e+01 1.00e-02 8.03e+01
  dihedral pdb=" CB  CYS B 286 "
           pdb=" SG  CYS B 286 "
           pdb=" SG  CYS B 311 "
           pdb=" CB  CYS B 311 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.57  -80.57     1      1.00e+01 1.00e-02 8.03e+01
  dihedral pdb=" CD  ARG A  59 "
           pdb=" NE  ARG A  59 "
           pdb=" CZ  ARG A  59 "
           pdb=" NH1 ARG A  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -62.80   62.80     1      1.00e+01 1.00e-02 5.21e+01
  ... (remaining 2944 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 454
       0.046 -    0.091: 278
       0.091 -    0.137: 77
       0.137 -    0.183: 25
       0.183 -    0.229: 6
  Chirality restraints: 840
  Sorted by residual:
  chirality pdb=" CA  ARG B 381 "
            pdb=" N   ARG B 381 "
            pdb=" C   ARG B 381 "
            pdb=" CB  ARG B 381 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  ARG A 381 "
            pdb=" N   ARG A 381 "
            pdb=" C   ARG A 381 "
            pdb=" CB  ARG A 381 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CA  ARG B  59 "
            pdb=" N   ARG B  59 "
            pdb=" C   ARG B  59 "
            pdb=" CB  ARG B  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.76e-01
  ... (remaining 837 not shown)

  Planarity restraints: 846
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  59 "    0.976 9.50e-02 1.11e+02   4.38e-01 1.16e+02
        pdb=" NE  ARG B  59 "   -0.058 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  59 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  59 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  59 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  59 "   -0.976 9.50e-02 1.11e+02   4.38e-01 1.16e+02
        pdb=" NE  ARG A  59 "    0.058 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  59 "    0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  59 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  59 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  30 "    0.574 9.50e-02 1.11e+02   2.57e-01 4.04e+01
        pdb=" NE  ARG B  30 "   -0.034 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  30 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  30 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  30 "    0.019 2.00e-02 2.50e+03
  ... (remaining 843 not shown)

  Histogram of nonbonded interaction distances:
        1.68 -     2.33: 19
        2.33 -     2.97: 2688
        2.97 -     3.61: 6670
        3.61 -     4.26: 9805
        4.26 -     4.90: 16492
  Nonbonded interactions: 35674
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 420 "
            pdb="ZN    ZN B 604 "
     model   vdw
     1.682 2.230
  nonbonded pdb=" OE2 GLU A 420 "
            pdb="ZN    ZN A 604 "
     model   vdw
     1.682 2.230
  nonbonded pdb=" OD2 ASP A 255 "
            pdb="ZN    ZN A 602 "
     model   vdw
     1.759 2.230
  nonbonded pdb=" OD2 ASP B 255 "
            pdb="ZN    ZN B 602 "
     model   vdw
     1.759 2.230
  nonbonded pdb=" OD2 ASP A  47 "
            pdb="ZN    ZN A 602 "
     model   vdw
     1.793 2.230
  ... (remaining 35669 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.420
  Find NCS groups from input model:        0.080
  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:             0.010
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
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      :  0.021   0.628   4969  Z= 0.813
  Angle     :  1.175  10.416   6754  Z= 0.696
  Chirality :  0.063   0.229    840
  Planarity :  0.025   0.438    846
  Dihedral  : 15.898  87.467   1698
  Min Nonbonded Distance : 1.682

