Starting phenix.real_space_refine
on Sat May 10 11:34:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qhs_18416/05_2025/8qhs_18416.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qhs_18416/05_2025/8qhs_18416.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qhs_18416/05_2025/8qhs_18416.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qhs_18416/05_2025/8qhs_18416.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qhs_18416/05_2025/8qhs_18416.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qhs_18416/05_2025/8qhs_18416.cif"
  }
  resolution = 2.3
  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=   0.001 sd=   0.055
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      30      5.16       5
     C    3725      2.51       5
     N     935      2.21       5
     O    1522      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6212
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1175
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1175
          Classifications: {'peptide': 157}
          Link IDs: {'PTRANS': 3, 'TRANS': 153}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 60
          Classifications: {'water': 60}
          Link IDs: {None: 59}
    Chain: "C"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 72
          Classifications: {'water': 72}
          Link IDs: {None: 71}
    Chain: "D"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 72
          Classifications: {'water': 72}
          Link IDs: {None: 71}
    Chain: "E"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 64
          Classifications: {'water': 64}
          Link IDs: {None: 63}
    Chain: "F"
      Number of atoms: 69
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 69, 69
          Classifications: {'water': 69}
          Link IDs: {None: 68}
  Restraints were copied for chains:
    C, E, D, F
  Time building chain proxies: 3.76, per 1000 atoms: 0.61
  Number of scatterers: 6212
  At special positions: 0
  Unit cell: (72.688, 99.12, 159.418, 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      30     16.00
     O    1522      8.00
     N     935      7.00
     C    3725      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   9 " - pdb=" SG  CYS C 104 " distance=3.00

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.58
  Conformation dependent library (CDL) restraints added in 913.5 milliseconds
  

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1400

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 3 sheets defined
      14.1% alpha, 26.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 7
      removed outlier: 3.514A  pdb=" N   ASN A   6 " --> pdb=" O   ALA A   2 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   LEU A   7 " --> pdb=" O   PHE A   3 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2 through 7'
    Processing helix  chain 'A' and resid 20 through 22
      No H-bonds generated for 'chain 'A' and resid 20 through 22'
    Processing helix  chain 'A' and resid 87 through 100
    Processing helix  chain 'C' and resid 3 through 7
      removed outlier: 3.906A  pdb=" N   LEU C   7 " --> pdb=" O   PHE C   3 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 3 through 7'
    Processing helix  chain 'C' and resid 20 through 22
      No H-bonds generated for 'chain 'C' and resid 20 through 22'
    Processing helix  chain 'C' and resid 87 through 100
    Processing helix  chain 'D' and resid 3 through 7
      removed outlier: 3.907A  pdb=" N   LEU D   7 " --> pdb=" O   PHE D   3 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 3 through 7'
    Processing helix  chain 'D' and resid 20 through 22
      No H-bonds generated for 'chain 'D' and resid 20 through 22'
    Processing helix  chain 'D' and resid 87 through 100
    Processing helix  chain 'E' and resid 3 through 7
      removed outlier: 3.906A  pdb=" N   LEU E   7 " --> pdb=" O   PHE E   3 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 3 through 7'
    Processing helix  chain 'E' and resid 20 through 22
      No H-bonds generated for 'chain 'E' and resid 20 through 22'
    Processing helix  chain 'E' and resid 87 through 100
    Processing helix  chain 'F' and resid 3 through 7
      removed outlier: 3.907A  pdb=" N   LEU F   7 " --> pdb=" O   PHE F   3 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 3 through 7'
    Processing helix  chain 'F' and resid 20 through 22
      No H-bonds generated for 'chain 'F' and resid 20 through 22'
    Processing helix  chain 'F' and resid 87 through 100
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 29
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 36 through 38
    current: chain 'A' and resid 68 through 82
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 68 through 82
    current: chain 'A' and resid 114 through 129
      removed outlier: 6.281A  pdb=" N   LYS A 141 " --> pdb=" O   ALA A 124 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   TYR A 126 " --> pdb=" O   SER A 139 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   SER A 139 " --> pdb=" O   TYR A 126 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   PHE A 128 " --> pdb=" O   THR A 137 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   THR A 137 " --> pdb=" O   PHE A 128 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 137 through 144
    current: chain 'D' and resid 36 through 38
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 36 through 38
    current: chain 'D' and resid 68 through 82
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 68 through 82
    current: chain 'D' and resid 114 through 129
      removed outlier: 6.281A  pdb=" N   LYS D 141 " --> pdb=" O   ALA D 124 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   TYR D 126 " --> pdb=" O   SER D 139 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   SER D 139 " --> pdb=" O   TYR D 126 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   PHE D 128 " --> pdb=" O   THR D 137 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   THR D 137 " --> pdb=" O   PHE D 128 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 24 through 29
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 36 through 38
    current: chain 'C' and resid 68 through 82
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 68 through 82
    current: chain 'C' and resid 114 through 129
      removed outlier: 6.282A  pdb=" N   LYS C 141 " --> pdb=" O   ALA C 124 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   TYR C 126 " --> pdb=" O   SER C 139 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   SER C 139 " --> pdb=" O   TYR C 126 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   PHE C 128 " --> pdb=" O   THR C 137 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   THR C 137 " --> pdb=" O   PHE C 128 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 137 through 144
    current: chain 'E' and resid 36 through 38
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 36 through 38
    current: chain 'E' and resid 68 through 82
  WARNING: can't find start of bonding for strands!
