Starting phenix.real_space_refine
on Thu May  1 00:22:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qki_18463/05_2025/8qki_18463_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qki_18463/05_2025/8qki_18463.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.46
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qki_18463/05_2025/8qki_18463.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qki_18463/05_2025/8qki_18463.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qki_18463/05_2025/8qki_18463_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qki_18463/05_2025/8qki_18463_neut.cif"
  }
  resolution = 3.46
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.000
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      90      5.16       5
     C    6780      2.51       5
     N    1680      2.21       5
     O    1638      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 10188
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1670
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1670
          Classifications: {'peptide': 207}
          Link IDs: {'PTRANS': 7, 'TRANS': 199}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 4.96, per 1000 atoms: 0.49
  Number of scatterers: 10188
  At special positions: 0
  Unit cell: (98.15, 101.4, 91.65, 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      90     16.00
     O    1638      8.00
     N    1680      7.00
     C    6780      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS A 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  53 " - pdb=" SG  CYS C 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  53 " - pdb=" SG  CYS B 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  53 " - pdb=" SG  CYS E 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  53 " - pdb=" SG  CYS D 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  53 " - pdb=" SG  CYS F 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  60 " - pdb=" SG  CYS C 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  60 " - pdb=" SG  CYS B 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  60 " - pdb=" SG  CYS E 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  60 " - pdb=" SG  CYS D 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  60 " - pdb=" SG  CYS F 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  64 " - pdb=" SG  CYS C 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  64 " - pdb=" SG  CYS B 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  64 " - pdb=" SG  CYS E 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  64 " - pdb=" SG  CYS D 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  64 " - pdb=" SG  CYS F 168 " distance=2.03

  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: 2.76
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2388

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 6 sheets defined
      75.8% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
    Processing helix  chain 'A' and resid 18 through 23
    Processing helix  chain 'A' and resid 23 through 42
    Processing helix  chain 'A' and resid 59 through 69
    Processing helix  chain 'A' and resid 72 through 108
      Proline residue:  A  87  - end of helix
      removed outlier: 3.760A  pdb=" N   ARG A 107 " --> pdb=" O   LYS A 103 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU A 108 " --> pdb=" O   LYS A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 157
    Processing helix  chain 'A' and resid 183 through 220
    Processing helix  chain 'B' and resid 2 through 11
    Processing helix  chain 'B' and resid 18 through 23
    Processing helix  chain 'B' and resid 23 through 42
    Processing helix  chain 'B' and resid 59 through 69
    Processing helix  chain 'B' and resid 72 through 108
      Proline residue:  B  87  - end of helix
      removed outlier: 3.760A  pdb=" N   ARG B 107 " --> pdb=" O   LYS B 103 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU B 108 " --> pdb=" O   LYS B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 157
    Processing helix  chain 'B' and resid 183 through 220
    Processing helix  chain 'C' and resid 2 through 11
    Processing helix  chain 'C' and resid 18 through 23
    Processing helix  chain 'C' and resid 23 through 42
    Processing helix  chain 'C' and resid 59 through 69
    Processing helix  chain 'C' and resid 72 through 108
      Proline residue:  C  87  - end of helix
      removed outlier: 3.760A  pdb=" N   ARG C 107 " --> pdb=" O   LYS C 103 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU C 108 " --> pdb=" O   LYS C 104 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 157
    Processing helix  chain 'C' and resid 183 through 220
    Processing helix  chain 'D' and resid 2 through 11
    Processing helix  chain 'D' and resid 18 through 23
    Processing helix  chain 'D' and resid 23 through 42
    Processing helix  chain 'D' and resid 59 through 69
    Processing helix  chain 'D' and resid 72 through 108
      Proline residue:  D  87  - end of helix
      removed outlier: 3.761A  pdb=" N   ARG D 107 " --> pdb=" O   LYS D 103 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU D 108 " --> pdb=" O   LYS D 104 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 157
    Processing helix  chain 'D' and resid 183 through 220
    Processing helix  chain 'E' and resid 2 through 11
    Processing helix  chain 'E' and resid 18 through 23
    Processing helix  chain 'E' and resid 23 through 42
    Processing helix  chain 'E' and resid 59 through 69
    Processing helix  chain 'E' and resid 72 through 108
      Proline residue:  E  87  - end of helix
      removed outlier: 3.760A  pdb=" N   ARG E 107 " --> pdb=" O   LYS E 103 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU E 108 " --> pdb=" O   LYS E 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 123 through 157
    Processing helix  chain 'E' and resid 183 through 220
    Processing helix  chain 'F' and resid 2 through 11
    Processing helix  chain 'F' and resid 18 through 23
    Processing helix  chain 'F' and resid 23 through 42
    Processing helix  chain 'F' and resid 59 through 69
    Processing helix  chain 'F' and resid 72 through 108
      Proline residue:  F  87  - end of helix
      removed outlier: 3.760A  pdb=" N   ARG F 107 " --> pdb=" O   LYS F 103 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU F 108 " --> pdb=" O   LYS F 104 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 123 through 157
    Processing helix  chain 'F' and resid 183 through 220
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53
    Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53
    Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53
    Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53
    Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53
    Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53

    780 hydrogen bonds defined for protein.