Molprobity Statistics.
  All-atom Clashscore : 16.25
  Ramachandran Plot:
    Outliers :  0.92 %
    Allowed  : 12.00 %
    Favored  : 87.08 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 16.14 %
    Favored  : 79.08 %
  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: -4.98 (0.24), residues: 650
  helix: -2.34 (0.21), residues: 378
  sheet: -6.06 (0.22), residues: 32
  loop : -4.39 (0.27), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.004   TRP A 375 
 HIS   0.005   0.001   HIS B 251 
 PHE   0.023   0.003   PHE A  21 
 TYR   0.010   0.002   TYR A 396 
 ARG   0.008   0.001   ARG B  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15082 (  262)
  hydrogen bonds       : angle       6.76006 (  780)
  metal coordination   : bond        0.38002 (   10)
  SS BOND              : bond        0.02893 (    3)
  SS BOND              : angle       1.46528 (    6)
  covalent geometry    : bond        0.01303 ( 4956)
  covalent geometry    : angle       1.17499 ( 6748)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 66
  time to evaluate  : 0.519 
Fit side-chains
REVERT: A  246 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.6383 (mmm160)
REVERT: A  312 TRP cc_start: 0.5026 (OUTLIER) cc_final: 0.4814 (t60)
REVERT: A  391 GLU cc_start: 0.7111 (tp30) cc_final: 0.6719 (pm20)
REVERT: B  246 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6340 (mmm160)
REVERT: B  312 TRP cc_start: 0.5213 (OUTLIER) cc_final: 0.4865 (t60)
REVERT: B  330 TYR cc_start: 0.8650 (t80) cc_final: 0.8430 (t80)
REVERT: B  391 GLU cc_start: 0.7164 (tp30) cc_final: 0.6721 (pm20)
  outliers start: 24
  outliers final: 18
  residues processed: 88
  average time/residue: 0.1927
  time to fit residues: 21.1497
Evaluate side-chains
  77 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 55
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ARG
Chi-restraints excluded: chain A residue   58 GLU
Chi-restraints excluded: chain A residue  246 ARG
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  312 TRP
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  317 ASP
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  381 ARG
Chi-restraints excluded: chain A residue  437 CYS
Chi-restraints excluded: chain A residue  441 CYS
Chi-restraints excluded: chain B residue   30 ARG
Chi-restraints excluded: chain B residue   58 GLU
Chi-restraints excluded: chain B residue  246 ARG
Chi-restraints excluded: chain B residue  252 VAL
Chi-restraints excluded: chain B residue  312 TRP
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  317 ASP
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  381 ARG
Chi-restraints excluded: chain B residue  437 CYS
Chi-restraints excluded: chain B residue  441 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.2980
   chunk 48 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A  65 HIS
A 108 HIS
B  65 HIS
B 108 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.188664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.161479 restraints weight = 4395.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.159838 restraints weight = 5894.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.160958 restraints weight = 5884.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   4969  Z= 0.138
  Angle     :  0.584   6.309   6754  Z= 0.308
  Chirality :  0.041   0.129    840
  Planarity :  0.003   0.028    846
  Dihedral  :  9.502  74.956    736
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.92 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 21.31 %
    Favored  : 76.10 %
  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: -2.40 (0.32), residues: 650
  helix: -0.14 (0.26), residues: 380
  sheet: -5.08 (0.53), residues: 42
  loop : -3.40 (0.35), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 375 