    previous: chain 'E' and resid 68 through 82
    current: chain 'E' and resid 114 through 129
      removed outlier: 6.281A  pdb=" N   LYS E 141 " --> pdb=" O   ALA E 124 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   TYR E 126 " --> pdb=" O   SER E 139 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   SER E 139 " --> pdb=" O   TYR E 126 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   PHE E 128 " --> pdb=" O   THR E 137 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   THR E 137 " --> pdb=" O   PHE E 128 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 24 through 29
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 36 through 38
    current: chain 'F' and resid 68 through 82
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 68 through 82
    current: chain 'F' and resid 114 through 129
      removed outlier: 6.281A  pdb=" N   LYS F 141 " --> pdb=" O   ALA F 124 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   TYR F 126 " --> pdb=" O   SER F 139 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   SER F 139 " --> pdb=" O   TYR F 126 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   PHE F 128 " --> pdb=" O   THR F 137 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   THR F 137 " --> pdb=" O   PHE F 128 " (cutoff:3.500A)

    71 hydrogen bonds defined for protein.
    213 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.34

  Time building geometry restraints manager: 1.86 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1915
        1.34 -     1.45: 1011
        1.45 -     1.57: 2989
        1.57 -     1.69: 0
        1.69 -     1.81: 50
  Bond restraints: 5965
  Sorted by residual:
  bond pdb=" C   ILE D  56 "
       pdb=" O   ILE D  56 "
    ideal  model  delta    sigma   weight residual
    1.236  1.223  0.014 1.19e-02 7.06e+03 1.31e+00
  bond pdb=" N   GLY C  44 "
       pdb=" CA  GLY C  44 "
    ideal  model  delta    sigma   weight residual
    1.454  1.443  0.011 9.90e-03 1.02e+04 1.29e+00
  bond pdb=" C   ILE C  56 "
       pdb=" O   ILE C  56 "
    ideal  model  delta    sigma   weight residual
    1.236  1.223  0.013 1.19e-02 7.06e+03 1.27e+00
  bond pdb=" C   ILE A  56 "
       pdb=" O   ILE A  56 "
    ideal  model  delta    sigma   weight residual
    1.236  1.223  0.013 1.19e-02 7.06e+03 1.25e+00
  bond pdb=" C   ILE E  56 "
       pdb=" O   ILE E  56 "
    ideal  model  delta    sigma   weight residual
    1.236  1.223  0.013 1.19e-02 7.06e+03 1.25e+00
  ... (remaining 5960 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.91: 6889
        0.91 -     1.82: 977
        1.82 -     2.73: 114
        2.73 -     3.64: 40
        3.64 -     4.55: 15
  Bond angle restraints: 8035
  Sorted by residual:
  angle pdb=" C   SER E 112 "
        pdb=" N   LYS E 113 "
        pdb=" CA  LYS E 113 "
      ideal   model   delta    sigma   weight residual
     122.19  125.30   -3.11 1.41e+00 5.03e-01 4.87e+00
  angle pdb=" C   SER A 112 "
        pdb=" N   LYS A 113 "
        pdb=" CA  LYS A 113 "
      ideal   model   delta    sigma   weight residual
     122.19  125.30   -3.11 1.41e+00 5.03e-01 4.87e+00
  angle pdb=" C   SER C 112 "
        pdb=" N   LYS C 113 "
        pdb=" CA  LYS C 113 "
      ideal   model   delta    sigma   weight residual
     122.19  125.28   -3.09 1.41e+00 5.03e-01 4.80e+00
  angle pdb=" C   SER D 112 "
        pdb=" N   LYS D 113 "
        pdb=" CA  LYS D 113 "
      ideal   model   delta    sigma   weight residual
     122.19  125.27   -3.08 1.41e+00 5.03e-01 4.76e+00
  angle pdb=" C   SER F 112 "
        pdb=" N   LYS F 113 "
        pdb=" CA  LYS F 113 "
      ideal   model   delta    sigma   weight residual
     122.19  125.26   -3.07 1.41e+00 5.03e-01 4.75e+00
  ... (remaining 8030 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.62: 3160
       16.62 -    33.24: 202
       33.24 -    49.85: 101
       49.85 -    66.47: 55
       66.47 -    83.09: 20
  Dihedral angle restraints: 3538
    sinusoidal: 1333
      harmonic: 2205
  Sorted by residual:
  dihedral pdb=" CA  ALA F 121 "
           pdb=" C   ALA F 121 "
           pdb=" N   ILE F 122 "
           pdb=" CA  ILE F 122 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.28   18.72     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  ALA A 121 "
           pdb=" C   ALA A 121 "
           pdb=" N   ILE A 122 "
           pdb=" CA  ILE A 122 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.29   18.71     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  ALA D 121 "
           pdb=" C   ALA D 121 "
           pdb=" N   ILE D 122 "
           pdb=" CA  ILE D 122 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.30   18.70     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 3535 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 453
       0.028 -    0.055: 257
