Starting phenix.real_space_refine
on Wed Sep 17 03:51:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zaj_39878/09_2025/8zaj_39878.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zaj_39878/09_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_39878/09_2025/8zaj_39878.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zaj_39878/09_2025/8zaj_39878.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zaj_39878/09_2025/8zaj_39878.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zaj_39878/09_2025/8zaj_39878.cif"
  }
  resolution = 2.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 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): 0.00s

  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: 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:
    B, C, D, E
  Time building chain proxies: 0.72, per 1000 atoms: 0.20
  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: 0.27
  Conformation dependent library (CDL) restraints added in 100.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.15
  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: 0.51

  Time building geometry restraints manager: 0.36 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             1.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.670
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.220
-------------------------------------------------------------------------------
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 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: -0.14 (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
 ARG   0.001   0.000   ARG B  87 
 TYR   0.007   0.002   TYR D  16 
 PHE   0.003   0.001   PHE D  81 
 TRP   0.002   0.001   TRP B   4 
 HIS   0.001   0.000   HIS B  90 

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

*********************** 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  : 0.171 
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: 0.5278
  time to fit residues: 50.6930
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  : 0.179 
-------------------------------------------------------------------------------
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 24 optimal weight:    0.9990
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    6.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  29 GLN
C  17 ASN
E  29 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.196371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.163847 restraints weight = 2686.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3944 rms_B_bonded: 1.54
r_work: 0.3821 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3716 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.1437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3695  Z= 0.141
  Angle     :  0.589   5.637   5005  Z= 0.301
  Chirality :  0.047   0.140    560
  Planarity :  0.005   0.046    660
  Dihedral  :  4.295  34.203    482
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 20.73 %
    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 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: -0.17 (0.39), residues: 465
  helix:  None (None), residues: 0
  sheet:  0.54 (0.39), residues: 180
  loop : -0.53 (0.36), residues: 285

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 3695)
  covalent geometry    : angle       0.58922 ( 5005)
  hydrogen bonds       : bond        0.03349 (  125)
  hydrogen bonds       : angle       6.59248 (  285)

*********************** 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
  99 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8029 (mmmt) cc_final: 0.7786 (mtmm)
REVERT: A   59 LEU cc_start: 0.7197 (mm) cc_final: 0.6982 (mt)
REVERT: A   73 ASP cc_start: 0.6720 (OUTLIER) cc_final: 0.6505 (p0)
REVERT: A   88 SER cc_start: 0.8303 (p) cc_final: 0.8043 (t)
REVERT: B    9 LYS cc_start: 0.8028 (mmmt) cc_final: 0.7731 (mtmm)
REVERT: B   16 TYR cc_start: 0.6955 (t80) cc_final: 0.6700 (t80)
REVERT: B   59 LEU cc_start: 0.7082 (mm) cc_final: 0.6855 (mt)
REVERT: B   73 ASP cc_start: 0.6783 (OUTLIER) cc_final: 0.6575 (p0)
REVERT: B   80 GLU cc_start: 0.7372 (tp30) cc_final: 0.7150 (tt0)
REVERT: B   88 SER cc_start: 0.8287 (p) cc_final: 0.8009 (t)
REVERT: C    9 LYS cc_start: 0.7977 (mmmt) cc_final: 0.7746 (mppt)
REVERT: C   40 LYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6551 (tttm)
REVERT: C   59 LEU cc_start: 0.7224 (mm) cc_final: 0.6986 (mt)
REVERT: C   73 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.6441 (p0)
REVERT: C   88 SER cc_start: 0.8272 (p) cc_final: 0.7985 (t)
REVERT: D   59 LEU cc_start: 0.7159 (mm) cc_final: 0.6915 (mt)
REVERT: D   73 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6537 (p0)
REVERT: D   88 SER cc_start: 0.8279 (p) cc_final: 0.8013 (t)
REVERT: E    9 LYS cc_start: 0.7989 (mmmt) cc_final: 0.7697 (mtmm)
REVERT: E   34 THR cc_start: 0.7389 (t) cc_final: 0.7050 (p)
REVERT: E   59 LEU cc_start: 0.7057 (mm) cc_final: 0.6814 (mt)
REVERT: E   73 ASP cc_start: 0.6807 (OUTLIER) cc_final: 0.6601 (p0)
REVERT: E   88 SER cc_start: 0.8236 (p) cc_final: 0.7995 (t)
  outliers start: 10
  outliers final: 0
  residues processed: 96
  average time/residue: 0.6079
  time to fit residues: 59.9298
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  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ASP
Chi-restraints excluded: chain B residue   73 ASP
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   73 ASP
Chi-restraints excluded: chain D residue   73 ASP
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 8 optimal weight:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 31 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 33 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.4203 r_free = 0.4203 target = 0.189350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.156479 restraints weight = 2615.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3860 rms_B_bonded: 1.47
r_work: 0.3735 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3626 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.040   3695  Z= 0.355
  Angle     :  0.831   6.598   5005  Z= 0.433
  Chirality :  0.052   0.143    560
  Planarity :  0.007   0.047    660
  Dihedral  :  4.790  15.009    480
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 19.76 %
    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 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: -0.45 (0.37), residues: 465
  helix:  None (None), residues: 0
  sheet: -0.08 (0.36), residues: 180
  loop : -0.38 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG D  87 
 TYR   0.019   0.006   TYR C  16 
 PHE   0.008   0.002   PHE B   3 
 TRP   0.007   0.003   TRP B   4 
 HIS   0.004   0.002   HIS C  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00682 ( 3695)
  covalent geometry    : angle       0.83089 ( 5005)
  hydrogen bonds       : bond        0.04100 (  125)
  hydrogen bonds       : angle       6.82729 (  285)