 HIS   0.009   0.002   HIS B 251 
 PHE   0.011   0.001   PHE A  21 
 TYR   0.007   0.001   TYR A 330 
 ARG   0.004   0.000   ARG B  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04737 (  262)
  hydrogen bonds       : angle       4.00101 (  780)
  metal coordination   : bond        0.00648 (   10)
  SS BOND              : bond        0.00140 (    3)
  SS BOND              : angle       1.24240 (    6)
  covalent geometry    : bond        0.00300 ( 4956)
  covalent geometry    : angle       0.58327 ( 6748)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.564 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7489 (tt)
REVERT: A  391 GLU cc_start: 0.6834 (tp30) cc_final: 0.6606 (pm20)
REVERT: B  314 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7383 (tt)
REVERT: B  391 GLU cc_start: 0.6818 (tp30) cc_final: 0.6554 (pm20)
  outliers start: 13
  outliers final: 3
  residues processed: 61
  average time/residue: 0.1982
  time to fit residues: 15.4974
Evaluate side-chains
  51 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   65 HIS
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  314 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 63 optimal weight:   10.0000
   chunk 59 optimal weight:    2.9990
   chunk 40 optimal weight:    0.4980
   chunk 46 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
B  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.187991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.159366 restraints weight = 4426.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.157284 restraints weight = 5883.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.158437 restraints weight = 5761.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4969  Z= 0.161
  Angle     :  0.585   6.574   6754  Z= 0.306
  Chirality :  0.042   0.131    840
  Planarity :  0.003   0.029    846
  Dihedral  :  5.623  53.420    690
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.85 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 21.31 %
    Favored  : 75.10 %
  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: -1.63 (0.33), residues: 650
  helix:  0.50 (0.27), residues: 378
  sheet: -5.58 (0.33), residues: 32
  loop : -3.08 (0.35), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 375 
 HIS   0.009   0.002   HIS B  65 
 PHE   0.012   0.001   PHE B  21 
 TYR   0.006   0.001   TYR A 396 
 ARG   0.004   0.000   ARG B  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04607 (  262)
  hydrogen bonds       : angle       3.72605 (  780)
  metal coordination   : bond        0.00262 (   10)
  SS BOND              : bond        0.00211 (    3)
  SS BOND              : angle       1.11319 (    6)
  covalent geometry    : bond        0.00382 ( 4956)
  covalent geometry    : angle       0.58474 ( 6748)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 41
  time to evaluate  : 0.567 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7591 (tt)
REVERT: B  314 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7573 (tt)
REVERT: B  391 GLU cc_start: 0.6872 (tp30) cc_final: 0.6560 (pm20)
  outliers start: 18
  outliers final: 14
  residues processed: 57
  average time/residue: 0.1382
  time to fit residues: 11.2794
Evaluate side-chains
  56 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 40
  time to evaluate  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue   65 HIS
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   78 GLU
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  342 ILE
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  397 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0570
   chunk 8 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 25 optimal weight:    0.2980
   chunk 29 optimal weight:    0.5980
   overall best weight:    0.9902

