Starting phenix.real_space_refine
on Wed Sep 17 05:10:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zb0_39893/09_2025/8zb0_39893.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zb0_39893/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zb0_39893/09_2025/8zb0_39893.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zb0_39893/09_2025/8zb0_39893.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zb0_39893/09_2025/8zb0_39893.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zb0_39893/09_2025/8zb0_39893.map"
  }
  resolution = 3.7
  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=   0.006
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'TYR:plan': 1, 'TRP:plan': 1, 'GLU:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2}
          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: 1.44, per 1000 atoms: 0.30
  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: 0.38
  Conformation dependent library (CDL) restraints added in 166.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  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: 0.08
  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: 0.65

  Time building geometry restraints manager: 0.49 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.730
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.620
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.720
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.008   0.001   ARG B  76 
 TYR   0.010   0.002   TYR A 396 
 PHE   0.023   0.003   PHE A  21 
 TRP   0.026   0.004   TRP A 375 
 HIS   0.005   0.001   HIS B 251 

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

*********************** 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  : 0.107 
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: 0.0885
  time to fit residues: 9.6996
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  : 0.193 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.0010
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   overall best weight:    1.1190

-------------------------------------------------------------------------------
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 = 0.4105 r_free = 0.4105 target = 0.186611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.159726 restraints weight = 4455.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.159201 restraints weight = 5515.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.159325 restraints weight = 5533.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.159932 restraints weight = 4786.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.159962 restraints weight = 4758.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4969  Z= 0.167
  Angle     :  0.614   6.611   6754  Z= 0.323
  Chirality :  0.043   0.133    840
  Planarity :  0.004   0.029    846
  Dihedral  :  9.645  74.070    736
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  7.69 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 19.72 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.53 (0.31), residues: 650
  helix: -0.24 (0.26), residues: 380
  sheet: -5.10 (0.52), residues: 42
  loop : -3.47 (0.34), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  76 
 TYR   0.009   0.001   TYR A 330 
 PHE   0.011   0.002   PHE A  21 
 TRP   0.010   0.002   TRP A 375 
 HIS   0.010   0.002   HIS B 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 4956)
  covalent geometry    : angle       0.61274 ( 6748)
  SS BOND              : bond        0.00270 (    3)
  SS BOND              : angle       1.20934 (    6)
  hydrogen bonds       : bond        0.04910 (  262)
  hydrogen bonds       : angle       4.10905 (  780)
  metal coordination   : bond        0.01017 (   10)

*********************** 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: 16
    poor density    : 46
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A  314 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7565 (tt)
REVERT: A  391 GLU cc_start: 0.6800 (tp30) cc_final: 0.6600 (pm20)
REVERT: B  314 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7554 (tt)
REVERT: B  391 GLU cc_start: 0.6853 (tp30) cc_final: 0.6576 (pm20)
  outliers start: 16
  outliers final: 9
  residues processed: 61
  average time/residue: 0.0617
  time to fit residues: 5.1552
Evaluate side-chains
  55 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 HIS
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  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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 48 optimal weight:   10.0000
   chunk 62 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0970
   chunk 56 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.7380

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.189078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.154154 restraints weight = 4423.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.156270 restraints weight = 3603.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.156943 restraints weight = 3105.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.158174 restraints weight = 2862.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.158554 restraints weight = 2644.748|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4969  Z= 0.131
  Angle     :  0.555   6.197   6754  Z= 0.292
  Chirality :  0.041   0.125    840
  Planarity :  0.003   0.030    846
  Dihedral  :  5.632  53.383    692
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.85 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 21.91 %
    Favored  : 74.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.34), residues: 650
  helix:  0.61 (0.28), residues: 378
  sheet: -5.55 (0.32), residues: 32
  loop : -3.03 (0.36), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  30 
 TYR   0.005   0.001   TYR B 330 
 PHE   0.011   0.001   PHE B  21 
 TRP   0.009   0.001   TRP A 375 
 HIS   0.007   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 4956)
  covalent geometry    : angle       0.55469 ( 6748)
  SS BOND              : bond        0.00182 (    3)
  SS BOND              : angle       1.10656 (    6)
  hydrogen bonds       : bond        0.04203 (  262)
  hydrogen bonds       : angle       3.61868 (  780)
  metal coordination   : bond        0.00195 (   10)