*********************** 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
  102 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7850 (mtmm)
REVERT: A   19 LYS cc_start: 0.6272 (OUTLIER) cc_final: 0.5575 (mtpt)
REVERT: A   59 LEU cc_start: 0.7380 (mm) cc_final: 0.7144 (mt)
REVERT: B    9 LYS cc_start: 0.8063 (mmmt) cc_final: 0.7753 (mtmm)
REVERT: B   19 LYS cc_start: 0.6310 (OUTLIER) cc_final: 0.5811 (mtmt)
REVERT: B   59 LEU cc_start: 0.7389 (mm) cc_final: 0.7104 (mt)
REVERT: C    9 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7802 (mtmm)
REVERT: C   19 LYS cc_start: 0.6320 (OUTLIER) cc_final: 0.5795 (mtmt)
REVERT: C   40 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6737 (tttm)
REVERT: C   59 LEU cc_start: 0.7360 (mm) cc_final: 0.7093 (mt)
REVERT: C   73 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6928 (p0)
REVERT: D   19 LYS cc_start: 0.6314 (OUTLIER) cc_final: 0.5646 (mtpt)
REVERT: D   40 LYS cc_start: 0.7204 (pttp) cc_final: 0.6916 (tmmt)
REVERT: D   59 LEU cc_start: 0.7378 (mm) cc_final: 0.7090 (mt)
REVERT: E    9 LYS cc_start: 0.8069 (mmmt) cc_final: 0.7759 (mtmm)
REVERT: E   19 LYS cc_start: 0.6221 (OUTLIER) cc_final: 0.5737 (mtmt)
REVERT: E   59 LEU cc_start: 0.7356 (mm) cc_final: 0.7074 (mt)
  outliers start: 14
  outliers final: 0
  residues processed: 94
  average time/residue: 0.7236
  time to fit residues: 69.6480
Evaluate side-chains
  94 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
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   19 LYS
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   73 ASP
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 34 optimal weight:    0.9980
   chunk 44 optimal weight:   10.0000
   chunk 11 optimal weight:    0.0870
   chunk 27 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 4 optimal weight:    7.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    0.9962