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

Flipped N/Q/H residues before XYZ refinement:
B  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.188188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.159053 restraints weight = 4478.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.156061 restraints weight = 5655.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.156717 restraints weight = 5795.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7255
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      :  0.004   0.032   4969  Z= 0.149
  Angle     :  0.555   5.952   6754  Z= 0.291
  Chirality :  0.041   0.129    840
  Planarity :  0.003   0.028    846
  Dihedral  :  5.444  51.336    690
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 20.32 %
    Favored  : 74.50 %
  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: -1.25 (0.34), residues: 650
  helix:  0.80 (0.28), residues: 380
  sheet: -5.38 (0.35), residues: 32
  loop : -2.96 (0.36), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 375 
 HIS   0.008   0.001   HIS B  65 
 PHE   0.012   0.001   PHE A  21 
 TYR   0.006   0.001   TYR A 396 
 ARG   0.003   0.000   ARG B  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04338 (  262)
  hydrogen bonds       : angle       3.53393 (  780)
  metal coordination   : bond        0.00232 (   10)
  SS BOND              : bond        0.00209 (    3)
  SS BOND              : angle       0.95802 (    6)
  covalent geometry    : bond        0.00352 ( 4956)
  covalent geometry    : angle       0.55479 ( 6748)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 36
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7541 (tt)
REVERT: A  391 GLU cc_start: 0.7088 (pm20) cc_final: 0.6746 (tp30)
REVERT: B  314 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7587 (tt)
REVERT: B  391 GLU cc_start: 0.6858 (tp30) cc_final: 0.6450 (pm20)
  outliers start: 26
  outliers final: 18
  residues processed: 60
  average time/residue: 0.1092
  time to fit residues: 9.7332
Evaluate side-chains
  55 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 35
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   65 HIS
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  397 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 20 optimal weight:    0.6980
   chunk 46 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 21 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  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.190445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.164621 restraints weight = 4433.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.161987 restraints weight = 5190.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.162680 restraints weight = 5414.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7181
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4969  Z= 0.128
  Angle     :  0.521   5.313   6754  Z= 0.273
  Chirality :  0.041   0.155    840
  Planarity :  0.003   0.027    846
  Dihedral  :  5.281  51.320    690
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  6.57 %
    Allowed  : 20.12 %
    Favored  : 73.31 %
  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: -0.65 (0.35), residues: 650
  helix:  1.37 (0.28), residues: 370
  sheet: -4.96 (0.48), residues: 32
  loop : -2.72 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 375 
 HIS   0.006   0.001   HIS B  65 
 PHE   0.011   0.001   PHE A  21 
 TYR   0.007   0.001   TYR A 330 
 ARG   0.002   0.000   ARG B  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03932 (  262)
  hydrogen bonds       : angle       3.31558 (  780)
  metal coordination   : bond        0.00217 (   10)
  SS BOND              : bond        0.00179 (    3)
  SS BOND              : angle       0.87892 (    6)
  covalent geometry    : bond        0.00295 ( 4956)
  covalent geometry    : angle       0.52048 ( 6748)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 37
  time to evaluate  : 0.482 
Fit side-chains
REVERT: A  255 ASP cc_start: 0.5307 (OUTLIER) cc_final: 0.4982 (m-30)
REVERT: B  255 ASP cc_start: 0.5346 (OUTLIER) cc_final: 0.5072 (m-30)
REVERT: B  314 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7609 (tt)
REVERT: B  391 GLU cc_start: 0.6839 (tp30) cc_final: 0.6491 (pm20)
  outliers start: 33
  outliers final: 22
  residues processed: 68
  average time/residue: 0.1182
  time to fit residues: 11.9097
Evaluate side-chains
  64 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 39
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  326 CYS
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain B residue   65 HIS
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  255 ASP
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  326 CYS
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  397 MET
Chi-restraints excluded: chain B residue  406 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 14 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.188437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.163016 restraints weight = 4383.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.160159 restraints weight = 5118.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.160769 restraints weight = 5675.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4969  Z= 0.150
  Angle     :  0.535   5.502   6754  Z= 0.280
  Chirality :  0.041   0.127    840
  Planarity :  0.003   0.026    846
  Dihedral  :  4.926  50.879    688
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  6.77 %
    Allowed  : 19.12 %
    Favored  : 74.10 %
  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: -0.36 (0.34), residues: 650
  helix:  1.65 (0.28), residues: 362
  sheet: -4.64 (0.54), residues: 32
  loop : -2.55 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 375 
 HIS   0.008   0.001   HIS B  65 
 PHE   0.012   0.001   PHE B  21 
 TYR   0.006   0.001   TYR B 396 
 ARG   0.002   0.000   ARG B  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04125 (  262)
  hydrogen bonds       : angle       3.32252 (  780)
  metal coordination   : bond        0.00241 (   10)
  SS BOND              : bond        0.00209 (    3)
  SS BOND              : angle       0.81120 (    6)
  covalent geometry    : bond        0.00359 ( 4956)
  covalent geometry    : angle       0.53456 ( 6748)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 42
  time to evaluate  : 0.480 
Fit side-chains
REVERT: A  255 ASP cc_start: 0.5294 (OUTLIER) cc_final: 0.4958 (m-30)
REVERT: B  255 ASP cc_start: 0.5381 (OUTLIER) cc_final: 0.5104 (m-30)
REVERT: B  314 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7591 (tt)
REVERT: B  368 GLU cc_start: 0.7620 (tt0) cc_final: 0.7236 (tt0)
REVERT: B  391 GLU cc_start: 0.6837 (tp30) cc_final: 0.6525 (pm20)
  outliers start: 34
  outliers final: 29
  residues processed: 74
  average time/residue: 0.1281
  time to fit residues: 13.8894
Evaluate side-chains
  74 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 42
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue  101 ILE
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  264 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  326 CYS
Chi-restraints excluded: chain A residue  332 THR
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain B residue   15 LEU
Chi-restraints excluded: chain B residue   65 HIS
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  255 ASP
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  325 VAL
Chi-restraints excluded: chain B residue  326 CYS
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  397 MET
Chi-restraints excluded: chain B residue  406 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0270
   chunk 46 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 3 optimal weight:    0.2980
   chunk 48 optimal weight:    0.0050
   chunk 42 optimal weight:    0.0040
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.2064

