Starting phenix.real_space_refine
on Wed Jul 23 14:43:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zaj_39878/07_2025/8zaj_39878.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zaj_39878/07_2025/8zaj_39878.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zaj_39878/07_2025/8zaj_39878.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zaj_39878/07_2025/8zaj_39878.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zaj_39878/07_2025/8zaj_39878.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zaj_39878/07_2025/8zaj_39878.cif"
  }
  resolution = 2.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    2290      2.51       5
     N     595      2.21       5
     O     715      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3620
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 724
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 7, 'TRANS': 87}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 2.10, per 1000 atoms: 0.58
  Number of scatterers: 3620
  At special positions: 0
  Unit cell: (74.06, 75.44, 53.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O     715      8.00
     N     595      7.00
     C    2290      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 413.1 milliseconds
  

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  860

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 10 sheets defined
      5.3% alpha, 44.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 21
    Processing helix  chain 'B' and resid 17 through 21
    Processing helix  chain 'C' and resid 17 through 21
    Processing helix  chain 'D' and resid 17 through 21
    Processing helix  chain 'E' and resid 17 through 21
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8
      removed outlier: 7.464A  pdb=" N   PHE A  94 " --> pdb=" O   VAL A  27 " (cutoff:3.500A)
      removed outlier: 5.447A  pdb=" N   VAL A  27 " --> pdb=" O   PHE A  94 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   GLN A  29 " --> pdb=" O   LEU A  68 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   LEU A  68 " --> pdb=" O   GLN A  29 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   THR A  31 " --> pdb=" O   CYS A  66 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   CYS A  66 " --> pdb=" O   THR A  31 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16
      removed outlier: 3.773A  pdb=" N   VAL A  79 " --> pdb=" O   TYR A  16 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE A  43 " --> pdb=" O   CYS A  56 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   CYS A  56 " --> pdb=" O   ILE A  43 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   CYS A  45 " --> pdb=" O   ALA A  54 " (cutoff:3.500A)
      removed outlier: 5.501A  pdb=" N   ALA A  54 " --> pdb=" O   CYS A  45 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 8
      removed outlier: 7.464A  pdb=" N   PHE B  94 " --> pdb=" O   VAL B  27 " (cutoff:3.500A)
      removed outlier: 5.447A  pdb=" N   VAL B  27 " --> pdb=" O   PHE B  94 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   GLN B  29 " --> pdb=" O   LEU B  68 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   LEU B  68 " --> pdb=" O   GLN B  29 " (cutoff:3.500A)
      removed outlier: 5.736A  pdb=" N   THR B  31 " --> pdb=" O   CYS B  66 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   CYS B  66 " --> pdb=" O   THR B  31 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 16
      removed outlier: 3.774A  pdb=" N   VAL B  79 " --> pdb=" O   TYR B  16 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE B  43 " --> pdb=" O   CYS B  56 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   CYS B  56 " --> pdb=" O   ILE B  43 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   CYS B  45 " --> pdb=" O   ALA B  54 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   ALA B  54 " --> pdb=" O   CYS B  45 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 8
      removed outlier: 7.464A  pdb=" N   PHE C  94 " --> pdb=" O   VAL C  27 " (cutoff:3.500A)
      removed outlier: 5.448A  pdb=" N   VAL C  27 " --> pdb=" O   PHE C  94 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   GLN C  29 " --> pdb=" O   LEU C  68 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   LEU C  68 " --> pdb=" O   GLN C  29 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   THR C  31 " --> pdb=" O   CYS C  66 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   CYS C  66 " --> pdb=" O   THR C  31 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 14 through 16
      removed outlier: 3.773A  pdb=" N   VAL C  79 " --> pdb=" O   TYR C  16 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE C  43 " --> pdb=" O   CYS C  56 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   CYS C  56 " --> pdb=" O   ILE C  43 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   CYS C  45 " --> pdb=" O   ALA C  54 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   ALA C  54 " --> pdb=" O   CYS C  45 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 8
      removed outlier: 7.464A  pdb=" N   PHE D  94 " --> pdb=" O   VAL D  27 " (cutoff:3.500A)
      removed outlier: 5.448A  pdb=" N   VAL D  27 " --> pdb=" O   PHE D  94 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   GLN D  29 " --> pdb=" O   LEU D  68 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   LEU D  68 " --> pdb=" O   GLN D  29 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   THR D  31 " --> pdb=" O   CYS D  66 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   CYS D  66 " --> pdb=" O   THR D  31 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 14 through 16
      removed outlier: 3.774A  pdb=" N   VAL D  79 " --> pdb=" O   TYR D  16 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE D  43 " --> pdb=" O   CYS D  56 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   CYS D  56 " --> pdb=" O   ILE D  43 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   CYS D  45 " --> pdb=" O   ALA D  54 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   ALA D  54 " --> pdb=" O   CYS D  45 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 8
      removed outlier: 7.464A  pdb=" N   PHE E  94 " --> pdb=" O   VAL E  27 " (cutoff:3.500A)
      removed outlier: 5.448A  pdb=" N   VAL E  27 " --> pdb=" O   PHE E  94 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   GLN E  29 " --> pdb=" O   LEU E  68 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   LEU E  68 " --> pdb=" O   GLN E  29 " (cutoff:3.500A)
      removed outlier: 5.736A  pdb=" N   THR E  31 " --> pdb=" O   CYS E  66 " (cutoff:3.500A)
      removed outlier: 7.576A  pdb=" N   CYS E  66 " --> pdb=" O   THR E  31 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 14 through 16
      removed outlier: 3.774A  pdb=" N   VAL E  79 " --> pdb=" O   TYR E  16 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE E  43 " --> pdb=" O   CYS E  56 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   CYS E  56 " --> pdb=" O   ILE E  43 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   CYS E  45 " --> pdb=" O   ALA E  54 " (cutoff:3.500A)
      removed outlier: 5.502A  pdb=" N   ALA E  54 " --> pdb=" O   CYS E  45 " (cutoff:3.500A)