       0.055 -    0.083: 115
       0.083 -    0.110: 50
       0.110 -    0.138: 20
  Chirality restraints: 895
  Sorted by residual:
  chirality pdb=" CA  ILE F 122 "
            pdb=" N   ILE F 122 "
            pdb=" C   ILE F 122 "
            pdb=" CB  ILE F 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.74e-01
  chirality pdb=" CA  ILE C 122 "
            pdb=" N   ILE C 122 "
            pdb=" C   ILE C 122 "
            pdb=" CB  ILE C 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.74e-01
  chirality pdb=" CA  ILE E 122 "
            pdb=" N   ILE E 122 "
            pdb=" C   ILE E 122 "
            pdb=" CB  ILE E 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.72e-01
  ... (remaining 892 not shown)

  Planarity restraints: 1035
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E 101 "    0.019 5.00e-02 4.00e+02   2.85e-02 1.30e+00
        pdb=" N   PRO E 102 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO E 102 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO E 102 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D 101 "   -0.019 5.00e-02 4.00e+02   2.83e-02 1.28e+00
        pdb=" N   PRO D 102 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO D 102 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO D 102 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER F 101 "   -0.019 5.00e-02 4.00e+02   2.82e-02 1.28e+00
        pdb=" N   PRO F 102 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO F 102 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO F 102 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1032 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 215
        2.65 -     3.21: 5559
        3.21 -     3.78: 10780
        3.78 -     4.34: 14721
        4.34 -     4.90: 22938
  Nonbonded interactions: 54213
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP E  60 "
            pdb=" O   HOH E 201 "
     model   vdw
     2.089 3.040
  nonbonded pdb=" O   HOH C 222 "
            pdb=" O   HOH C 243 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" OD1 ASP F 150 "
            pdb=" OG1 THR F 152 "
     model   vdw
     2.158 3.040
  nonbonded pdb=" OD1 ASP D 150 "
            pdb=" OG1 THR D 152 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" OD1 ASP C 150 "
            pdb=" OG1 THR C 152 "
     model   vdw
     2.159 3.040
  ... (remaining 54208 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

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:             3.490
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     17.820
  Find NCS groups from input model:        0.150
  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:           0.010
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
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      :  0.014   0.967   5966  Z= 0.693
  Angle     :  0.688   8.800   8037  Z= 0.407
  Chirality :  0.045   0.138    895
  Planarity :  0.003   0.028   1035
  Dihedral  : 17.608  83.088   2135
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  6.56 %
    Allowed  :  6.56 %
    Favored  : 86.89 %
  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: -0.18 (0.27), residues: 765
  helix: -0.27 (0.50), residues: 70
  sheet:  0.11 (0.29), residues: 290
  loop : -0.15 (0.26), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.003   TRP D  75 
 HIS   0.005   0.003   HIS E  90 
 PHE   0.015   0.002   PHE D 128 
 TYR   0.006   0.002   TYR F 138 
 ARG   0.000   0.000   ARG F  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15643 (   71)
  hydrogen bonds       : angle       5.38717 (  213)
  SS BOND              : bond        0.96731 (    1)
  SS BOND              : angle       8.14900 (    2)
  covalent geometry    : bond        0.00645 ( 5965)
  covalent geometry    : angle       0.67646 ( 8035)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 128
  time to evaluate  : 0.677 
Fit side-chains
REVERT: C   17 LYS cc_start: 0.7992 (ttmt) cc_final: 0.6800 (ttpt)
REVERT: C  145 MET cc_start: 0.9166 (mtp) cc_final: 0.8881 (mtp)
REVERT: E   17 LYS cc_start: 0.7917 (ttmt) cc_final: 0.6997 (ttpt)
REVERT: F  145 MET cc_start: 0.9120 (mtp) cc_final: 0.8795 (mtp)
  outliers start: 40
  outliers final: 1
  residues processed: 141
  average time/residue: 1.4852
  time to fit residues: 217.2638
Evaluate side-chains
  96 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  108 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0370
   chunk 19 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 30 optimal weight:    8.9990
   chunk 58 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.6860

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

Flipped N/Q/H residues before XYZ refinement:
A  43 GLN
A 159 GLN
C  43 GLN
C 159 GLN
D  43 GLN
D 159 GLN
E  43 GLN
E 159 GLN
F  43 GLN