-------------------------------------------------------------------------------
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  44 GLN
C  29 GLN
C  44 GLN
D  44 GLN
E  44 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.195365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.163306 restraints weight = 2555.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 1.45
r_work: 0.3813 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3706 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.2684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3695  Z= 0.145
  Angle     :  0.585   6.070   5005  Z= 0.297
  Chirality :  0.047   0.142    560
  Planarity :  0.005   0.044    660
  Dihedral  :  4.205  13.340    480
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 19.02 %
    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 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: -0.27 (0.38), residues: 465
  helix:  None (None), residues: 0
  sheet:  0.15 (0.37), residues: 180
  loop : -0.35 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  87 
 TYR   0.008   0.002   TYR A  16 
 PHE   0.003   0.001   PHE B  81 
 TRP   0.002   0.001   TRP C   4 
 HIS   0.002   0.001   HIS C  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3695)
  covalent geometry    : angle       0.58495 ( 5005)
  hydrogen bonds       : bond        0.02826 (  125)
  hydrogen bonds       : angle       6.07089 (  285)

*********************** 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: 8
    poor density    : 82
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7820 (mppt)
REVERT: A   19 LYS cc_start: 0.6178 (OUTLIER) cc_final: 0.5544 (mtpt)
REVERT: A   59 LEU cc_start: 0.7259 (mm) cc_final: 0.7013 (mt)
REVERT: B   16 TYR cc_start: 0.6941 (t80) cc_final: 0.6688 (t80)
REVERT: B   19 LYS cc_start: 0.6247 (OUTLIER) cc_final: 0.5622 (mtpt)
REVERT: B   59 LEU cc_start: 0.7239 (mm) cc_final: 0.6981 (mt)
REVERT: C    9 LYS cc_start: 0.8076 (mmmt) cc_final: 0.7873 (mppt)
REVERT: C   19 LYS cc_start: 0.6169 (OUTLIER) cc_final: 0.5539 (mtpt)
REVERT: C   59 LEU cc_start: 0.7236 (mm) cc_final: 0.6980 (mt)
REVERT: D   19 LYS cc_start: 0.6206 (OUTLIER) cc_final: 0.5564 (mtpt)
REVERT: D   59 LEU cc_start: 0.7219 (mm) cc_final: 0.6949 (mt)
REVERT: E   19 LYS cc_start: 0.6105 (OUTLIER) cc_final: 0.5814 (mptt)
REVERT: E   59 LEU cc_start: 0.7228 (mm) cc_final: 0.6960 (mt)
  outliers start: 8
  outliers final: 0
  residues processed: 89
  average time/residue: 0.6971
  time to fit residues: 63.5399
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  : 0.146 
-------------------------------------------------------------------------------
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   19 LYS
Chi-restraints excluded: chain D residue   19 LYS
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 41 optimal weight:    0.1980
   chunk 38 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9980
   chunk 11 optimal weight:    8.9990
   chunk 22 optimal weight:   10.0000
   chunk 35 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 26 optimal weight:    7.9990
   chunk 6 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   overall best weight:    3.2386

-------------------------------------------------------------------------------
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  29 GLN
C  44 GLN
D  44 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.190226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.157426 restraints weight = 2607.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 1.47
r_work: 0.3748 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3639 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.3071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   3695  Z= 0.299
  Angle     :  0.748   6.634   5005  Z= 0.388
  Chirality :  0.049   0.145    560
  Planarity :  0.006   0.049    660
  Dihedral  :  4.720  15.348    480
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 17.80 %
    Favored  : 79.51 %
  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: -0.62 (0.37), residues: 465
  helix:  None (None), residues: 0
  sheet: -0.28 (0.35), residues: 180
  loop : -0.44 (0.36), residues: 285

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00577 ( 3695)
  covalent geometry    : angle       0.74761 ( 5005)
  hydrogen bonds       : bond        0.03597 (  125)
  hydrogen bonds       : angle       6.59740 (  285)