    125 hydrogen bonds defined for protein.
    285 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: 0.85

  Time building geometry restraints manager: 0.91 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1195
        1.34 -     1.46: 671
        1.46 -     1.57: 1809
        1.57 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 3695
  Sorted by residual:
  bond pdb=" CB  PRO B  78 "
       pdb=" CG  PRO B  78 "
    ideal  model  delta    sigma   weight residual
    1.492  1.533 -0.041 5.00e-02 4.00e+02 6.65e-01
  bond pdb=" CB  PRO A  78 "
       pdb=" CG  PRO A  78 "
    ideal  model  delta    sigma   weight residual
    1.492  1.532 -0.040 5.00e-02 4.00e+02 6.41e-01
  bond pdb=" CB  PRO D  78 "
       pdb=" CG  PRO D  78 "
    ideal  model  delta    sigma   weight residual
    1.492  1.532 -0.040 5.00e-02 4.00e+02 6.36e-01
  bond pdb=" CB  PRO E  78 "
       pdb=" CG  PRO E  78 "
    ideal  model  delta    sigma   weight residual
    1.492  1.532 -0.040 5.00e-02 4.00e+02 6.36e-01
  bond pdb=" CB  PRO C  78 "
       pdb=" CG  PRO C  78 "
    ideal  model  delta    sigma   weight residual
    1.492  1.532 -0.040 5.00e-02 4.00e+02 6.27e-01
  ... (remaining 3690 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 4787
        1.15 -     2.30: 150
        2.30 -     3.45: 58
        3.45 -     4.59: 5
        4.59 -     5.74: 5
  Bond angle restraints: 5005
  Sorted by residual:
  angle pdb=" CA  ILE D  25 "
        pdb=" CB  ILE D  25 "
        pdb=" CG1 ILE D  25 "
      ideal   model   delta    sigma   weight residual
     110.40  113.21   -2.81 1.70e+00 3.46e-01 2.73e+00
  angle pdb=" CA  ILE A  25 "
        pdb=" CB  ILE A  25 "
        pdb=" CG1 ILE A  25 "
      ideal   model   delta    sigma   weight residual
     110.40  113.17   -2.77 1.70e+00 3.46e-01 2.66e+00
  angle pdb=" CA  ILE B  25 "
        pdb=" CB  ILE B  25 "
        pdb=" CG1 ILE B  25 "
      ideal   model   delta    sigma   weight residual
     110.40  113.15   -2.75 1.70e+00 3.46e-01 2.62e+00
  angle pdb=" CA  ILE E  25 "
        pdb=" CB  ILE E  25 "
        pdb=" CG1 ILE E  25 "
      ideal   model   delta    sigma   weight residual
     110.40  113.14   -2.74 1.70e+00 3.46e-01 2.59e+00
  angle pdb=" CA  ILE C  25 "
        pdb=" CB  ILE C  25 "
        pdb=" CG1 ILE C  25 "
      ideal   model   delta    sigma   weight residual
     110.40  113.13   -2.73 1.70e+00 3.46e-01 2.58e+00
  ... (remaining 5000 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.59: 1755
       11.59 -    23.19: 273
       23.19 -    34.78: 157
       34.78 -    46.37: 40
       46.37 -    57.97: 20
  Dihedral angle restraints: 2245
    sinusoidal: 910
      harmonic: 1335
  Sorted by residual:
  dihedral pdb=" CG  LYS E  50 "
           pdb=" CD  LYS E  50 "
           pdb=" CE  LYS E  50 "
           pdb=" NZ  LYS E  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.66   57.34     3      1.50e+01 4.44e-03 9.44e+00
  dihedral pdb=" CG  LYS D  50 "
           pdb=" CD  LYS D  50 "
           pdb=" CE  LYS D  50 "
           pdb=" NZ  LYS D  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.66   57.34     3      1.50e+01 4.44e-03 9.44e+00
  dihedral pdb=" CG  LYS A  50 "
           pdb=" CD  LYS A  50 "
           pdb=" CE  LYS A  50 "
           pdb=" NZ  LYS A  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.66   57.34     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 2242 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 326
       0.027 -    0.055: 132
       0.055 -    0.082: 27
       0.082 -    0.109: 56
       0.109 -    0.137: 19
  Chirality restraints: 560
  Sorted by residual:
  chirality pdb=" CA  ILE C  63 "
            pdb=" N   ILE C  63 "
            pdb=" C   ILE C  63 "
            pdb=" CB  ILE C  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.67e-01
  chirality pdb=" CA  ILE A  63 "
            pdb=" N   ILE A  63 "
            pdb=" C   ILE A  63 "
            pdb=" CB  ILE A  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.64e-01
  chirality pdb=" CA  ILE B  63 "
            pdb=" N   ILE B  63 "
            pdb=" C   ILE B  63 "
            pdb=" CB  ILE B  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.63e-01
  ... (remaining 557 not shown)