F 159 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.125424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.107805 restraints weight = 5783.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 1.17
r_work: 0.3075 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 2.67 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8860
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   5966  Z= 0.100
  Angle     :  0.413   3.010   8037  Z= 0.236
  Chirality :  0.043   0.147    895
  Planarity :  0.002   0.018   1035
  Dihedral  :  4.993  52.049    812
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 13.11 %
    Favored  : 86.07 %
  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:  0.51 (0.28), residues: 765
  helix:  2.09 (0.65), residues: 70
  sheet:  0.25 (0.30), residues: 290
  loop :  0.22 (0.27), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  65 
 HIS   0.002   0.001   HIS F  90 
 PHE   0.014   0.001   PHE C 128 
 TYR   0.004   0.001   TYR A  83 
 ARG   0.002   0.001   ARG E  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02465 (   71)
  hydrogen bonds       : angle       3.88726 (  213)
  SS BOND              : bond        0.00745 (    1)
  SS BOND              : angle       0.17495 (    2)
  covalent geometry    : bond        0.00221 ( 5965)
  covalent geometry    : angle       0.41292 ( 8035)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.731 
Fit side-chains
REVERT: C   17 LYS cc_start: 0.7990 (ttmt) cc_final: 0.6757 (ttpt)
REVERT: C  145 MET cc_start: 0.9313 (mtp) cc_final: 0.9002 (mtp)
REVERT: D  129 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8480 (tm-30)
REVERT: E   17 LYS cc_start: 0.7882 (ttmt) cc_final: 0.6739 (ttpt)
REVERT: F  113 LYS cc_start: 0.8552 (mtmm) cc_final: 0.7844 (mptp)
  outliers start: 5
  outliers final: 0
  residues processed: 103
  average time/residue: 1.6443
  time to fit residues: 175.4329
Evaluate side-chains
  104 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  129 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 16 optimal weight:    0.0670
   chunk 61 optimal weight:    4.9990
   chunk 34 optimal weight:    4.9990
   chunk 9 optimal weight:    0.1980
   chunk 56 optimal weight:    5.9990
   chunk 28 optimal weight:    7.9990
   chunk 42 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.0322

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.127974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.111252 restraints weight = 5887.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 1.05
r_work: 0.3059 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 2.38 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8876
moved from start:          0.1517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5966  Z= 0.115
  Angle     :  0.410   3.013   8037  Z= 0.233
  Chirality :  0.043   0.146    895
  Planarity :  0.002   0.016   1035
  Dihedral  :  4.559  16.852    810
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 13.28 %
    Favored  : 85.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.84 (0.29), residues: 765
  helix:  2.50 (0.66), residues: 70
  sheet:  0.36 (0.30), residues: 290
  loop :  0.50 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP E  65 
 HIS   0.003   0.001   HIS F  90 
 PHE   0.011   0.001   PHE C 128 
 TYR   0.005   0.001   TYR A  83 
 ARG   0.001   0.000   ARG C  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02458 (   71)
  hydrogen bonds       : angle       3.81950 (  213)
  SS BOND              : bond        0.00197 (    1)
  SS BOND              : angle       0.16470 (    2)
  covalent geometry    : bond        0.00256 ( 5965)
  covalent geometry    : angle       0.40983 ( 8035)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.664 
Fit side-chains
REVERT: C    5 GLU cc_start: 0.8190 (mp0) cc_final: 0.7619 (mp0)
REVERT: C   17 LYS cc_start: 0.7934 (ttmt) cc_final: 0.6730 (ttpt)
REVERT: C  114 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8728 (mmmt)
REVERT: D  129 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8528 (tm-30)
REVERT: E   17 LYS cc_start: 0.7887 (ttmt) cc_final: 0.6789 (ttpt)
REVERT: E  129 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8469 (tp30)
REVERT: F  113 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8003 (mptp)
  outliers start: 9
  outliers final: 2
  residues processed: 106
  average time/residue: 1.6391
  time to fit residues: 179.9583
Evaluate side-chains
  102 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain D residue  129 GLU
Chi-restraints excluded: chain E residue  129 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 65 optimal weight:    8.9990
   chunk 61 optimal weight:    2.9990
   chunk 29 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 71 optimal weight:    9.9990