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

Flipped N/Q/H residues before XYZ refinement:
B  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.194621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.169633 restraints weight = 4333.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.167201 restraints weight = 5379.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.167620 restraints weight = 5327.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   4969  Z= 0.095
  Angle     :  0.479   5.542   6754  Z= 0.252
  Chirality :  0.040   0.118    840
  Planarity :  0.003   0.029    846
  Dihedral  :  4.681  53.243    688
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 22.91 %
    Favored  : 73.51 %
  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:  0.17 (0.35), residues: 650
  helix:  2.07 (0.28), residues: 370
  sheet: -3.49 (0.66), residues: 48
  loop : -2.47 (0.39), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 375 
 HIS   0.007   0.001   HIS B  65 
 PHE   0.009   0.001   PHE A  21 
 TYR   0.005   0.001   TYR B 330 
 ARG   0.002   0.000   ARG B  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03219 (  262)
  hydrogen bonds       : angle       2.98396 (  780)
  metal coordination   : bond        0.00217 (   10)
  SS BOND              : bond        0.00113 (    3)
  SS BOND              : angle       0.75428 (    6)
  covalent geometry    : bond        0.00203 ( 4956)
  covalent geometry    : angle       0.47832 ( 6748)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 45
  time to evaluate  : 0.571 
Fit side-chains
REVERT: A  391 GLU cc_start: 0.6828 (pm20) cc_final: 0.6512 (tp30)
REVERT: B  314 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7595 (tt)
REVERT: B  368 GLU cc_start: 0.7552 (tt0) cc_final: 0.7196 (tt0)
REVERT: B  391 GLU cc_start: 0.6759 (tp30) cc_final: 0.6531 (pm20)
  outliers start: 18
  outliers final: 11
  residues processed: 62
  average time/residue: 0.1389
  time to fit residues: 12.3610
Evaluate side-chains
  54 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  326 CYS
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  326 CYS
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  397 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 63 optimal weight:    0.0980
   chunk 44 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 25 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.6782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.190981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.154487 restraints weight = 4400.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.156911 restraints weight = 3425.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.158123 restraints weight = 2854.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4969  Z= 0.118
  Angle     :  0.500   5.737   6754  Z= 0.262
  Chirality :  0.040   0.121    840
  Planarity :  0.003   0.032    846
  Dihedral  :  4.666  52.706    688
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 23.31 %
    Favored  : 73.31 %
  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:  0.56 (0.35), residues: 650
  helix:  2.40 (0.28), residues: 362
  sheet: -3.90 (0.70), residues: 32
  loop : -2.19 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 375 
 HIS   0.005   0.001   HIS A 251 
 PHE   0.012   0.001   PHE A  21 
 TYR   0.005   0.001   TYR A 396 
 ARG   0.002   0.000   ARG B  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03627 (  262)
  hydrogen bonds       : angle       3.02619 (  780)
  metal coordination   : bond        0.00199 (   10)
  SS BOND              : bond        0.00153 (    3)
  SS BOND              : angle       0.68168 (    6)
  covalent geometry    : bond        0.00274 ( 4956)
  covalent geometry    : angle       0.49994 ( 6748)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 44
  time to evaluate  : 0.519 
Fit side-chains
REVERT: A  391 GLU cc_start: 0.6931 (pm20) cc_final: 0.6545 (tp30)
REVERT: B  314 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7586 (tt)
REVERT: B  368 GLU cc_start: 0.7585 (tt0) cc_final: 0.7275 (tt0)
REVERT: B  391 GLU cc_start: 0.6960 (tp30) cc_final: 0.6460 (pm20)
  outliers start: 17
  outliers final: 13
  residues processed: 60
  average time/residue: 0.1371
  time to fit residues: 12.1328
Evaluate side-chains
  58 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  326 CYS
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  397 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 29 optimal weight:    0.4980
   chunk 0 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 48 optimal weight:    7.9990
   chunk 8 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0980
   chunk 41 optimal weight:    0.0020
   overall best weight:    0.6990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.191116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.154664 restraints weight = 4341.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.157192 restraints weight = 3383.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.158624 restraints weight = 2820.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7149
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4969  Z= 0.119
  Angle     :  0.494   6.005   6754  Z= 0.259
  Chirality :  0.040   0.118    840
  Planarity :  0.003   0.033    846
  Dihedral  :  4.656  52.189    688
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 23.90 %
    Favored  : 73.11 %
  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:  0.72 (0.35), residues: 650
  helix:  2.55 (0.27), residues: 362
  sheet: -3.24 (0.66), residues: 48
  loop : -2.13 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 375 
 HIS   0.004   0.001   HIS A 251 
 PHE   0.010   0.001   PHE B  21 
 TYR   0.005   0.001   TYR B 396 
 ARG   0.002   0.000   ARG B  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03553 (  262)
  hydrogen bonds       : angle       3.00500 (  780)
  metal coordination   : bond        0.00218 (   10)
  SS BOND              : bond        0.00158 (    3)
  SS BOND              : angle       0.61293 (    6)
  covalent geometry    : bond        0.00279 ( 4956)
  covalent geometry    : angle       0.49407 ( 6748)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.540 
Fit side-chains
REVERT: A  391 GLU cc_start: 0.6823 (pm20) cc_final: 0.6498 (tp30)
REVERT: B  314 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7561 (tt)
REVERT: B  368 GLU cc_start: 0.7614 (tt0) cc_final: 0.7372 (tt0)
REVERT: B  391 GLU cc_start: 0.6952 (tp30) cc_final: 0.6462 (pm20)
  outliers start: 15
  outliers final: 13
  residues processed: 61
  average time/residue: 0.1813
  time to fit residues: 15.2664
Evaluate side-chains
  61 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  326 CYS
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  326 CYS
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  397 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 33 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 49 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0270
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.7038