    2304 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: 2.68

  Time building geometry restraints manager: 3.22 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3030
        1.35 -     1.46: 2697
        1.46 -     1.58: 4615
        1.58 -     1.70: 2
        1.70 -     1.82: 132
  Bond restraints: 10476
  Sorted by residual:
  bond pdb=" C6  CLR E 501 "
       pdb=" C7  CLR E 501 "
    ideal  model  delta    sigma   weight residual
    1.492  1.542 -0.050 2.00e-02 2.50e+03 6.29e+00
  bond pdb=" C6  CLR D 501 "
       pdb=" C7  CLR D 501 "
    ideal  model  delta    sigma   weight residual
    1.492  1.542 -0.050 2.00e-02 2.50e+03 6.28e+00
  bond pdb=" C6  CLR F 501 "
       pdb=" C7  CLR F 501 "
    ideal  model  delta    sigma   weight residual
    1.492  1.542 -0.050 2.00e-02 2.50e+03 6.25e+00
  bond pdb=" C6  CLR A 501 "
       pdb=" C7  CLR A 501 "
    ideal  model  delta    sigma   weight residual
    1.492  1.542 -0.050 2.00e-02 2.50e+03 6.14e+00
  bond pdb=" C6  CLR B 501 "
       pdb=" C7  CLR B 501 "
    ideal  model  delta    sigma   weight residual
    1.492  1.541 -0.049 2.00e-02 2.50e+03 6.12e+00
  ... (remaining 10471 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 13804
        1.66 -     3.31: 332
        3.31 -     4.97: 106
        4.97 -     6.63: 44
        6.63 -     8.28: 18
  Bond angle restraints: 14304
  Sorted by residual:
  angle pdb=" CB  GLN A  98 "
        pdb=" CG  GLN A  98 "
        pdb=" CD  GLN A  98 "
      ideal   model   delta    sigma   weight residual
     112.60  117.32   -4.72 1.70e+00 3.46e-01 7.72e+00
  angle pdb=" CB  GLN D  98 "
        pdb=" CG  GLN D  98 "
        pdb=" CD  GLN D  98 "
      ideal   model   delta    sigma   weight residual
     112.60  117.31   -4.71 1.70e+00 3.46e-01 7.67e+00
  angle pdb=" CB  GLN C  98 "
        pdb=" CG  GLN C  98 "
        pdb=" CD  GLN C  98 "
      ideal   model   delta    sigma   weight residual
     112.60  117.30   -4.70 1.70e+00 3.46e-01 7.64e+00
  angle pdb=" C22 CLR C 501 "
        pdb=" C23 CLR C 501 "
        pdb=" C24 CLR C 501 "
      ideal   model   delta    sigma   weight residual
     111.95  103.67    8.28 3.00e+00 1.11e-01 7.63e+00
  angle pdb=" CB  GLN E  98 "
        pdb=" CG  GLN E  98 "
        pdb=" CD  GLN E  98 "
      ideal   model   delta    sigma   weight residual
     112.60  117.28   -4.68 1.70e+00 3.46e-01 7.57e+00
  ... (remaining 14299 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.70: 5503
       11.70 -    23.40: 545
       23.40 -    35.11: 240
       35.11 -    46.81: 96
       46.81 -    58.51: 36
  Dihedral angle restraints: 6420
    sinusoidal: 2748
      harmonic: 3672
  Sorted by residual:
  dihedral pdb=" CA  ASP B  46 "
           pdb=" C   ASP B  46 "
           pdb=" N   GLU B  47 "
           pdb=" CA  GLU B  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.87   16.13     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CA  ASP F  46 "
           pdb=" C   ASP F  46 "
           pdb=" N   GLU F  47 "
           pdb=" CA  GLU F  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.89   16.11     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CA  ASP A  46 "
           pdb=" C   ASP A  46 "
           pdb=" N   GLU A  47 "
           pdb=" CA  GLU A  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.89   16.11     0      5.00e+00 4.00e-02 1.04e+01
  ... (remaining 6417 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1583
       0.073 -    0.147: 97
       0.147 -    0.220: 0
       0.220 -    0.293: 7
       0.293 -    0.367: 17
  Chirality restraints: 1704
  Sorted by residual:
  chirality pdb=" C17 CLR B 501 "
            pdb=" C13 CLR B 501 "
            pdb=" C16 CLR B 501 "
            pdb=" C20 CLR B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.92   -0.37 2.00e-01 2.50e+01 3.36e+00
  chirality pdb=" C17 CLR D 501 "
            pdb=" C13 CLR D 501 "
            pdb=" C16 CLR D 501 "
            pdb=" C20 CLR D 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.92   -0.37 2.00e-01 2.50e+01 3.34e+00
  chirality pdb=" C17 CLR E 501 "
            pdb=" C13 CLR E 501 "
            pdb=" C16 CLR E 501 "