  Planarity restraints: 660
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN E  17 "    0.034 5.00e-02 4.00e+02   5.22e-02 4.36e+00
        pdb=" N   PRO E  18 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO E  18 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO E  18 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A  17 "    0.034 5.00e-02 4.00e+02   5.22e-02 4.35e+00
        pdb=" N   PRO A  18 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A  18 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A  18 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D  17 "    0.034 5.00e-02 4.00e+02   5.20e-02 4.33e+00
        pdb=" N   PRO D  18 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO D  18 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO D  18 "    0.029 5.00e-02 4.00e+02
  ... (remaining 657 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 806
        2.79 -     3.32: 3041
        3.32 -     3.85: 6060
        3.85 -     4.37: 7593
        4.37 -     4.90: 12164
  Nonbonded interactions: 29664
  Sorted by model distance:
  nonbonded pdb=" N   GLY A   2 "
            pdb=" OD2 ASP B  73 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" N   GLU C  21 "
            pdb=" OE1 GLU C  21 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" N   GLU B  21 "
            pdb=" OE1 GLU B  21 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" N   GLU D  21 "
            pdb=" OE1 GLU D  21 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" N   GLU E  21 "
            pdb=" OE1 GLU E  21 "
     model   vdw
     2.275 3.120
  ... (remaining 29659 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.360
  Find NCS groups from input model:        0.070
  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:11.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6296
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      :  0.003   0.041   3695  Z= 0.130
  Angle     :  0.550   5.743   5005  Z= 0.275
  Chirality :  0.046   0.137    560
  Planarity :  0.006   0.052    660
  Dihedral  : 16.017  57.968   1385
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 25.37 %
    Favored  : 71.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.39), residues: 465
  helix:  None (None), residues: 0
  sheet:  0.75 (0.41), residues: 175
  loop : -0.64 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B   4 
 HIS   0.001   0.000   HIS B  90 
 PHE   0.003   0.001   PHE D  81 
 TYR   0.007   0.002   TYR D  16 
 ARG   0.001   0.000   ARG B  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20257 (  125)
  hydrogen bonds       : angle       8.91909 (  285)
  covalent geometry    : bond        0.00301 ( 3695)
  covalent geometry    : angle       0.54957 ( 5005)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
REVERT: A    7 GLU cc_start: 0.6554 (tt0) cc_final: 0.6181 (tt0)
REVERT: A    9 LYS cc_start: 0.6515 (mmmt) cc_final: 0.5847 (mtmt)
REVERT: A   24 LYS cc_start: 0.6320 (ttmt) cc_final: 0.6118 (ttpt)
REVERT: A   44 GLN cc_start: 0.6633 (mt0) cc_final: 0.6303 (mt0)
REVERT: A   59 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5701 (mt)
REVERT: A   62 LYS cc_start: 0.6534 (mttt) cc_final: 0.6298 (mtmt)
REVERT: A   80 GLU cc_start: 0.6527 (tp30) cc_final: 0.6049 (tp30)
REVERT: A   88 SER cc_start: 0.7308 (p) cc_final: 0.6685 (t)
REVERT: A   89 ILE cc_start: 0.6411 (mt) cc_final: 0.6044 (mp)
REVERT: A   96 GLU cc_start: 0.6353 (mt-10) cc_final: 0.6126 (mt-10)
REVERT: B    7 GLU cc_start: 0.6544 (tt0) cc_final: 0.6138 (tt0)
REVERT: B    9 LYS cc_start: 0.6566 (mmmt) cc_final: 0.5924 (mtmm)
REVERT: B   16 TYR cc_start: 0.6197 (t80) cc_final: 0.5773 (t80)
REVERT: B   24 LYS cc_start: 0.6385 (ttmt) cc_final: 0.6152 (ttpt)
REVERT: B   41 SER cc_start: 0.6540 (m) cc_final: 0.6090 (t)
REVERT: B   44 GLN cc_start: 0.6574 (mt0) cc_final: 0.6235 (mt0)
REVERT: B   59 LEU cc_start: 0.6044 (mm) cc_final: 0.5580 (mt)
REVERT: B   62 LYS cc_start: 0.6431 (mttt) cc_final: 0.6212 (mttt)
REVERT: B   73 ASP cc_start: 0.5847 (p0) cc_final: 0.5640 (p0)
REVERT: B   80 GLU cc_start: 0.6670 (tp30) cc_final: 0.6093 (tp30)
REVERT: B   88 SER cc_start: 0.7327 (p) cc_final: 0.6705 (t)
REVERT: B   89 ILE cc_start: 0.6471 (mt) cc_final: 0.6206 (mp)
REVERT: C    7 GLU cc_start: 0.6494 (tt0) cc_final: 0.5749 (tp30)
REVERT: C    9 LYS cc_start: 0.6327 (mmmt) cc_final: 0.5503 (mppt)
REVERT: C   24 LYS cc_start: 0.6244 (ttmt) cc_final: 0.6005 (ttpt)
REVERT: C   44 GLN cc_start: 0.6525 (mt0) cc_final: 0.6235 (mt0)
REVERT: C   59 LEU cc_start: 0.6218 (mm) cc_final: 0.5752 (mt)
REVERT: C   62 LYS cc_start: 0.6512 (mttt) cc_final: 0.6267 (mtmt)
REVERT: C   80 GLU cc_start: 0.6462 (tp30) cc_final: 0.5022 (tp30)
REVERT: C   89 ILE cc_start: 0.6332 (mt) cc_final: 0.5989 (mp)
REVERT: C   96 GLU cc_start: 0.6251 (mt-10) cc_final: 0.5904 (mt-10)
REVERT: D    7 GLU cc_start: 0.6543 (tt0) cc_final: 0.6127 (tt0)
REVERT: D   24 LYS cc_start: 0.6311 (ttmt) cc_final: 0.6102 (ttpt)
REVERT: D   34 THR cc_start: 0.5965 (t) cc_final: 0.5584 (p)
REVERT: D   41 SER cc_start: 0.6261 (m) cc_final: 0.5779 (t)
REVERT: D   44 GLN cc_start: 0.6768 (mt0) cc_final: 0.6465 (mt0)
REVERT: D   59 LEU cc_start: 0.6025 (mm) cc_final: 0.5600 (mt)
REVERT: D   62 LYS cc_start: 0.6297 (mttt) cc_final: 0.6087 (mttt)
REVERT: D   80 GLU cc_start: 0.6607 (tp30) cc_final: 0.6015 (tp30)
REVERT: D   88 SER cc_start: 0.7546 (p) cc_final: 0.6792 (t)
REVERT: D   89 ILE cc_start: 0.6454 (mt) cc_final: 0.6230 (mp)
REVERT: D   96 GLU cc_start: 0.6335 (mt-10) cc_final: 0.6116 (mt-10)
REVERT: E    7 GLU cc_start: 0.6468 (tt0) cc_final: 0.6181 (tt0)
REVERT: E    9 LYS cc_start: 0.6680 (mmmt) cc_final: 0.6071 (mtmm)
REVERT: E   16 TYR cc_start: 0.6112 (t80) cc_final: 0.5887 (t80)
REVERT: E   24 LYS cc_start: 0.6366 (ttmt) cc_final: 0.6161 (ttpt)
REVERT: E   34 THR cc_start: 0.5976 (t) cc_final: 0.5542 (p)
REVERT: E   41 SER cc_start: 0.6306 (m) cc_final: 0.5961 (t)
REVERT: E   44 GLN cc_start: 0.6770 (mt0) cc_final: 0.6410 (mt0)
REVERT: E   59 LEU cc_start: 0.5900 (mm) cc_final: 0.5415 (mt)
REVERT: E   62 LYS cc_start: 0.6274 (mttt) cc_final: 0.6021 (mttt)
REVERT: E   73 ASP cc_start: 0.5871 (p0) cc_final: 0.5655 (p0)
REVERT: E   80 GLU cc_start: 0.6791 (tp30) cc_final: 0.5944 (tt0)
REVERT: E   88 SER cc_start: 0.7008 (p) cc_final: 0.6473 (t)
REVERT: E   89 ILE cc_start: 0.6364 (mt) cc_final: 0.6090 (mp)
REVERT: E   96 GLU cc_start: 0.6361 (mt-10) cc_final: 0.6142 (mt-10)
  outliers start: 11
  outliers final: 0
  residues processed: 93
  average time/residue: 1.0637
  time to fit residues: 102.3558
Evaluate side-chains
  87 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 34 optimal weight:    7.9990
   chunk 18 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 23 optimal weight:    0.0470
   chunk 35 optimal weight:    8.9990
   chunk 13 optimal weight:    5.9990
   chunk 21 optimal weight:    7.9990
   chunk 26 optimal weight:    0.7980
   chunk 40 optimal weight:    7.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    2.9082