   chunk 52 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    2.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.122288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.104848 restraints weight = 5970.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 1.08
r_work: 0.2992 rms_B_bonded: 1.45 restraints_weight: 0.5000
r_work: 0.2888 rms_B_bonded: 2.44 restraints_weight: 0.2500
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8921
moved from start:          0.1331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   5966  Z= 0.213
  Angle     :  0.518   3.838   8037  Z= 0.288
  Chirality :  0.045   0.157    895
  Planarity :  0.003   0.021   1035
  Dihedral  :  5.156  20.014    810
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 13.77 %
    Favored  : 84.59 %
  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:  0.89 (0.29), residues: 765
  helix:  2.23 (0.63), residues: 70
  sheet:  0.36 (0.30), residues: 290
  loop :  0.63 (0.28), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP E  75 
 HIS   0.004   0.002   HIS A  90 
 PHE   0.016   0.002   PHE C 128 
 TYR   0.008   0.002   TYR A 138 
 ARG   0.001   0.000   ARG A  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03459 (   71)
  hydrogen bonds       : angle       4.11705 (  213)
  SS BOND              : bond        0.00007 (    1)
  SS BOND              : angle       0.06155 (    2)
  covalent geometry    : bond        0.00478 ( 5965)
  covalent geometry    : angle       0.51856 ( 8035)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.665 
Fit side-chains
REVERT: C    5 GLU cc_start: 0.8203 (mp0) cc_final: 0.7645 (mp0)
REVERT: C   17 LYS cc_start: 0.7991 (ttmt) cc_final: 0.6734 (ttpt)
REVERT: C  114 LYS cc_start: 0.9075 (mmmm) cc_final: 0.8866 (mmmt)
REVERT: C  129 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8302 (tp30)
REVERT: E   17 LYS cc_start: 0.8021 (ttmt) cc_final: 0.6892 (ttpp)
REVERT: E  113 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8414 (mppt)
REVERT: E  129 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8461 (tp30)
REVERT: F  113 LYS cc_start: 0.8644 (mtmm) cc_final: 0.7957 (mptp)
  outliers start: 10
  outliers final: 0
  residues processed: 105
  average time/residue: 1.6151
  time to fit residues: 175.6625
Evaluate side-chains
  107 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 104
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain E residue  113 LYS
Chi-restraints excluded: chain E residue  129 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 57 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.1586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.127853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.110973 restraints weight = 5981.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 1.06
r_work: 0.3060 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 2.41 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8886
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5966  Z= 0.122
  Angle     :  0.417   3.045   8037  Z= 0.237
  Chirality :  0.043   0.145    895
  Planarity :  0.002   0.016   1035
  Dihedral  :  4.632  17.249    810
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 14.43 %
    Favored  : 84.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.29), residues: 765
  helix:  2.65 (0.67), residues: 70
  sheet:  0.40 (0.30), residues: 290
  loop :  0.75 (0.29), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP E  65 
 HIS   0.003   0.001   HIS F  90 
 PHE   0.011   0.001   PHE C 128 
 TYR   0.005   0.001   TYR F  83 
 ARG   0.001   0.000   ARG E  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02286 (   71)
  hydrogen bonds       : angle       3.93961 (  213)
  SS BOND              : bond        0.00040 (    1)
  SS BOND              : angle       0.16366 (    2)
  covalent geometry    : bond        0.00268 ( 5965)
  covalent geometry    : angle       0.41738 ( 8035)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.768 
Fit side-chains
REVERT: C    5 GLU cc_start: 0.8159 (mp0) cc_final: 0.7613 (mp0)
REVERT: C   17 LYS cc_start: 0.7928 (ttmt) cc_final: 0.6725 (ttpt)
REVERT: C  114 LYS cc_start: 0.8947 (mmmm) cc_final: 0.8712 (mmmt)
REVERT: C  129 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8345 (tp30)
REVERT: D  129 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8551 (tm-30)
REVERT: E   17 LYS cc_start: 0.7911 (ttmt) cc_final: 0.6848 (ttpt)
REVERT: E  129 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8484 (tp30)
REVERT: F  113 LYS cc_start: 0.8550 (mtmm) cc_final: 0.7952 (mptp)
  outliers start: 7
  outliers final: 5
  residues processed: 105
  average time/residue: 1.7800
  time to fit residues: 193.3895
Evaluate side-chains
  110 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain D residue  139 SER
Chi-restraints excluded: chain E residue  129 GLU