            pdb=" C20 CLR E 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.92   -0.36 2.00e-01 2.50e+01 3.31e+00
  ... (remaining 1701 not shown)

  Planarity restraints: 1674
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 211 "   -0.005 2.00e-02 2.50e+03   7.56e-03 1.14e+00
        pdb=" CG  TYR B 211 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 211 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 211 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 211 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 211 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 211 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 211 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 211 "   -0.004 2.00e-02 2.50e+03   7.51e-03 1.13e+00
        pdb=" CG  TYR A 211 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 211 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 211 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 211 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 211 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 211 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A 211 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR E 211 "    0.004 2.00e-02 2.50e+03   7.51e-03 1.13e+00
        pdb=" CG  TYR E 211 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR E 211 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR E 211 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR E 211 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR E 211 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR E 211 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR E 211 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1671 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 45
        2.64 -     3.20: 9475
        3.20 -     3.77: 16878
        3.77 -     4.33: 20935
        4.33 -     4.90: 35726
  Nonbonded interactions: 83059
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 182 "
            pdb=" NZ  LYS F  48 "
     model   vdw
     2.071 3.120
  nonbonded pdb=" O   ILE C  71 "
            pdb=" OH  TYR C 157 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" O   ILE F  71 "
            pdb=" OH  TYR F 157 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" O   ILE A  71 "
            pdb=" OH  TYR A 157 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" O   ILE E  71 "
            pdb=" OH  TYR E 157 "
     model   vdw
     2.199 3.040
  ... (remaining 83054 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  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:             4.100
  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:          0.490
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     23.950
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
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      :  0.004   0.050  10494  Z= 0.185
  Angle     :  0.751   8.284  14340  Z= 0.354
  Chirality :  0.052   0.367   1704
  Planarity :  0.002   0.014   1674
  Dihedral  : 12.595  58.509   3978
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  3.76 %
    Favored  : 95.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.24), residues: 1218
  helix:  2.50 (0.16), residues: 882
  sheet: -0.88 (0.47), residues: 102
  loop : -1.88 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E 132 
 HIS   0.005   0.001   HIS F  94 
 PHE   0.006   0.001   PHE B 149 
 TYR   0.018   0.002   TYR B 211 
 ARG   0.003   0.000   ARG B 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09225 (  780)
  hydrogen bonds       : angle       4.40385 ( 2304)
  SS BOND              : bond        0.00136 (   18)
  SS BOND              : angle       0.20668 (   36)
  covalent geometry    : bond        0.00377 (10476)
  covalent geometry    : angle       0.75204 (14304)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 314
  time to evaluate  : 1.124 
Fit side-chains
REVERT: A   13 VAL cc_start: 0.9149 (m) cc_final: 0.8898 (p)
REVERT: A   34 MET cc_start: 0.7579 (mmm) cc_final: 0.7370 (mmt)
REVERT: B   66 ASP cc_start: 0.7978 (t0) cc_final: 0.7717 (t0)
REVERT: B  150 MET cc_start: 0.7869 (mmp) cc_final: 0.6999 (tmm)
REVERT: C   34 MET cc_start: 0.7996 (mmm) cc_final: 0.7641 (mmt)
REVERT: C   54 ASN cc_start: 0.8937 (t0) cc_final: 0.8634 (t0)