*********************** 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
  55 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 39
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A  102 GLU cc_start: 0.6101 (mm-30) cc_final: 0.5898 (mt-10)
REVERT: A  314 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7481 (tt)
REVERT: A  391 GLU cc_start: 0.6824 (tp30) cc_final: 0.6600 (pm20)
REVERT: B  102 GLU cc_start: 0.6092 (mm-30) cc_final: 0.5829 (mt-10)
REVERT: B  314 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7587 (tt)
REVERT: B  391 GLU cc_start: 0.6938 (tp30) cc_final: 0.6591 (pm20)
  outliers start: 16
  outliers final: 12
  residues processed: 53
  average time/residue: 0.0446
  time to fit residues: 3.5190
Evaluate side-chains
  51 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 37
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue   67 THR
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  326 CYS
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  326 CYS
Chi-restraints excluded: chain B residue  341 LEU
Chi-restraints excluded: chain B residue  366 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0980
   chunk 55 optimal weight:    3.9990
   chunk 62 optimal weight:    0.2980
   chunk 15 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 6 optimal weight:    0.2980
   chunk 47 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    0.6782

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.191189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.164165 restraints weight = 4412.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.162312 restraints weight = 5280.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.162927 restraints weight = 5960.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.163188 restraints weight = 4824.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.163921 restraints weight = 4224.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.2544

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= 0.121
  Angle     :  0.514   5.643   6754  Z= 0.271
  Chirality :  0.040   0.124    840
  Planarity :  0.003   0.030    846
  Dihedral  :  5.395  51.962    692
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 19.92 %
    Favored  : 74.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.02 (0.35), residues: 650
  helix:  0.97 (0.28), residues: 380
  sheet: -5.26 (0.37), residues: 32
  loop : -2.80 (0.38), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  30 
 TYR   0.005   0.001   TYR A 396 
 PHE   0.011   0.001   PHE A  21 
 TRP   0.009   0.001   TRP A 375 
 HIS   0.007   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 4956)
  covalent geometry    : angle       0.51348 ( 6748)
  SS BOND              : bond        0.00167 (    3)
  SS BOND              : angle       0.97073 (    6)
  hydrogen bonds       : bond        0.03882 (  262)
  hydrogen bonds       : angle       3.36948 (  780)
  metal coordination   : bond        0.00220 (   10)

*********************** 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
  64 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 37
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A  255 ASP cc_start: 0.5302 (OUTLIER) cc_final: 0.4925 (m-30)
REVERT: A  314 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7549 (tt)
REVERT: A  391 GLU cc_start: 0.6827 (tp30) cc_final: 0.6604 (pm20)
REVERT: B  314 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7606 (tt)
REVERT: B  391 GLU cc_start: 0.6843 (tp30) cc_final: 0.6476 (pm20)
  outliers start: 27
  outliers final: 16
  residues processed: 61
  average time/residue: 0.0415
  time to fit residues: 3.8447
Evaluate side-chains
  56 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 37
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue   67 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  255 ASP
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  326 CYS
Chi-restraints excluded: chain A residue  341 LEU
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 1 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 6 optimal weight:    0.3980
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.7380

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.192450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.166451 restraints weight = 4432.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.165450 restraints weight = 6234.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.163854 restraints weight = 5894.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.163621 restraints weight = 4533.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.163969 restraints weight = 3548.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7181
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4969  Z= 0.125
  Angle     :  0.514   5.270   6754  Z= 0.269
  Chirality :  0.041   0.160    840
  Planarity :  0.003   0.029    846
  Dihedral  :  5.260  51.646    691
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  6.37 %
    Allowed  : 19.52 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.35), residues: 650
  helix:  1.44 (0.28), residues: 370
  sheet: -4.82 (0.48), residues: 32
  loop : -2.63 (0.38), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  30 
 TYR   0.007   0.001   TYR B 330 
 PHE   0.012   0.001   PHE B  21 
 TRP   0.011   0.001   TRP A 375 
 HIS   0.006   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4956)
  covalent geometry    : angle       0.51369 ( 6748)
  SS BOND              : bond        0.00176 (    3)
  SS BOND              : angle       0.86813 (    6)
  hydrogen bonds       : bond        0.03811 (  262)
  hydrogen bonds       : angle       3.25588 (  780)
  metal coordination   : bond        0.00212 (   10)