*********************** 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
  95 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7842 (mtmm)
REVERT: A   19 LYS cc_start: 0.6205 (OUTLIER) cc_final: 0.5707 (mtmt)
REVERT: A   59 LEU cc_start: 0.7367 (mm) cc_final: 0.7126 (mt)
REVERT: B    9 LYS cc_start: 0.8145 (mptm) cc_final: 0.7853 (mppt)
REVERT: B   19 LYS cc_start: 0.6254 (OUTLIER) cc_final: 0.5779 (mtmt)
REVERT: B   59 LEU cc_start: 0.7350 (mm) cc_final: 0.7077 (mt)
REVERT: C    9 LYS cc_start: 0.8119 (mmmt) cc_final: 0.7788 (mtmm)
REVERT: C   19 LYS cc_start: 0.6246 (OUTLIER) cc_final: 0.5553 (mtpt)
REVERT: C   59 LEU cc_start: 0.7318 (mm) cc_final: 0.7047 (mt)
REVERT: D    9 LYS cc_start: 0.8060 (mptm) cc_final: 0.7765 (mppt)
REVERT: D   19 LYS cc_start: 0.6202 (OUTLIER) cc_final: 0.5504 (mtpt)
REVERT: D   59 LEU cc_start: 0.7375 (mm) cc_final: 0.7096 (mt)
REVERT: E    9 LYS cc_start: 0.8103 (mptm) cc_final: 0.7841 (mppt)
REVERT: E   19 LYS cc_start: 0.6162 (OUTLIER) cc_final: 0.5686 (mtmt)
REVERT: E   59 LEU cc_start: 0.7349 (mm) cc_final: 0.7055 (mt)
  outliers start: 11
  outliers final: 0
  residues processed: 94
  average time/residue: 0.6792
  time to fit residues: 65.3868
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  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LYS
Chi-restraints excluded: chain A residue   19 LYS
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 28 optimal weight:    2.9990
   chunk 18 optimal weight:   10.0000
   chunk 1 optimal weight:    0.2980
   chunk 0 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 42 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 27 optimal weight:    7.9990
   overall best weight:    1.9986

-------------------------------------------------------------------------------
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  29 GLN
C  44 GLN
D  44 GLN
E  44 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.191514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.160844 restraints weight = 2646.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 1.39
r_work: 0.3787 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3684 rms_B_bonded: 3.13 restraints_weight: 0.2500
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3695  Z= 0.214
  Angle     :  0.656   6.472   5005  Z= 0.339
  Chirality :  0.048   0.144    560
  Planarity :  0.006   0.047    660
  Dihedral  :  4.619  15.116    480
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.56 %
    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 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: -0.53 (0.37), residues: 465
  helix:  None (None), residues: 0
  sheet: -0.22 (0.35), residues: 180
  loop : -0.38 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG E  87 
 TYR   0.013   0.003   TYR C  16 
 PHE   0.005   0.001   PHE E  81 
 TRP   0.004   0.002   TRP A   4 
 HIS   0.003   0.001   HIS C  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 3695)
  covalent geometry    : angle       0.65640 ( 5005)
  hydrogen bonds       : bond        0.03176 (  125)
  hydrogen bonds       : angle       6.34613 (  285)

*********************** 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
  93 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7990 (mppt)
REVERT: A   19 LYS cc_start: 0.6206 (OUTLIER) cc_final: 0.5750 (mtmt)
REVERT: A   59 LEU cc_start: 0.7385 (mm) cc_final: 0.7158 (mt)
REVERT: B    9 LYS cc_start: 0.8205 (mptm) cc_final: 0.7967 (mppt)
REVERT: B   19 LYS cc_start: 0.6284 (OUTLIER) cc_final: 0.5826 (mtmt)
REVERT: B   59 LEU cc_start: 0.7340 (mm) cc_final: 0.7102 (mt)
REVERT: C   19 LYS cc_start: 0.6231 (OUTLIER) cc_final: 0.5592 (mtpt)
REVERT: C   59 LEU cc_start: 0.7350 (mm) cc_final: 0.7114 (mt)
REVERT: D    9 LYS cc_start: 0.8190 (mptm) cc_final: 0.7918 (mppt)
REVERT: D   19 LYS cc_start: 0.6257 (OUTLIER) cc_final: 0.5616 (mtpt)
REVERT: D   59 LEU cc_start: 0.7411 (mm) cc_final: 0.7163 (mt)
REVERT: E    9 LYS cc_start: 0.8180 (mptm) cc_final: 0.7956 (mppt)
REVERT: E   19 LYS cc_start: 0.6182 (OUTLIER) cc_final: 0.5732 (mtmt)
REVERT: E   59 LEU cc_start: 0.7380 (mm) cc_final: 0.7122 (mt)
  outliers start: 13
  outliers final: 0
  residues processed: 91
  average time/residue: 0.7098
  time to fit residues: 66.1711
Evaluate side-chains
  84 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 78
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LYS
Chi-restraints excluded: chain A residue   19 LYS
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 8 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 34 optimal weight:    7.9990
   chunk 30 optimal weight:    0.7980
   chunk 40 optimal weight:    8.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    3.3588