REVERT: C   66 ASP cc_start: 0.7819 (t0) cc_final: 0.7543 (t0)
REVERT: C  150 MET cc_start: 0.7649 (mmp) cc_final: 0.6819 (tmm)
REVERT: D   54 ASN cc_start: 0.8893 (t0) cc_final: 0.8609 (t0)
REVERT: D   66 ASP cc_start: 0.7719 (t0) cc_final: 0.7501 (t0)
REVERT: D  150 MET cc_start: 0.7655 (mmp) cc_final: 0.6816 (tmm)
REVERT: E   54 ASN cc_start: 0.8943 (t0) cc_final: 0.8601 (t0)
REVERT: E   66 ASP cc_start: 0.7866 (t0) cc_final: 0.7598 (t0)
REVERT: E  150 MET cc_start: 0.7793 (mmp) cc_final: 0.6954 (tmm)
REVERT: F   34 MET cc_start: 0.8005 (mmm) cc_final: 0.7698 (mmt)
REVERT: F   54 ASN cc_start: 0.8975 (t0) cc_final: 0.8654 (t0)
REVERT: F   66 ASP cc_start: 0.7668 (t0) cc_final: 0.7443 (t0)
REVERT: F  150 MET cc_start: 0.7706 (mmp) cc_final: 0.6814 (tmm)
  outliers start: 6
  outliers final: 0
  residues processed: 315
  average time/residue: 0.2113
  time to fit residues: 93.7899
Evaluate side-chains
  259 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 1.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.7980
   chunk 90 optimal weight:    0.0980
   chunk 50 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 61 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   chunk 36 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 108 optimal weight:    2.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
C  16 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.076867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.067526 restraints weight = 30058.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 3.03
r_work: 0.3094 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10494  Z= 0.112
  Angle     :  0.551   5.997  14340  Z= 0.275
  Chirality :  0.037   0.125   1704
  Planarity :  0.003   0.018   1674
  Dihedral  :  4.983  54.452   1746
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 11.83 %
    Favored  : 86.38 %
  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:  3.22 (0.24), residues: 1218
  helix:  3.29 (0.16), residues: 894
  sheet: -0.62 (0.48), residues: 102
  loop : -1.70 (0.42), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D  24 
 HIS   0.004   0.001   HIS D 123 
 PHE   0.007   0.001   PHE F  31 
 TYR   0.013   0.001   TYR A 157 
 ARG   0.002   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02881 (  780)
  hydrogen bonds       : angle       3.03719 ( 2304)
  SS BOND              : bond        0.00096 (   18)
  SS BOND              : angle       0.26145 (   36)
  covalent geometry    : bond        0.00249 (10476)
  covalent geometry    : angle       0.55177 (14304)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 243
  time to evaluate  : 1.333 
Fit side-chains
REVERT: B   54 ASN cc_start: 0.9414 (t0) cc_final: 0.9161 (t0)
REVERT: B   98 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8210 (mm-40)
REVERT: B  150 MET cc_start: 0.9209 (mmp) cc_final: 0.7454 (tmm)
REVERT: B  178 ASP cc_start: 0.8916 (p0) cc_final: 0.8690 (p0)
REVERT: C   14 ASN cc_start: 0.8196 (t0) cc_final: 0.7995 (t0)
REVERT: C   54 ASN cc_start: 0.9278 (t0) cc_final: 0.9032 (t0)
REVERT: C   66 ASP cc_start: 0.8784 (t0) cc_final: 0.8583 (t0)
REVERT: C   94 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.7887 (t-90)
REVERT: C  144 LEU cc_start: 0.8804 (mm) cc_final: 0.8460 (mm)
REVERT: C  150 MET cc_start: 0.9204 (mmp) cc_final: 0.7454 (tmm)
REVERT: D   54 ASN cc_start: 0.9296 (t0) cc_final: 0.9089 (t0)
REVERT: D   98 GLN cc_start: 0.8456 (mm-40) cc_final: 0.8125 (mm-40)
REVERT: D  144 LEU cc_start: 0.8801 (mm) cc_final: 0.8469 (mm)
REVERT: D  150 MET cc_start: 0.9109 (mmp) cc_final: 0.7354 (tmm)
REVERT: E   14 ASN cc_start: 0.8213 (t0) cc_final: 0.8010 (t0)
REVERT: E  150 MET cc_start: 0.9219 (mmp) cc_final: 0.7455 (tmm)
REVERT: F   14 ASN cc_start: 0.8165 (t0) cc_final: 0.7955 (t0)
REVERT: F   48 LYS cc_start: 0.8501 (tmmt) cc_final: 0.8251 (mptt)
REVERT: F   54 ASN cc_start: 0.9335 (t0) cc_final: 0.9126 (t0)
REVERT: F  144 LEU cc_start: 0.8760 (mm) cc_final: 0.8418 (mm)
REVERT: F  150 MET cc_start: 0.9189 (mmp) cc_final: 0.7419 (tmm)
  outliers start: 20
  outliers final: 14
  residues processed: 252
  average time/residue: 0.2600
  time to fit residues: 90.6932