*********************** 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
  71 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 39
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A  391 GLU cc_start: 0.6822 (tp30) cc_final: 0.6540 (pm20)
REVERT: B  255 ASP cc_start: 0.5408 (OUTLIER) cc_final: 0.5139 (m-30)
REVERT: B  314 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7609 (tt)
REVERT: B  391 GLU cc_start: 0.6830 (tp30) cc_final: 0.6490 (pm20)
  outliers start: 32
  outliers final: 24
  residues processed: 68
  average time/residue: 0.0445
  time to fit residues: 4.6057
Evaluate side-chains
  65 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 39
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
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  264 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  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  326 CYS
Chi-restraints excluded: chain B residue  332 THR
Chi-restraints excluded: chain B residue  341 LEU
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 35 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 17 optimal weight:    0.2980
   chunk 2 optimal weight:    0.4980
   chunk 23 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0980
   chunk 58 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.4154 r_free = 0.4154 target = 0.193317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.166661 restraints weight = 4436.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.166507 restraints weight = 6419.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.168007 restraints weight = 5480.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.163986 restraints weight = 3432.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.163885 restraints weight = 3312.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4969  Z= 0.103
  Angle     :  0.477   5.061   6754  Z= 0.251
  Chirality :  0.040   0.123    840
  Planarity :  0.003   0.028    846
  Dihedral  :  4.709  52.240    688
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 21.31 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.12 (0.35), residues: 650
  helix:  1.77 (0.28), residues: 370
  sheet: -4.29 (0.62), residues: 32
  loop : -2.51 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  30 
 TYR   0.005   0.001   TYR B 330 
 PHE   0.012   0.001   PHE A  21 
 TRP   0.008   0.001   TRP A 375 
 HIS   0.007   0.001   HIS B  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 4956)
  covalent geometry    : angle       0.47656 ( 6748)
  SS BOND              : bond        0.00136 (    3)
  SS BOND              : angle       0.80424 (    6)
  hydrogen bonds       : bond        0.03439 (  262)
  hydrogen bonds       : angle       3.07069 (  780)
  metal coordination   : bond        0.00219 (   10)

*********************** 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
  66 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 45
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  368 GLU cc_start: 0.7728 (tt0) cc_final: 0.7334 (tt0)
REVERT: A  391 GLU cc_start: 0.6877 (tp30) cc_final: 0.6528 (pm20)
REVERT: B  314 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7569 (tt)
REVERT: B  368 GLU cc_start: 0.7694 (tt0) cc_final: 0.7349 (tt0)
REVERT: B  391 GLU cc_start: 0.6890 (tp30) cc_final: 0.6499 (pm20)
  outliers start: 21
  outliers final: 13
  residues processed: 63
  average time/residue: 0.0449
  time to fit residues: 4.2569
Evaluate side-chains
  55 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
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  341 LEU
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain B residue   29 SER
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  397 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 60 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 50 optimal weight:   20.0000
   chunk 55 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 418 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.182252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.156064 restraints weight = 4509.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.153652 restraints weight = 6097.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.154395 restraints weight = 5684.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.154557 restraints weight = 4606.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.154636 restraints weight = 4363.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   4969  Z= 0.255
  Angle     :  0.660   6.302   6754  Z= 0.344
  Chirality :  0.046   0.146    840
  Planarity :  0.003   0.027    846
  Dihedral  :  5.293  48.385    688
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 22.11 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.64 (0.33), residues: 650
  helix:  1.40 (0.27), residues: 366
  sheet: -4.33 (0.61), residues: 32
  loop : -2.77 (0.35), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  30 
 TYR   0.008   0.002   TYR A 396 
 PHE   0.018   0.002   PHE A  21 
 TRP   0.016   0.002   TRP B 375 
 HIS   0.010   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00623 ( 4956)
  covalent geometry    : angle       0.66019 ( 6748)
  SS BOND              : bond        0.00364 (    3)
  SS BOND              : angle       0.78566 (    6)
  hydrogen bonds       : bond        0.05369 (  262)
  hydrogen bonds       : angle       3.78390 (  780)
  metal coordination   : bond        0.00480 (   10)