Chi-restraints excluded: chain E residue  155 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 14 optimal weight:    0.2980
   chunk 16 optimal weight:    0.0000
   chunk 30 optimal weight:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 45 optimal weight:   10.0000
   chunk 56 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.8588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.130168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.113523 restraints weight = 5896.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 1.05
r_work: 0.3087 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 2.38 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5966  Z= 0.103
  Angle     :  0.398   3.582   8037  Z= 0.227
  Chirality :  0.042   0.145    895
  Planarity :  0.002   0.017   1035
  Dihedral  :  4.391  16.333    810
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 14.59 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.30), residues: 765
  helix:  2.78 (0.67), residues: 70
  sheet:  0.52 (0.32), residues: 280
  loop :  0.90 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP E  65 
 HIS   0.002   0.001   HIS F  90 
 PHE   0.010   0.001   PHE C 128 
 TYR   0.004   0.001   TYR F  83 
 ARG   0.001   0.000   ARG E  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01963 (   71)
  hydrogen bonds       : angle       3.91850 (  213)
  SS BOND              : bond        0.00047 (    1)
  SS BOND              : angle       0.15962 (    2)
  covalent geometry    : bond        0.00229 ( 5965)
  covalent geometry    : angle       0.39789 ( 8035)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.784 
Fit side-chains
REVERT: C    5 GLU cc_start: 0.8104 (mp0) cc_final: 0.7553 (mp0)
REVERT: C   17 LYS cc_start: 0.7912 (ttmt) cc_final: 0.6726 (ttpt)
REVERT: C  114 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8682 (mmmt)
REVERT: C  129 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8320 (tp30)
REVERT: E   17 LYS cc_start: 0.7891 (ttmt) cc_final: 0.6833 (ttpt)
REVERT: E  129 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8471 (tp30)
  outliers start: 9
  outliers final: 5
  residues processed: 107
  average time/residue: 1.7101
  time to fit residues: 189.5102
Evaluate side-chains
  104 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain D residue  139 SER
Chi-restraints excluded: chain E residue  129 GLU
Chi-restraints excluded: chain E residue  155 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 42 optimal weight:    0.0870
   chunk 27 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 72 optimal weight:    0.9980
   overall best weight:    1.0162

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.130768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.113891 restraints weight = 5879.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 1.07
r_work: 0.3071 rms_B_bonded: 1.46 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 2.47 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8885
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5966  Z= 0.113
  Angle     :  0.410   3.017   8037  Z= 0.234
  Chirality :  0.043   0.145    895
  Planarity :  0.002   0.017   1035
  Dihedral  :  4.425  16.989    810
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 15.74 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.30), residues: 765
  helix:  2.76 (0.67), residues: 70
  sheet:  0.47 (0.32), residues: 280
  loop :  0.99 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP E  65 
 HIS   0.002   0.001   HIS F  90 
 PHE   0.010   0.001   PHE C 128 
 TYR   0.004   0.001   TYR A  83 
 ARG   0.001   0.000   ARG E  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02092 (   71)
  hydrogen bonds       : angle       3.99718 (  213)
  SS BOND              : bond        0.00024 (    1)
  SS BOND              : angle       0.10876 (    2)
  covalent geometry    : bond        0.00251 ( 5965)
  covalent geometry    : angle       0.41005 ( 8035)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.744 
Fit side-chains
REVERT: C    5 GLU cc_start: 0.8142 (mp0) cc_final: 0.7617 (mp0)
REVERT: C   17 LYS cc_start: 0.7930 (ttmt) cc_final: 0.6743 (ttpt)
REVERT: C  114 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8745 (mmmt)
REVERT: C  129 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8347 (tp30)
REVERT: E   17 LYS cc_start: 0.7893 (ttmt) cc_final: 0.6753 (ttpt)
REVERT: E  129 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8500 (tp30)
REVERT: F  113 LYS cc_start: 0.8565 (mtmm) cc_final: 0.8008 (mptp)
  outliers start: 7
  outliers final: 5
  residues processed: 104
  average time/residue: 1.8228
  time to fit residues: 196.1681
Evaluate side-chains
  110 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain D residue  139 SER
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue  129 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 73 optimal weight:    8.9990