Evaluate side-chains
  233 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 218
  time to evaluate  : 1.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ASP
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain B residue   46 ASP
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  126 HIS
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain C residue   46 ASP
Chi-restraints excluded: chain C residue   94 HIS
Chi-restraints excluded: chain D residue   46 ASP
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue   83 LEU
Chi-restraints excluded: chain E residue  126 HIS
Chi-restraints excluded: chain E residue  144 LEU
Chi-restraints excluded: chain F residue   46 ASP
Chi-restraints excluded: chain F residue  178 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0870
   chunk 93 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 68 optimal weight:    5.9990
   chunk 85 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 105 optimal weight:   10.0000
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.9760

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.071801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.062327 restraints weight = 30961.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 2.98
r_work: 0.2983 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.3360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10494  Z= 0.110
  Angle     :  0.528   9.204  14340  Z= 0.261
  Chirality :  0.038   0.152   1704
  Planarity :  0.002   0.023   1674
  Dihedral  :  5.009  57.677   1746
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.16 %
    Favored  : 83.42 %
  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:  3.52 (0.24), residues: 1218
  helix:  3.46 (0.16), residues: 894
  sheet: -0.26 (0.52), residues: 102
  loop : -1.53 (0.42), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  44 
 HIS   0.002   0.001   HIS F  94 
 PHE   0.009   0.001   PHE D  68 
 TYR   0.006   0.001   TYR A 211 
 ARG   0.002   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02790 (  780)
  hydrogen bonds       : angle       2.97211 ( 2304)
  SS BOND              : bond        0.00138 (   18)
  SS BOND              : angle       0.26401 (   36)
  covalent geometry    : bond        0.00243 (10476)
  covalent geometry    : angle       0.52898 (14304)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 219
  time to evaluate  : 1.548 
Fit side-chains
REVERT: A   41 GLU cc_start: 0.6924 (tt0) cc_final: 0.6535 (tt0)
REVERT: A   48 LYS cc_start: 0.9211 (tppp) cc_final: 0.8942 (mmtp)
REVERT: A  105 MET cc_start: 0.8498 (mtt) cc_final: 0.8133 (mtm)
REVERT: B   48 LYS cc_start: 0.8990 (tppp) cc_final: 0.8684 (mmmm)
REVERT: B   98 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8204 (mp10)
REVERT: B  102 GLU cc_start: 0.8937 (tp30) cc_final: 0.8658 (tp30)
REVERT: B  144 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8777 (mm)
REVERT: C   48 LYS cc_start: 0.8918 (tppp) cc_final: 0.8592 (mmmm)
REVERT: C   94 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.8391 (t-90)
REVERT: C  102 GLU cc_start: 0.8914 (tp30) cc_final: 0.8495 (mm-30)
REVERT: C  144 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8758 (mm)
REVERT: D   48 LYS cc_start: 0.8828 (tppp) cc_final: 0.8491 (mmmm)
REVERT: D   54 ASN cc_start: 0.9343 (t0) cc_final: 0.9054 (t0)
REVERT: D  102 GLU cc_start: 0.8928 (tp30) cc_final: 0.8504 (mm-30)
REVERT: E   14 ASN cc_start: 0.8521 (t0) cc_final: 0.8307 (t0)
REVERT: E   48 LYS cc_start: 0.8963 (tppp) cc_final: 0.8607 (mmmm)
REVERT: E   98 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8394 (mm-40)
REVERT: E  102 GLU cc_start: 0.8918 (tp30) cc_final: 0.8647 (tp30)
REVERT: E  144 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8795 (mm)
REVERT: F   14 ASN cc_start: 0.8526 (t0) cc_final: 0.8316 (t0)
REVERT: F   54 ASN cc_start: 0.9352 (t0) cc_final: 0.9144 (t0)
REVERT: F   94 HIS cc_start: 0.8674 (OUTLIER) cc_final: 0.8416 (t-90)
REVERT: F   98 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8506 (mp10)
REVERT: F  102 GLU cc_start: 0.8908 (tp30) cc_final: 0.8499 (mm-30)
REVERT: F  144 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8736 (mm)
  outliers start: 27
  outliers final: 15