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.190760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.161227 restraints weight = 2704.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3935 rms_B_bonded: 1.36
r_work: 0.3796 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3693 rms_B_bonded: 3.10 restraints_weight: 0.2500
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.3408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   3695  Z= 0.309
  Angle     :  0.762   7.019   5005  Z= 0.395
  Chirality :  0.049   0.143    560
  Planarity :  0.006   0.049    660
  Dihedral  :  4.929  15.633    480
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.80 %
    Favored  : 79.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.37), residues: 465
  helix:  None (None), residues: 0
  sheet: -0.46 (0.35), residues: 180
  loop : -0.41 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E  87 
 TYR   0.017   0.005   TYR C  16 
 PHE   0.005   0.002   PHE B   3 
 TRP   0.006   0.003   TRP C   4 
 HIS   0.003   0.001   HIS B  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00594 ( 3695)
  covalent geometry    : angle       0.76224 ( 5005)
  hydrogen bonds       : bond        0.03656 (  125)
  hydrogen bonds       : angle       6.65138 (  285)

*********************** 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
  96 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A    9 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7990 (mtmm)
REVERT: A   19 LYS cc_start: 0.6251 (OUTLIER) cc_final: 0.5775 (mtmt)
REVERT: A   59 LEU cc_start: 0.7444 (mm) cc_final: 0.7228 (mt)
REVERT: B    9 LYS cc_start: 0.8234 (mptm) cc_final: 0.8019 (mppt)
REVERT: B   19 LYS cc_start: 0.6294 (OUTLIER) cc_final: 0.5819 (mtmt)
REVERT: B   59 LEU cc_start: 0.7465 (mm) cc_final: 0.7231 (mt)
REVERT: C   19 LYS cc_start: 0.6297 (OUTLIER) cc_final: 0.5628 (mtpt)
REVERT: C   59 LEU cc_start: 0.7392 (mm) cc_final: 0.7169 (mt)
REVERT: D    9 LYS cc_start: 0.8197 (mptm) cc_final: 0.7951 (mppt)
REVERT: D   19 LYS cc_start: 0.6333 (OUTLIER) cc_final: 0.5678 (mtpt)
REVERT: D   59 LEU cc_start: 0.7471 (mm) cc_final: 0.7230 (mt)
REVERT: E   19 LYS cc_start: 0.6243 (OUTLIER) cc_final: 0.5766 (mtmt)
REVERT: E   59 LEU cc_start: 0.7437 (mm) cc_final: 0.7182 (mt)
  outliers start: 10
  outliers final: 1
  residues processed: 94
  average time/residue: 0.6833
  time to fit residues: 65.8370
Evaluate side-chains
  90 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LYS
Chi-restraints excluded: chain A residue   19 LYS
Chi-restraints excluded: chain B residue   19 LYS
Chi-restraints excluded: chain B residue   47 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 31 optimal weight:    8.9990
   chunk 34 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 8 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0870
   chunk 3 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    1.1964

-------------------------------------------------------------------------------
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
E  44 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.194533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.164670 restraints weight = 2668.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3973 rms_B_bonded: 1.38
r_work: 0.3839 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3738 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3695  Z= 0.161
  Angle     :  0.598   6.425   5005  Z= 0.306
  Chirality :  0.047   0.144    560
  Planarity :  0.005   0.047    660
  Dihedral  :  4.453  14.360    480
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 19.76 %
    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 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: -0.51 (0.37), residues: 465
  helix:  None (None), residues: 0
  sheet: -0.27 (0.35), residues: 180
  loop : -0.31 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  87 
 TYR   0.009   0.002   TYR C  16 
 PHE   0.004   0.001   PHE D  81 
 TRP   0.006   0.002   TRP A   4 
 HIS   0.002   0.001   HIS D  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3695)
  covalent geometry    : angle       0.59810 ( 5005)
  hydrogen bonds       : bond        0.02839 (  125)
  hydrogen bonds       : angle       6.12737 (  285)