*********************** 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
  69 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 43
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  368 GLU cc_start: 0.7626 (tt0) cc_final: 0.7235 (tt0)
REVERT: B  314 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7753 (tt)
REVERT: B  368 GLU cc_start: 0.7560 (tt0) cc_final: 0.7189 (tt0)
REVERT: B  391 GLU cc_start: 0.6803 (tp30) cc_final: 0.6603 (pm20)
  outliers start: 26
  outliers final: 25
  residues processed: 68
  average time/residue: 0.0495
  time to fit residues: 5.0627
Evaluate side-chains
  69 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 43
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
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  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   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  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  342 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 17 optimal weight:    5.9990
   chunk 61 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 50 optimal weight:   20.0000
   chunk 7 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 58 optimal weight:    0.5980
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4114 r_free = 0.4114 target = 0.189128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.154096 restraints weight = 4457.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.156142 restraints weight = 3616.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.157736 restraints weight = 3073.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.158345 restraints weight = 2733.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.158677 restraints weight = 2565.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4969  Z= 0.120
  Angle     :  0.514   5.785   6754  Z= 0.270
  Chirality :  0.041   0.121    840
  Planarity :  0.003   0.027    846
  Dihedral  :  4.894  51.079    688
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 23.71 %
    Favored  : 72.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.34), residues: 650
  helix:  1.92 (0.28), residues: 368
  sheet: -4.01 (0.68), residues: 32
  loop : -2.65 (0.36), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  30 
 TYR   0.005   0.001   TYR A 396 
 PHE   0.011   0.001   PHE A  21 
 TRP   0.010   0.001   TRP B 375 
 HIS   0.005   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4956)
  covalent geometry    : angle       0.51368 ( 6748)
  SS BOND              : bond        0.00142 (    3)
  SS BOND              : angle       0.72903 (    6)
  hydrogen bonds       : bond        0.03885 (  262)
  hydrogen bonds       : angle       3.23156 (  780)
  metal coordination   : bond        0.00179 (   10)

*********************** 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
  59 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 39
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A  368 GLU cc_start: 0.7575 (tt0) cc_final: 0.7248 (tt0)
REVERT: A  391 GLU cc_start: 0.6905 (pm20) cc_final: 0.6540 (tp30)
REVERT: B  368 GLU cc_start: 0.7556 (tt0) cc_final: 0.7287 (tt0)
  outliers start: 20
  outliers final: 16
  residues processed: 58
  average time/residue: 0.0475
  time to fit residues: 4.1519
Evaluate side-chains
  54 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 38
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
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  264 VAL
Chi-restraints excluded: chain A residue  325 VAL
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   71 THR
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  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 41 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 42 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   chunk 50 optimal weight:   20.0000
   chunk 52 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0970
   chunk 46 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 21 optimal weight:    0.4980
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 = 0.4132 r_free = 0.4132 target = 0.191624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.165613 restraints weight = 4404.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.164221 restraints weight = 6775.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.165851 restraints weight = 6028.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.165817 restraints weight = 4346.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.165979 restraints weight = 3998.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7129
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4969  Z= 0.112
  Angle     :  0.499   6.040   6754  Z= 0.262
  Chirality :  0.040   0.118    840
  Planarity :  0.003   0.030    846
  Dihedral  :  4.243  27.576    686
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 22.71 %
    Favored  : 73.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.35), residues: 650
  helix:  2.41 (0.27), residues: 362
  sheet: -3.91 (0.72), residues: 32
  loop : -2.30 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  30 
 TYR   0.004   0.001   TYR B 396 
 PHE   0.011   0.001   PHE A  21 
 TRP   0.009   0.001   TRP A 375 
 HIS   0.004   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 4956)
  covalent geometry    : angle       0.49845 ( 6748)
  SS BOND              : bond        0.00139 (    3)
  SS BOND              : angle       0.65518 (    6)
  hydrogen bonds       : bond        0.03446 (  262)
  hydrogen bonds       : angle       3.01602 (  780)
  metal coordination   : bond        0.00221 (   10)