  residues processed: 233
  average time/residue: 0.3276
  time to fit residues: 107.2258
Evaluate side-chains
  217 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 196
  time to evaluate  : 1.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ASP
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain B residue   46 ASP
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  126 HIS
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain C residue   46 ASP
Chi-restraints excluded: chain C residue   94 HIS
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain D residue   46 ASP
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue   83 LEU
Chi-restraints excluded: chain E residue  126 HIS
Chi-restraints excluded: chain E residue  144 LEU
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain F residue   46 ASP
Chi-restraints excluded: chain F residue   94 HIS
Chi-restraints excluded: chain F residue  144 LEU
Chi-restraints excluded: chain F residue  178 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 95 optimal weight:    0.2980
   chunk 33 optimal weight:    5.9990
   chunk 47 optimal weight:    0.4980
   chunk 1 optimal weight:    0.9980
   chunk 113 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 54 optimal weight:    0.1980
   chunk 10 optimal weight:    9.9990
   chunk 82 optimal weight:    1.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  94 HIS
A  98 GLN
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 ASN
B  67 GLN
C  54 ASN
** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  67 GLN
F  67 GLN
** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.071114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.061620 restraints weight = 30556.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 2.94
r_work: 0.2957 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.3808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  10494  Z= 0.102
  Angle     :  0.522   7.603  14340  Z= 0.257
  Chirality :  0.037   0.152   1704
  Planarity :  0.002   0.022   1674
  Dihedral  :  4.994  57.855   1746
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 13.80 %
    Favored  : 83.15 %
  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:  3.63 (0.24), residues: 1218
  helix:  3.51 (0.16), residues: 894
  sheet: -0.17 (0.53), residues: 102
  loop : -1.38 (0.42), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  44 
 HIS   0.003   0.001   HIS C 123 
 PHE   0.007   0.001   PHE E  68 
 TYR   0.010   0.001   TYR F 151 
 ARG   0.003   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02635 (  780)
  hydrogen bonds       : angle       2.92806 ( 2304)
  SS BOND              : bond        0.00115 (   18)
  SS BOND              : angle       0.15080 (   36)
  covalent geometry    : bond        0.00225 (10476)
  covalent geometry    : angle       0.52289 (14304)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 209
  time to evaluate  : 1.121 
Fit side-chains
REVERT: A   41 GLU cc_start: 0.7106 (tt0) cc_final: 0.6707 (tt0)
REVERT: A   94 HIS cc_start: 0.8926 (t70) cc_final: 0.8648 (t-90)
REVERT: A  105 MET cc_start: 0.8510 (mtt) cc_final: 0.8164 (mtm)
REVERT: A  123 HIS cc_start: 0.8224 (t70) cc_final: 0.7853 (t70)
REVERT: B   48 LYS cc_start: 0.9024 (tppp) cc_final: 0.8750 (mmmm)
REVERT: B   66 ASP cc_start: 0.8939 (t0) cc_final: 0.8691 (t0)
REVERT: B   98 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8488 (mp10)
REVERT: B  102 GLU cc_start: 0.8977 (tp30) cc_final: 0.8729 (tp30)
REVERT: B  144 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8853 (mm)
REVERT: C   48 LYS cc_start: 0.8995 (tppp) cc_final: 0.8712 (mmmm)
REVERT: C  102 GLU cc_start: 0.8960 (tp30) cc_final: 0.8560 (mm-30)
REVERT: C  144 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8794 (mm)
REVERT: D   48 LYS cc_start: 0.8869 (tppp) cc_final: 0.8632 (mmmm)
REVERT: D   66 ASP cc_start: 0.8851 (t0) cc_final: 0.8567 (t0)
REVERT: D  102 GLU cc_start: 0.8966 (tp30) cc_final: 0.8556 (mm-30)
REVERT: E   14 ASN cc_start: 0.8566 (t0) cc_final: 0.8324 (t0)
REVERT: E   48 LYS cc_start: 0.9025 (tppp) cc_final: 0.8754 (mmmm)
REVERT: E   66 ASP cc_start: 0.8960 (t0) cc_final: 0.8699 (t0)
REVERT: E   98 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8445 (mp10)