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

Flipped N/Q/H residues before XYZ refinement:
C  17 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.189654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.156506 restraints weight = 2640.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 1.50
r_work: 0.3744 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3637 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   3695  Z= 0.283
  Angle     :  0.755   6.293   5005  Z= 0.393
  Chirality :  0.049   0.145    560
  Planarity :  0.007   0.048    660
  Dihedral  :  4.909  38.816    482
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 19.02 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.38), residues: 465
  helix:  None (None), residues: 0
  sheet:  0.24 (0.37), residues: 180
  loop : -0.46 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A   4 
 HIS   0.003   0.002   HIS D  90 
 PHE   0.006   0.001   PHE B   3 
 TYR   0.018   0.004   TYR C  16 
 ARG   0.002   0.001   ARG D  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04214 (  125)
  hydrogen bonds       : angle       7.05222 (  285)
  covalent geometry    : bond        0.00552 ( 3695)
  covalent geometry    : angle       0.75491 ( 5005)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 LYS cc_start: 0.8046 (mmmt) cc_final: 0.7840 (mtmm)
REVERT: A   19 LYS cc_start: 0.6290 (OUTLIER) cc_final: 0.5613 (mtpt)
REVERT: A   40 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6718 (tttm)
REVERT: A   59 LEU cc_start: 0.7333 (mm) cc_final: 0.7106 (mt)
REVERT: A   73 ASP cc_start: 0.7000 (OUTLIER) cc_final: 0.6769 (p0)
REVERT: B    9 LYS cc_start: 0.8028 (mmmt) cc_final: 0.7795 (mtmm)
REVERT: B   19 LYS cc_start: 0.6366 (OUTLIER) cc_final: 0.5712 (mtpt)
REVERT: B   59 LEU cc_start: 0.7321 (mm) cc_final: 0.7069 (mt)
REVERT: B   73 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6854 (p0)
REVERT: C    9 LYS cc_start: 0.8053 (mmmt) cc_final: 0.7817 (mtmm)
REVERT: C   19 LYS cc_start: 0.6252 (OUTLIER) cc_final: 0.5572 (mtpt)
REVERT: C   40 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6687 (tttm)
REVERT: C   59 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7050 (mt)
REVERT: D   19 LYS cc_start: 0.6373 (OUTLIER) cc_final: 0.5732 (mtpt)
REVERT: D   40 LYS cc_start: 0.7031 (OUTLIER) cc_final: 0.6680 (tttm)
REVERT: D   59 LEU cc_start: 0.7329 (mm) cc_final: 0.7029 (mt)
REVERT: D   73 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6806 (p0)
REVERT: E    9 LYS cc_start: 0.8046 (mmmt) cc_final: 0.7783 (mtmm)
REVERT: E   19 LYS cc_start: 0.6255 (OUTLIER) cc_final: 0.5903 (mptt)
REVERT: E   59 LEU cc_start: 0.7308 (mm) cc_final: 0.7017 (mt)
REVERT: E   73 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6924 (p0)
  outliers start: 16
  outliers final: 0
  residues processed: 96
  average time/residue: 1.3882
  time to fit residues: 136.7223
Evaluate side-chains
  95 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue   40 LYS
Chi-restraints excluded: chain A residue   73 ASP
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain C residue   19 LYS
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain D residue   19 LYS
Chi-restraints excluded: chain D residue   40 LYS
Chi-restraints excluded: chain D residue   73 ASP
Chi-restraints excluded: chain E residue   19 LYS
Chi-restraints excluded: chain E residue   73 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 6 optimal weight:    6.9990
   chunk 26 optimal weight:    0.7980
   chunk 39 optimal weight:    9.9990
   chunk 43 optimal weight:    0.0040
   chunk 8 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 0 optimal weight:    8.9990
   chunk 23 optimal weight:    0.4980
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.7994