*********************** 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
  87 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A   19 LYS cc_start: 0.6226 (OUTLIER) cc_final: 0.5619 (mtpt)
REVERT: A   59 LEU cc_start: 0.7395 (mm) cc_final: 0.7174 (mt)
REVERT: B    9 LYS cc_start: 0.8225 (mptm) cc_final: 0.7998 (mppt)
REVERT: B   59 LEU cc_start: 0.7343 (mm) cc_final: 0.7117 (mt)
REVERT: C   19 LYS cc_start: 0.6218 (OUTLIER) cc_final: 0.5607 (mtpt)
REVERT: C   59 LEU cc_start: 0.7323 (mm) cc_final: 0.7107 (mt)
REVERT: D    9 LYS cc_start: 0.8210 (mptm) cc_final: 0.7950 (mppt)
REVERT: D   19 LYS cc_start: 0.6268 (OUTLIER) cc_final: 0.5665 (mtpt)
REVERT: D   59 LEU cc_start: 0.7394 (mm) cc_final: 0.7147 (mt)
REVERT: E    9 LYS cc_start: 0.8209 (mptm) cc_final: 0.7997 (mppt)
REVERT: E   19 LYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5570 (mtpt)
REVERT: E   59 LEU cc_start: 0.7382 (mm) cc_final: 0.7124 (mt)
  outliers start: 7
  outliers final: 0
  residues processed: 87
  average time/residue: 0.7307
  time to fit residues: 65.0992
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  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 13 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 22 optimal weight:    6.9990
   chunk 24 optimal weight:    0.4980
   chunk 31 optimal weight:    9.9990
   chunk 16 optimal weight:    0.3980
   chunk 17 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   overall best weight:    1.2982

-------------------------------------------------------------------------------
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 = 0.4259 r_free = 0.4259 target = 0.194636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.165336 restraints weight = 2635.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3975 rms_B_bonded: 1.34
r_work: 0.3843 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3743 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.3309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3695  Z= 0.165
  Angle     :  0.603   6.493   5005  Z= 0.307
  Chirality :  0.047   0.144    560
  Planarity :  0.005   0.047    660
  Dihedral  :  4.341  14.503    480
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  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 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: -0.48 (0.37), residues: 465
  helix:  None (None), residues: 0
  sheet: -0.24 (0.35), residues: 180
  loop : -0.30 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  87 
 TYR   0.007   0.002   TYR D  16 
 PHE   0.004   0.001   PHE D  81 
 TRP   0.007   0.002   TRP A   4 
 HIS   0.002   0.001   HIS D  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 3695)
  covalent geometry    : angle       0.60297 ( 5005)
  hydrogen bonds       : bond        0.02921 (  125)
  hydrogen bonds       : angle       6.03385 (  285)

*********************** 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
  86 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A   19 LYS cc_start: 0.6229 (OUTLIER) cc_final: 0.5638 (mtpt)
REVERT: A   59 LEU cc_start: 0.7357 (mm) cc_final: 0.7137 (mt)
REVERT: B    9 LYS cc_start: 0.8209 (mptm) cc_final: 0.7992 (mppt)
REVERT: B   59 LEU cc_start: 0.7318 (mm) cc_final: 0.7088 (mt)
REVERT: C   19 LYS cc_start: 0.6217 (OUTLIER) cc_final: 0.5590 (mtpt)
REVERT: C   59 LEU cc_start: 0.7319 (mm) cc_final: 0.7089 (mt)
REVERT: D    9 LYS cc_start: 0.8181 (mptm) cc_final: 0.7929 (mppt)
REVERT: D   19 LYS cc_start: 0.6286 (OUTLIER) cc_final: 0.5680 (mtpt)
REVERT: D   59 LEU cc_start: 0.7374 (mm) cc_final: 0.7134 (mt)
REVERT: E    9 LYS cc_start: 0.8181 (mptm) cc_final: 0.7956 (mppt)
REVERT: E   19 LYS cc_start: 0.6208 (OUTLIER) cc_final: 0.5587 (mtpt)
REVERT: E   59 LEU cc_start: 0.7334 (mm) cc_final: 0.7087 (mt)
REVERT: E   89 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7621 (mp)
  outliers start: 6
  outliers final: 0
  residues processed: 86
  average time/residue: 0.6999
  time to fit residues: 61.6554
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  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A 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
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 6 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 37 optimal weight:    0.7980
   chunk 4 optimal weight:    9.9990
   chunk 43 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 41 optimal weight:    0.1980
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.4265 r_free = 0.4265 target = 0.195394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.164970 restraints weight = 2702.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 1.41
r_work: 0.3841 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3741 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.3292