REVERT: E  102 GLU cc_start: 0.8965 (tp30) cc_final: 0.8691 (tp30)
REVERT: E  144 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8863 (mm)
REVERT: F   14 ASN cc_start: 0.8561 (t0) cc_final: 0.8323 (t0)
REVERT: F   94 HIS cc_start: 0.8761 (t-90) cc_final: 0.8482 (t-90)
REVERT: F  102 GLU cc_start: 0.8957 (tp30) cc_final: 0.8559 (mm-30)
REVERT: F  144 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8762 (mm)
  outliers start: 34
  outliers final: 17
  residues processed: 238
  average time/residue: 0.2331
  time to fit residues: 77.2110
Evaluate side-chains
  223 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 202
  time to evaluate  : 1.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   46 ASP
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain B residue   46 ASP
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  126 HIS
Chi-restraints excluded: chain B residue  143 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain C residue  143 LEU
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue  126 HIS
Chi-restraints excluded: chain E residue  143 LEU
Chi-restraints excluded: chain E residue  144 LEU
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain F residue  143 LEU
Chi-restraints excluded: chain F residue  144 LEU
Chi-restraints excluded: chain F residue  178 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 70 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 109 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 30 optimal weight:    0.3980
   chunk 33 optimal weight:    5.9990
   chunk 101 optimal weight:    5.9990
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A  94 HIS
A  98 GLN
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  67 GLN
C 205 ASN
** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  67 GLN
F  67 GLN
** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.065253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.056120 restraints weight = 31058.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 2.80
r_work: 0.2848 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8811
moved from start:          0.4791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10494  Z= 0.155
  Angle     :  0.581   7.518  14340  Z= 0.292
  Chirality :  0.040   0.154   1704
  Planarity :  0.003   0.025   1674
  Dihedral  :  5.478  57.815   1746
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 13.26 %
    Favored  : 83.33 %
  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:  3.50 (0.24), residues: 1218
  helix:  3.42 (0.16), residues: 888
  sheet: -0.27 (0.52), residues: 102
  loop : -1.24 (0.43), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  44 
 HIS   0.003   0.001   HIS E  16 
 PHE   0.009   0.001   PHE C  68 
 TYR   0.008   0.001   TYR F   7 
 ARG   0.002   0.000   ARG E 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02873 (  780)
  hydrogen bonds       : angle       3.06801 ( 2304)
  SS BOND              : bond        0.00217 (   18)
  SS BOND              : angle       0.29283 (   36)
  covalent geometry    : bond        0.00347 (10476)
  covalent geometry    : angle       0.58121 (14304)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 215
  time to evaluate  : 1.081 
Fit side-chains
REVERT: A   57 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8428 (tm-30)
REVERT: A  123 HIS cc_start: 0.8239 (t70) cc_final: 0.7915 (t70)
REVERT: B  144 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9023 (mm)
REVERT: C   48 LYS cc_start: 0.9190 (tppp) cc_final: 0.8962 (mmmm)
REVERT: C   94 HIS cc_start: 0.8909 (t-90) cc_final: 0.8450 (t-90)
REVERT: C  102 GLU cc_start: 0.9007 (tp30) cc_final: 0.8618 (mm-30)
REVERT: C  144 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.8990 (mm)
REVERT: D   66 ASP cc_start: 0.8879 (t0) cc_final: 0.8657 (t0)
REVERT: D  102 GLU cc_start: 0.9010 (tp30) cc_final: 0.8518 (mm-30)
REVERT: D  144 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.8998 (mm)
REVERT: D  151 TYR cc_start: 0.8544 (t80) cc_final: 0.8332 (t80)
REVERT: E   14 ASN cc_start: 0.8737 (t0) cc_final: 0.8525 (t0)
REVERT: E   98 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8471 (mp10)