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A  44 GLN
B  29 GLN
B  44 GLN
C  29 GLN
C  44 GLN
D  44 GLN
E  29 GLN
E  44 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.196821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.165070 restraints weight = 2544.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3954 rms_B_bonded: 1.44
r_work: 0.3833 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3728 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3695  Z= 0.130
  Angle     :  0.567   5.788   5005  Z= 0.287
  Chirality :  0.047   0.140    560
  Planarity :  0.005   0.043    660
  Dihedral  :  4.023  12.545    480
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 20.24 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.38), residues: 465
  helix:  None (None), residues: 0
  sheet:  0.39 (0.37), residues: 180
  loop : -0.38 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A   4 
 HIS   0.002   0.001   HIS C  90 
 PHE   0.003   0.001   PHE B   3 
 TYR   0.004   0.001   TYR D  16 
 ARG   0.001   0.000   ARG A  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02898 (  125)
  hydrogen bonds       : angle       6.05145 (  285)
  covalent geometry    : bond        0.00283 ( 3695)
  covalent geometry    : angle       0.56659 ( 5005)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.410 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8020 (mmmt) cc_final: 0.7776 (mppt)
REVERT: A   19 LYS cc_start: 0.6202 (OUTLIER) cc_final: 0.5561 (mtpt)
REVERT: A   59 LEU cc_start: 0.7259 (mm) cc_final: 0.7032 (mt)
REVERT: A   73 ASP cc_start: 0.6892 (OUTLIER) cc_final: 0.6680 (p0)
REVERT: B    9 LYS cc_start: 0.8049 (mmmt) cc_final: 0.7789 (mppt)
REVERT: B   16 TYR cc_start: 0.6936 (t80) cc_final: 0.6722 (t80)
REVERT: B   19 LYS cc_start: 0.6310 (OUTLIER) cc_final: 0.5670 (mtpt)
REVERT: B   59 LEU cc_start: 0.7190 (mm) cc_final: 0.6948 (mt)
REVERT: C    9 LYS cc_start: 0.8043 (mmmt) cc_final: 0.7831 (mppt)
REVERT: C   19 LYS cc_start: 0.6136 (OUTLIER) cc_final: 0.5498 (mtpt)
REVERT: C   59 LEU cc_start: 0.7183 (mm) cc_final: 0.6939 (mt)
REVERT: C   96 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6794 (mt-10)
REVERT: D   19 LYS cc_start: 0.6251 (OUTLIER) cc_final: 0.5622 (mtpt)
REVERT: D   59 LEU cc_start: 0.7235 (mm) cc_final: 0.6979 (mt)
REVERT: E   19 LYS cc_start: 0.6110 (OUTLIER) cc_final: 0.5790 (mptt)
REVERT: E   59 LEU cc_start: 0.7172 (mm) cc_final: 0.6924 (mt)
  outliers start: 12
  outliers final: 0
  residues processed: 89
  average time/residue: 1.5669
  time to fit residues: 142.8544
Evaluate side-chains
  85 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue   73 ASP
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain C residue   19 LYS
Chi-restraints excluded: chain D residue   19 LYS
Chi-restraints excluded: chain E residue   19 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 23 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   chunk 26 optimal weight:    8.9990
   chunk 36 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 17 optimal weight:    8.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
C  44 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.191263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.158408 restraints weight = 2583.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3886 rms_B_bonded: 1.46
r_work: 0.3759 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3651 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   3695  Z= 0.256
  Angle     :  0.707   6.372   5005  Z= 0.365
  Chirality :  0.049   0.144    560
  Planarity :  0.006   0.046    660
  Dihedral  :  4.500  14.783    480
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.80 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.37), residues: 465
  helix:  None (None), residues: 0
  sheet: -0.02 (0.36), residues: 180
  loop : -0.33 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP C   4 
 HIS   0.004   0.002   HIS C  90 
 PHE   0.006   0.001   PHE B   3 
 TYR   0.017   0.004   TYR D  16 
 ARG   0.002   0.001   ARG E  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03456 (  125)
  hydrogen bonds       : angle       6.48431 (  285)
  covalent geometry    : bond        0.00498 ( 3695)
  covalent geometry    : angle       0.70722 ( 5005)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7802 (mtmm)
REVERT: A   19 LYS cc_start: 0.6208 (OUTLIER) cc_final: 0.5713 (mtmt)
REVERT: A   59 LEU cc_start: 0.7335 (mm) cc_final: 0.7099 (mt)
REVERT: A   73 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6944 (p0)
REVERT: B    9 LYS cc_start: 0.8057 (mmmt) cc_final: 0.7766 (mtmm)
REVERT: B   16 TYR cc_start: 0.7013 (t80) cc_final: 0.6809 (t80)
REVERT: B   19 LYS cc_start: 0.6275 (OUTLIER) cc_final: 0.5797 (mtmt)
REVERT: B   59 LEU cc_start: 0.7265 (mm) cc_final: 0.7010 (mt)
REVERT: C    9 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7753 (mtmm)
REVERT: C   59 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7016 (mt)
REVERT: D   59 LEU cc_start: 0.7319 (mm) cc_final: 0.7043 (mt)
REVERT: E    9 LYS cc_start: 0.8077 (mptm) cc_final: 0.7831 (mppt)
REVERT: E   19 LYS cc_start: 0.6126 (OUTLIER) cc_final: 0.5651 (mtmt)
REVERT: E   59 LEU cc_start: 0.7295 (mm) cc_final: 0.7003 (mt)
  outliers start: 9
  outliers final: 0
  residues processed: 88
  average time/residue: 1.4571
  time to fit residues: 131.4569
Evaluate side-chains
  83 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 78
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain A residue   73 ASP
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain E residue   19 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 29 optimal weight:    7.9990
   chunk 1 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 44 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 18 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 43 optimal weight:    0.0270
   overall best weight:    1.8044