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= 0.153
  Angle     :  0.591   6.349   5005  Z= 0.299
  Chirality :  0.047   0.141    560
  Planarity :  0.005   0.046    660
  Dihedral  :  4.248  14.254    480
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 20.00 %
    Favored  : 78.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.37), residues: 465
  helix:  None (None), residues: 0
  sheet: -0.18 (0.35), residues: 180
  loop : -0.29 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  87 
 TYR   0.007   0.002   TYR D  16 
 PHE   0.004   0.001   PHE B  81 
 TRP   0.010   0.002   TRP B   4 
 HIS   0.002   0.001   HIS D  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 3695)
  covalent geometry    : angle       0.59128 ( 5005)
  hydrogen bonds       : bond        0.02776 (  125)
  hydrogen bonds       : angle       5.90439 (  285)

********************** 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
  88 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A   19 LYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5621 (mtpt)
REVERT: A   59 LEU cc_start: 0.7354 (mm) cc_final: 0.7133 (mt)
REVERT: B    9 LYS cc_start: 0.8216 (mptm) cc_final: 0.7975 (mppt)
REVERT: B   59 LEU cc_start: 0.7312 (mm) cc_final: 0.7082 (mt)
REVERT: C   19 LYS cc_start: 0.6196 (OUTLIER) cc_final: 0.5580 (mtpt)
REVERT: C   59 LEU cc_start: 0.7293 (mm) cc_final: 0.7074 (mt)
REVERT: D    9 LYS cc_start: 0.8184 (mptm) cc_final: 0.7921 (mppt)
REVERT: D   19 LYS cc_start: 0.6260 (OUTLIER) cc_final: 0.5659 (mtpt)
REVERT: D   59 LEU cc_start: 0.7371 (mm) cc_final: 0.7125 (mt)
REVERT: E    9 LYS cc_start: 0.8187 (mptm) cc_final: 0.7956 (mppt)
REVERT: E   19 LYS cc_start: 0.6183 (OUTLIER) cc_final: 0.5566 (mtpt)
REVERT: E   59 LEU cc_start: 0.7304 (mm) cc_final: 0.7064 (mt)
REVERT: E   89 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7613 (mp)
  outliers start: 8
  outliers final: 1
  residues processed: 88
  average time/residue: 0.6635
  time to fit residues: 59.7931
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  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A 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
Chi-restraints excluded: chain E residue   47 ILE
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 1 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0770
   chunk 43 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 18 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.7940

-------------------------------------------------------------------------------
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 = 0.4283 r_free = 0.4283 target = 0.197190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.167204 restraints weight = 2627.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3995 rms_B_bonded: 1.39
r_work: 0.3864 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3763 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.3270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3695  Z= 0.127
  Angle     :  0.562   6.194   5005  Z= 0.282
  Chirality :  0.047   0.140    560
  Planarity :  0.005   0.046    660
  Dihedral  :  4.013  13.431    480
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 20.73 %
    Favored  : 78.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.37), residues: 465
  helix:  None (None), residues: 0
  sheet: -0.05 (0.36), residues: 180
  loop : -0.24 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  87 
 TYR   0.006   0.001   TYR D  16 
 PHE   0.004   0.001   PHE B  81 
 TRP   0.014   0.003   TRP B   4 
 HIS   0.002   0.001   HIS D  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 3695)
  covalent geometry    : angle       0.56196 ( 5005)
  hydrogen bonds       : bond        0.02619 (  125)
  hydrogen bonds       : angle       5.70525 (  285)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2166.91 seconds
wall clock time: 37 minutes 43.21 seconds (2263.21 seconds total)