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.196658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.171727 restraints weight = 4440.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.169867 restraints weight = 5944.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.170144 restraints weight = 5099.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.3329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4969  Z= 0.119
  Angle     :  0.514   8.395   6754  Z= 0.263
  Chirality :  0.041   0.118    840
  Planarity :  0.003   0.034    846
  Dihedral  :  4.641  52.287    688
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 24.10 %
    Favored  : 72.71 %
  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:  0.78 (0.35), residues: 650
  helix:  2.49 (0.27), residues: 370
  sheet: -3.54 (0.72), residues: 32
  loop : -2.14 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 375 
 HIS   0.004   0.001   HIS A 251 
 PHE   0.009   0.001   PHE B  21 
 TYR   0.005   0.001   TYR A 396 
 ARG   0.002   0.000   ARG B  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03585 (  262)
  hydrogen bonds       : angle       3.00159 (  780)
  metal coordination   : bond        0.00208 (   10)
  SS BOND              : bond        0.00152 (    3)
  SS BOND              : angle       0.57850 (    6)
  covalent geometry    : bond        0.00278 ( 4956)
  covalent geometry    : angle       0.51384 ( 6748)

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

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

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1300 Ramachandran restraints generated.
    650 Oldfield, 0 Emsley, 650 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 45
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A  391 GLU cc_start: 0.6761 (pm20) cc_final: 0.6516 (tp30)
REVERT: B  314 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7648 (tt)
REVERT: B  368 GLU cc_start: 0.7579 (tt0) cc_final: 0.7305 (tt0)
REVERT: B  391 GLU cc_start: 0.6730 (tp30) cc_final: 0.6469 (pm20)
  outliers start: 16
  outliers final: 15
  residues processed: 60
  average time/residue: 0.1858
  time to fit residues: 16.0816
Evaluate side-chains
  61 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 45
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  326 CYS
Chi-restraints excluded: chain A residue  341 LEU
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  326 CYS
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  397 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 51 optimal weight:    0.0170
   chunk 1 optimal weight:    0.9990
   chunk 7 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 53 optimal weight:    0.1980
   chunk 62 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 48 optimal weight:   10.0000
   overall best weight:    0.6022

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.192058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.166239 restraints weight = 4368.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.165012 restraints weight = 6415.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.165871 restraints weight = 5946.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.3477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4969  Z= 0.110
  Angle     :  0.496   7.375   6754  Z= 0.255
  Chirality :  0.040   0.118    840
  Planarity :  0.003   0.035    846
  Dihedral  :  4.572  52.418    688
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 23.11 %
    Favored  : 73.11 %
  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:  0.97 (0.36), residues: 650
  helix:  2.51 (0.27), residues: 376
  sheet: -3.00 (0.66), residues: 48
  loop : -1.87 (0.43), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 375 
 HIS   0.004   0.001   HIS A 251 
 PHE   0.010   0.001   PHE B  21 
 TYR   0.004   0.001   TYR A 396 
 ARG   0.002   0.000   ARG B  30 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03362 (  262)
  hydrogen bonds       : angle       2.93658 (  780)
  metal coordination   : bond        0.00198 (   10)
  SS BOND              : bond        0.00131 (    3)
  SS BOND              : angle       0.56270 (    6)
  covalent geometry    : bond        0.00257 ( 4956)
  covalent geometry    : angle       0.49628 ( 6748)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2065.92 seconds
wall clock time: 38 minutes 52.72 seconds (2332.72 seconds total)