   chunk 36 optimal weight:    0.8980
   chunk 30 optimal weight:   10.0000
   chunk 18 optimal weight:    4.9990
   chunk 23 optimal weight:    0.0470
   chunk 37 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9980
   chunk 69 optimal weight:    0.1980
   chunk 44 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.2280

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.127947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.111169 restraints weight = 5861.642|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 1.04
r_work: 0.3046 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 2.39 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8872
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5966  Z= 0.127
  Angle     :  0.427   3.536   8037  Z= 0.243
  Chirality :  0.043   0.146    895
  Planarity :  0.002   0.018   1035
  Dihedral  :  4.537  17.618    810
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 15.25 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.30), residues: 765
  helix:  2.72 (0.67), residues: 70
  sheet:  0.46 (0.32), residues: 280
  loop :  1.00 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP E  65 
 HIS   0.003   0.001   HIS F  90 
 PHE   0.011   0.001   PHE C 128 
 TYR   0.005   0.001   TYR F  83 
 ARG   0.001   0.000   ARG E  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02275 (   71)
  hydrogen bonds       : angle       4.04655 (  213)
  SS BOND              : bond        0.00016 (    1)
  SS BOND              : angle       0.11790 (    2)
  covalent geometry    : bond        0.00281 ( 5965)
  covalent geometry    : angle       0.42728 ( 8035)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.733 
Fit side-chains
REVERT: C    5 GLU cc_start: 0.8085 (mp0) cc_final: 0.7564 (mp0)
REVERT: C   17 LYS cc_start: 0.7925 (ttmt) cc_final: 0.6711 (ttpt)
REVERT: C  114 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8735 (mmmt)
REVERT: C  129 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8316 (tp30)
REVERT: D  129 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8543 (tm-30)
REVERT: E   17 LYS cc_start: 0.7912 (ttmt) cc_final: 0.6747 (ttpt)
REVERT: E  129 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8464 (tp30)
REVERT: F  113 LYS cc_start: 0.8562 (mtmm) cc_final: 0.7968 (mptp)
  outliers start: 9
  outliers final: 6
  residues processed: 109
  average time/residue: 1.7009
  time to fit residues: 192.0380
Evaluate side-chains
  112 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain D residue  129 GLU
Chi-restraints excluded: chain D residue  139 SER
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue  129 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 46 optimal weight:    8.9990
   chunk 63 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   overall best weight:    2.3788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.125942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.109234 restraints weight = 6043.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 1.04
r_work: 0.3021 rms_B_bonded: 1.40 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 2.37 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8906
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   5966  Z= 0.198
  Angle     :  0.507   3.656   8037  Z= 0.284
  Chirality :  0.045   0.153    895
  Planarity :  0.003   0.017   1035
  Dihedral  :  4.990  19.694    810
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.25 %
    Favored  : 82.95 %
  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:  1.21 (0.30), residues: 765
  helix:  2.39 (0.65), residues: 70
  sheet:  0.45 (0.31), residues: 280
  loop :  0.96 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP E  75 
 HIS   0.004   0.002   HIS A  90 
 PHE   0.015   0.002   PHE C 128 
 TYR   0.008   0.002   TYR F  83 
 ARG   0.002   0.000   ARG A  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03057 (   71)
  hydrogen bonds       : angle       4.18323 (  213)
  SS BOND              : bond        0.00034 (    1)
  SS BOND              : angle       0.09975 (    2)
  covalent geometry    : bond        0.00443 ( 5965)
  covalent geometry    : angle       0.50746 ( 8035)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.740 
Fit side-chains
REVERT: A   62 VAL cc_start: 0.8584 (m) cc_final: 0.8334 (t)
REVERT: C    5 GLU cc_start: 0.8085 (mp0) cc_final: 0.7552 (mp0)
REVERT: C   17 LYS cc_start: 0.7984 (ttmt) cc_final: 0.6709 (ttpt)
REVERT: C  129 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8339 (tp30)
REVERT: E   17 LYS cc_start: 0.7985 (ttmt) cc_final: 0.6866 (ttpt)
REVERT: E  129 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8456 (tp30)
REVERT: F  113 LYS cc_start: 0.8647 (mtmm) cc_final: 0.7990 (mptp)
  outliers start: 11
  outliers final: 5