*********************** 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
  60 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 42
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A  368 GLU cc_start: 0.7568 (tt0) cc_final: 0.7259 (tt0)
REVERT: A  391 GLU cc_start: 0.6758 (pm20) cc_final: 0.6557 (tp30)
REVERT: B  368 GLU cc_start: 0.7556 (tt0) cc_final: 0.7261 (tt0)
REVERT: B  391 GLU cc_start: 0.6764 (pm20) cc_final: 0.6523 (tp30)
  outliers start: 18
  outliers final: 15
  residues processed: 59
  average time/residue: 0.0549
  time to fit residues: 4.6298
Evaluate side-chains
  57 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
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  121 VAL
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  264 VAL
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 34 optimal weight:    5.9990
   chunk 17 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0040
   chunk 23 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 55 optimal weight:    0.5980
   chunk 32 optimal weight:    4.9990
   chunk 18 optimal weight:    6.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.6794

-------------------------------------------------------------------------------
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 = 0.4120 r_free = 0.4120 target = 0.190326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.154144 restraints weight = 4462.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.156578 restraints weight = 3793.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.158769 restraints weight = 3178.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.159697 restraints weight = 2759.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.160939 restraints weight = 2488.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.3375

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= 0.121
  Angle     :  0.506   5.538   6754  Z= 0.266
  Chirality :  0.040   0.119    840
  Planarity :  0.003   0.033    846
  Dihedral  :  4.231  27.383    686
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 22.31 %
    Favored  : 73.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.35), residues: 650
  helix:  2.56 (0.27), residues: 362
  sheet: -3.67 (0.73), residues: 32
  loop : -2.21 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  30 
 TYR   0.004   0.001   TYR B 396 
 PHE   0.011   0.001   PHE A  21 
 TRP   0.010   0.001   TRP B 375 
 HIS   0.004   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4956)
  covalent geometry    : angle       0.50636 ( 6748)
  SS BOND              : bond        0.00135 (    3)
  SS BOND              : angle       0.59129 (    6)
  hydrogen bonds       : bond        0.03537 (  262)
  hydrogen bonds       : angle       3.02219 (  780)
  metal coordination   : bond        0.00215 (   10)

********************** 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
  62 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 43
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A  368 GLU cc_start: 0.7545 (tt0) cc_final: 0.7227 (tt0)
REVERT: A  391 GLU cc_start: 0.6808 (pm20) cc_final: 0.6583 (tp30)
REVERT: B  368 GLU cc_start: 0.7561 (tt0) cc_final: 0.7300 (tt0)
REVERT: B  391 GLU cc_start: 0.6818 (pm20) cc_final: 0.6554 (tp30)
  outliers start: 19
  outliers final: 17
  residues processed: 61
  average time/residue: 0.0551
  time to fit residues: 4.7323
Evaluate side-chains
  60 residues out of total 568 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 43
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
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  264 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  264 VAL
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 48 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 60 optimal weight:    0.0570
   chunk 27 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0670
   chunk 59 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 50 optimal weight:   10.0000
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.5036

-------------------------------------------------------------------------------
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 = 0.4162 r_free = 0.4162 target = 0.194088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.164984 restraints weight = 4436.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.164427 restraints weight = 5884.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.165149 restraints weight = 5194.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.165804 restraints weight = 4383.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.165963 restraints weight = 4001.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.3555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   4969  Z= 0.107
  Angle     :  0.501   8.132   6754  Z= 0.259
  Chirality :  0.040   0.118    840
  Planarity :  0.003   0.034    846
  Dihedral  :  4.105  26.675    686
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 23.11 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.36), residues: 650
  helix:  2.44 (0.27), residues: 376
  sheet: -3.05 (0.67), residues: 48
  loop : -2.06 (0.42), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  30 
 TYR   0.004   0.001   TYR A 396 
 PHE   0.009   0.001   PHE A  21 
 TRP   0.008   0.001   TRP A 375 
 HIS   0.003   0.001   HIS A 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 4956)
  covalent geometry    : angle       0.50090 ( 6748)
  SS BOND              : bond        0.00109 (    3)
  SS BOND              : angle       0.55319 (    6)
  hydrogen bonds       : bond        0.03250 (  262)
  hydrogen bonds       : angle       2.91492 (  780)
  metal coordination   : bond        0.00221 (   10)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 821.38 seconds
wall clock time: 14 minutes 50.41 seconds (890.41 seconds total)