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
C  44 GLN
D  44 GLN
E  44 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.193893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.163597 restraints weight = 2649.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3965 rms_B_bonded: 1.39
r_work: 0.3829 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3726 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3695  Z= 0.200
  Angle     :  0.638   6.318   5005  Z= 0.328
  Chirality :  0.047   0.144    560
  Planarity :  0.006   0.046    660
  Dihedral  :  4.435  14.562    480
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 19.27 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.37), residues: 465
  helix:  None (None), residues: 0
  sheet: -0.09 (0.36), residues: 180
  loop : -0.36 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.002   TRP A   4 
 HIS   0.003   0.001   HIS C  90 
 PHE   0.004   0.001   PHE E  81 
 TYR   0.012   0.003   TYR C  16 
 ARG   0.001   0.000   ARG E  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03079 (  125)
  hydrogen bonds       : angle       6.27514 (  285)
  covalent geometry    : bond        0.00400 ( 3695)
  covalent geometry    : angle       0.63816 ( 5005)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 0.429 
Fit side-chains
REVERT: A   19 LYS cc_start: 0.6201 (OUTLIER) cc_final: 0.5745 (mtmt)
REVERT: A   59 LEU cc_start: 0.7379 (mm) cc_final: 0.7166 (mt)
REVERT: B    9 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7905 (mtmm)
REVERT: B   19 LYS cc_start: 0.6265 (OUTLIER) cc_final: 0.5822 (mtmt)
REVERT: B   59 LEU cc_start: 0.7355 (mm) cc_final: 0.7126 (mt)
REVERT: C   59 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7092 (mt)
REVERT: D   19 LYS cc_start: 0.6246 (OUTLIER) cc_final: 0.5602 (mtpt)
REVERT: D   59 LEU cc_start: 0.7413 (mm) cc_final: 0.7176 (mt)
REVERT: E   19 LYS cc_start: 0.6155 (OUTLIER) cc_final: 0.5713 (mtmt)
REVERT: E   59 LEU cc_start: 0.7357 (mm) cc_final: 0.7109 (mt)
  outliers start: 7
  outliers final: 0
  residues processed: 86
  average time/residue: 1.3498
  time to fit residues: 119.2086
Evaluate side-chains
  84 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain D residue   19 LYS
Chi-restraints excluded: chain E residue   19 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 40 optimal weight:   10.0000
   chunk 22 optimal weight:    8.9990
   chunk 7 optimal weight:    0.7980
   chunk 9 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 30 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 2 optimal weight:    0.2980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
C  44 GLN
D  29 GLN
D  44 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.199533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.170837 restraints weight = 2665.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.4053 rms_B_bonded: 1.35
r_work: 0.3921 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3821 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3695  Z= 0.119
  Angle     :  0.550   5.953   5005  Z= 0.276
  Chirality :  0.047   0.140    560
  Planarity :  0.005   0.043    660
  Dihedral  :  3.885  12.806    480
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 19.51 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.38), residues: 465
  helix:  None (None), residues: 0
  sheet:  0.12 (0.36), residues: 180
  loop : -0.29 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A   4 
 HIS   0.002   0.001   HIS C  90 
 PHE   0.003   0.001   PHE D  81 
 TYR   0.005   0.001   TYR D  16 
 ARG   0.001   0.000   ARG A  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02608 (  125)
  hydrogen bonds       : angle       5.76616 (  285)
  covalent geometry    : bond        0.00271 ( 3695)
  covalent geometry    : angle       0.54957 ( 5005)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.401 
Fit side-chains
REVERT: A   19 LYS cc_start: 0.6150 (OUTLIER) cc_final: 0.5565 (mtpt)
REVERT: B   19 LYS cc_start: 0.6171 (OUTLIER) cc_final: 0.5618 (mtpt)
REVERT: B   59 LEU cc_start: 0.7235 (mm) cc_final: 0.7033 (mt)
REVERT: C   59 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6981 (mt)
REVERT: D   19 LYS cc_start: 0.6208 (OUTLIER) cc_final: 0.5618 (mtpt)
REVERT: D   59 LEU cc_start: 0.7291 (mm) cc_final: 0.7075 (mt)
REVERT: E   19 LYS cc_start: 0.6087 (OUTLIER) cc_final: 0.5515 (mtpt)
REVERT: E   59 LEU cc_start: 0.7224 (mm) cc_final: 0.7020 (mt)
  outliers start: 8
  outliers final: 0
  residues processed: 87
  average time/residue: 1.4736
  time to fit residues: 131.3851
Evaluate side-chains
  84 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain C residue   59 LEU
Chi-restraints excluded: chain D residue   19 LYS
Chi-restraints excluded: chain E residue   19 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 16 optimal weight:    0.0070
   chunk 39 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 40 optimal weight:    8.9990
   chunk 20 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    9.9990
   chunk 34 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.9600