  residues processed: 111
  average time/residue: 1.6271
  time to fit residues: 187.1891
Evaluate side-chains
  107 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain D residue  139 SER
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue  129 GLU
Chi-restraints excluded: chain E residue  155 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 44 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0060
   chunk 73 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.3802

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.126595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.109586 restraints weight = 5984.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 1.06
r_work: 0.3037 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 2.41 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8879
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5966  Z= 0.136
  Angle     :  0.440   3.287   8037  Z= 0.250
  Chirality :  0.043   0.146    895
  Planarity :  0.002   0.019   1035
  Dihedral  :  4.671  18.042    810
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 15.41 %
    Favored  : 82.95 %
  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:  1.27 (0.30), residues: 765
  helix:  2.62 (0.66), residues: 70
  sheet:  0.47 (0.32), residues: 280
  loop :  0.99 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP E  65 
 HIS   0.003   0.002   HIS F  90 
 PHE   0.012   0.001   PHE C 128 
 TYR   0.005   0.001   TYR A  83 
 ARG   0.001   0.000   ARG F  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02338 (   71)
  hydrogen bonds       : angle       4.11505 (  213)
  SS BOND              : bond        0.00022 (    1)
  SS BOND              : angle       0.10533 (    2)
  covalent geometry    : bond        0.00302 ( 5965)
  covalent geometry    : angle       0.44030 ( 8035)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.681 
Fit side-chains
REVERT: A   62 VAL cc_start: 0.8530 (m) cc_final: 0.8275 (t)
REVERT: C    5 GLU cc_start: 0.8046 (mp0) cc_final: 0.7520 (mp0)
REVERT: C   17 LYS cc_start: 0.7937 (ttmt) cc_final: 0.6693 (ttpt)
REVERT: C  129 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8315 (tp30)
REVERT: D  129 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8563 (tm-30)
REVERT: E   17 LYS cc_start: 0.7909 (ttmt) cc_final: 0.6739 (ttpt)
REVERT: E  129 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8466 (tp30)
REVERT: F  113 LYS cc_start: 0.8561 (mtmm) cc_final: 0.7936 (mptp)
  outliers start: 10
  outliers final: 7
  residues processed: 107
  average time/residue: 1.6642
  time to fit residues: 184.2997
Evaluate side-chains
  108 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 SER
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  129 GLU
Chi-restraints excluded: chain D residue   67 SER
Chi-restraints excluded: chain D residue  139 SER
Chi-restraints excluded: chain E residue   67 SER
Chi-restraints excluded: chain E residue  129 GLU
Chi-restraints excluded: chain E residue  155 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 14 optimal weight:    0.0670
   chunk 6 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   chunk 61 optimal weight:    0.0470
   chunk 5 optimal weight:    0.9990
   chunk 16 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   overall best weight:    1.2222

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.128045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.111142 restraints weight = 6030.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 1.06
r_work: 0.3053 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.2951 rms_B_bonded: 2.41 restraints_weight: 0.2500
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8877
moved from start:          0.1671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5966  Z= 0.128
  Angle     :  0.435   4.442   8037  Z= 0.248
  Chirality :  0.043   0.145    895
  Planarity :  0.002   0.019   1035
  Dihedral  :  4.582  17.712    810
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 15.90 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.30), residues: 765
  helix:  2.70 (0.66), residues: 70
  sheet:  0.46 (0.32), residues: 280
  loop :  1.05 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP E  65 
 HIS   0.003   0.001   HIS F  90 
 PHE   0.011   0.001   PHE C 128 
 TYR   0.005   0.001   TYR F  83 
 ARG   0.001   0.000   ARG E  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02221 (   71)
  hydrogen bonds       : angle       4.05407 (  213)
  SS BOND              : bond        0.00016 (    1)
  SS BOND              : angle       0.11933 (    2)
  covalent geometry    : bond        0.00286 ( 5965)
  covalent geometry    : angle       0.43544 ( 8035)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6519.03 seconds
wall clock time: 112 minutes 58.72 seconds (6778.72 seconds total)