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
C  44 GLN
D  44 GLN
E  44 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.198733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.169298 restraints weight = 2632.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.4022 rms_B_bonded: 1.36
r_work: 0.3888 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3788 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3695  Z= 0.138
  Angle     :  0.571   6.098   5005  Z= 0.286
  Chirality :  0.047   0.141    560
  Planarity :  0.005   0.045    660
  Dihedral  :  3.941  13.729    480
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 19.27 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.38), residues: 465
  helix:  None (None), residues: 0
  sheet:  0.20 (0.36), residues: 180
  loop : -0.23 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B   4 
 HIS   0.002   0.001   HIS C  90 
 PHE   0.004   0.001   PHE D  81 
 TYR   0.012   0.002   TYR B  16 
 ARG   0.000   0.000   ARG A  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02679 (  125)
  hydrogen bonds       : angle       5.79073 (  285)
  covalent geometry    : bond        0.00297 ( 3695)
  covalent geometry    : angle       0.57107 ( 5005)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.403 
Fit side-chains
REVERT: A   19 LYS cc_start: 0.6167 (OUTLIER) cc_final: 0.5578 (mtpt)
REVERT: B   19 LYS cc_start: 0.6104 (OUTLIER) cc_final: 0.5566 (mtpt)
REVERT: B   59 LEU cc_start: 0.7235 (mm) cc_final: 0.7034 (mt)
REVERT: D   19 LYS cc_start: 0.6211 (OUTLIER) cc_final: 0.5610 (mtpt)
REVERT: D   59 LEU cc_start: 0.7298 (mm) cc_final: 0.7082 (mt)
REVERT: E   19 LYS cc_start: 0.6104 (OUTLIER) cc_final: 0.5524 (mtpt)
REVERT: E   59 LEU cc_start: 0.7219 (mm) cc_final: 0.7012 (mt)
  outliers start: 7
  outliers final: 0
  residues processed: 86
  average time/residue: 1.4104
  time to fit residues: 124.3613
Evaluate side-chains
  84 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain D residue   19 LYS
Chi-restraints excluded: chain E residue   19 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 11 optimal weight:    8.9990
   chunk 17 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 27 optimal weight:    7.9990
   chunk 30 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
B  44 GLN
C  44 GLN
D  44 GLN
E  44 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.198581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.168978 restraints weight = 2640.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3992 rms_B_bonded: 1.36
r_work: 0.3862 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3760 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.3120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3695  Z= 0.145
  Angle     :  0.588   6.068   5005  Z= 0.294
  Chirality :  0.047   0.142    560
  Planarity :  0.005   0.045    660
  Dihedral  :  3.980  13.930    480
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 19.76 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.38), residues: 465
  helix:  None (None), residues: 0
  sheet:  0.24 (0.36), residues: 180
  loop : -0.22 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B   4 
 HIS   0.002   0.001   HIS B  90 
 PHE   0.004   0.001   PHE D  81 
 TYR   0.014   0.002   TYR B  16 
 ARG   0.000   0.000   ARG A  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02706 (  125)
  hydrogen bonds       : angle       5.80871 (  285)
  covalent geometry    : bond        0.00313 ( 3695)
  covalent geometry    : angle       0.58760 ( 5005)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.408 
Fit side-chains
REVERT: A   19 LYS cc_start: 0.6134 (OUTLIER) cc_final: 0.5557 (mtpt)
REVERT: B   19 LYS cc_start: 0.6103 (OUTLIER) cc_final: 0.5559 (mtpt)
REVERT: D   19 LYS cc_start: 0.6191 (OUTLIER) cc_final: 0.5590 (mtpt)
REVERT: D   59 LEU cc_start: 0.7298 (mm) cc_final: 0.7086 (mt)
REVERT: E   19 LYS cc_start: 0.6122 (OUTLIER) cc_final: 0.5534 (mtpt)
REVERT: E   89 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7615 (mp)
  outliers start: 6
  outliers final: 0
  residues processed: 86
  average time/residue: 1.4093
  time to fit residues: 124.3486
Evaluate side-chains
  84 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain D residue   19 LYS
Chi-restraints excluded: chain E residue   19 LYS
Chi-restraints excluded: chain E residue   89 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   chunk 41 optimal weight:    0.4980
   chunk 35 optimal weight:    0.8980
   chunk 13 optimal weight:    9.9990
   chunk 24 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 36 optimal weight:    7.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
B  44 GLN
C  44 GLN
D  44 GLN
E  44 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.194507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.163797 restraints weight = 2626.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3959 rms_B_bonded: 1.39
r_work: 0.3826 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3724 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.3224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3695  Z= 0.192
  Angle     :  0.647   6.243   5005  Z= 0.328
  Chirality :  0.048   0.142    560
  Planarity :  0.005   0.046    660
  Dihedral  :  4.255  14.802    480
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 19.51 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.37), residues: 465
  helix:  None (None), residues: 0
  sheet:  0.10 (0.36), residues: 180
  loop : -0.22 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.003   TRP B   4 
 HIS   0.002   0.001   HIS C  90 
 PHE   0.005   0.001   PHE B   3 
 TYR   0.020   0.003   TYR B  16 
 ARG   0.001   0.000   ARG E  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03020 (  125)
  hydrogen bonds       : angle       6.03425 (  285)
  covalent geometry    : bond        0.00389 ( 3695)
  covalent geometry    : angle       0.64689 ( 5005)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.407 
Fit side-chains
REVERT: A   19 LYS cc_start: 0.6186 (OUTLIER) cc_final: 0.5587 (mtpt)
REVERT: D   19 LYS cc_start: 0.6208 (OUTLIER) cc_final: 0.5575 (mtpt)
REVERT: D   59 LEU cc_start: 0.7366 (mm) cc_final: 0.7129 (mt)
REVERT: E   19 LYS cc_start: 0.6116 (OUTLIER) cc_final: 0.5678 (mtmt)
REVERT: E   89 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7633 (mp)
  outliers start: 5
  outliers final: 0
  residues processed: 85
  average time/residue: 1.3725
  time to fit residues: 119.6902
Evaluate side-chains
  82 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain D residue   19 LYS
Chi-restraints excluded: chain E residue   19 LYS
Chi-restraints excluded: chain E residue   89 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 16 optimal weight:    0.4980
   chunk 35 optimal weight:    7.9990
   chunk 27 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 21 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 12 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 9 optimal weight:    7.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
B  44 GLN
C  44 GLN
D  44 GLN
E  44 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.194671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.163983 restraints weight = 2636.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.3961 rms_B_bonded: 1.39
r_work: 0.3828 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3726 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.3253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3695  Z= 0.187
  Angle     :  0.656   7.627   5005  Z= 0.332
  Chirality :  0.047   0.142    560
  Planarity :  0.005   0.047    660
  Dihedral  :  4.315  14.713    480
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 20.00 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.37), residues: 465
  helix:  None (None), residues: 0
  sheet:  0.01 (0.35), residues: 180
  loop : -0.26 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP B   4 
 HIS   0.003   0.001   HIS C  90 
 PHE   0.005   0.001   PHE A  81 
 TYR   0.017   0.003   TYR B  16 
 ARG   0.000   0.000   ARG E  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02993 (  125)
  hydrogen bonds       : angle       6.06176 (  285)
  covalent geometry    : bond        0.00382 ( 3695)
  covalent geometry    : angle       0.65642 ( 5005)

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

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

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  930 Ramachandran restraints generated.
    465 Oldfield, 0 Emsley, 465 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.452 
Fit side-chains
REVERT: A   19 LYS cc_start: 0.6199 (OUTLIER) cc_final: 0.5598 (mtpt)
REVERT: D   19 LYS cc_start: 0.6194 (OUTLIER) cc_final: 0.5566 (mtpt)
REVERT: D   59 LEU cc_start: 0.7378 (mm) cc_final: 0.7138 (mt)
REVERT: E   19 LYS cc_start: 0.6118 (OUTLIER) cc_final: 0.5680 (mtmt)
REVERT: E   89 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7672 (mp)
  outliers start: 4
  outliers final: 0
  residues processed: 84
  average time/residue: 1.3942
  time to fit residues: 120.2322
Evaluate side-chains
  84 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain D residue   19 LYS
Chi-restraints excluded: chain E residue   19 LYS
Chi-restraints excluded: chain E residue   89 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 8 optimal weight:    0.6980
   chunk 20 optimal weight:   10.0000
   chunk 28 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0000
   chunk 18 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   chunk 41 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    1.4588

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

Flipped N/Q/H residues before XYZ refinement:
A  44 GLN
B  44 GLN
C  44 GLN
D  44 GLN
E  44 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.194991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.164444 restraints weight = 2623.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3965 rms_B_bonded: 1.38
r_work: 0.3833 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3730 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.3262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3695  Z= 0.177
  Angle     :  0.652   6.712   5005  Z= 0.328
  Chirality :  0.047   0.141    560
  Planarity :  0.005   0.046    660
  Dihedral  :  4.264  14.583    480
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 20.00 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.37), residues: 465
  helix:  None (None), residues: 0
  sheet:  0.01 (0.35), residues: 180
  loop : -0.25 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP B   4 
 HIS   0.002   0.001   HIS C  26 
 PHE   0.005   0.001   PHE B  81 
 TYR   0.016   0.003   TYR B  16 
 ARG   0.000   0.000   ARG E  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02921 (  125)
  hydrogen bonds       : angle       6.00747 (  285)
  covalent geometry    : bond        0.00365 ( 3695)
  covalent geometry    : angle       0.65193 ( 5005)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4374.28 seconds
wall clock time: 75 minutes 1.64 seconds (4501.64 seconds total)