REVERT: E  102 GLU cc_start: 0.9027 (tp30) cc_final: 0.8814 (tp30)
REVERT: E  144 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9032 (mm)
REVERT: E  167 LYS cc_start: 0.9353 (mmtp) cc_final: 0.9132 (mmtm)
REVERT: F   14 ASN cc_start: 0.8725 (t0) cc_final: 0.8479 (t0)
REVERT: F  102 GLU cc_start: 0.8996 (tp30) cc_final: 0.8586 (mm-30)
REVERT: F  144 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8935 (mm)
  outliers start: 38
  outliers final: 23
  residues processed: 237
  average time/residue: 0.2280
  time to fit residues: 74.6407
Evaluate side-chains
  225 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 197
  time to evaluate  : 1.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ASP
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain B residue   46 ASP
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain C residue   46 ASP
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain D residue   46 ASP
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue  144 LEU
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain F residue   56 LEU
Chi-restraints excluded: chain F residue  144 LEU
Chi-restraints excluded: chain F residue  178 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 13 optimal weight:    7.9990
   chunk 101 optimal weight:    0.0570
   chunk 39 optimal weight:    0.8980
   chunk 76 optimal weight:    4.9990
   chunk 28 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 71 optimal weight:    7.9990
   chunk 75 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.7900

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  94 HIS
B  98 GLN
B 123 HIS
** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  94 HIS
** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.066934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.057819 restraints weight = 30902.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 2.84
r_work: 0.2868 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8757
moved from start:          0.4952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10494  Z= 0.111
  Angle     :  0.560   6.811  14340  Z= 0.282
  Chirality :  0.038   0.158   1704
  Planarity :  0.003   0.028   1674
  Dihedral  :  5.241  59.652   1746
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 14.52 %
    Favored  : 83.33 %
  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:  3.60 (0.24), residues: 1218
  helix:  3.48 (0.16), residues: 888
  sheet: -0.39 (0.52), residues: 102
  loop : -1.11 (0.44), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP F  44 
 HIS   0.003   0.001   HIS C 123 
 PHE   0.007   0.001   PHE A 149 
 TYR   0.007   0.001   TYR C 171 
 ARG   0.003   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02608 (  780)
  hydrogen bonds       : angle       2.98417 ( 2304)
  SS BOND              : bond        0.00081 (   18)
  SS BOND              : angle       0.17573 (   36)
  covalent geometry    : bond        0.00237 (10476)
  covalent geometry    : angle       0.56105 (14304)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 216
  time to evaluate  : 1.212 
Fit side-chains
REVERT: A  105 MET cc_start: 0.8507 (mtt) cc_final: 0.8178 (mtm)
REVERT: B    7 TYR cc_start: 0.8849 (t80) cc_final: 0.8392 (t80)
REVERT: B  102 GLU cc_start: 0.9020 (tp30) cc_final: 0.8806 (mm-30)
REVERT: B  144 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9027 (mm)
REVERT: C   41 GLU cc_start: 0.7407 (tt0) cc_final: 0.7157 (tt0)
REVERT: C   48 LYS cc_start: 0.9224 (tppp) cc_final: 0.8917 (mmmm)
REVERT: C   57 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8376 (tm-30)
REVERT: C   94 HIS cc_start: 0.8880 (t-90) cc_final: 0.8413 (t-90)
REVERT: C  102 GLU cc_start: 0.9040 (tp30) cc_final: 0.8677 (mm-30)
REVERT: C  144 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.8956 (mm)
REVERT: D   66 ASP cc_start: 0.8870 (t70) cc_final: 0.8587 (t0)
REVERT: D  102 GLU cc_start: 0.8990 (tp30) cc_final: 0.8596 (mm-30)
REVERT: D  144 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.8993 (mm)
REVERT: D  151 TYR cc_start: 0.8410 (t80) cc_final: 0.8208 (t80)
REVERT: D  208 GLU cc_start: 0.8571 (tp30) cc_final: 0.8345 (tp30)
REVERT: E   14 ASN cc_start: 0.8686 (t0) cc_final: 0.8479 (t0)
REVERT: E   47 GLU cc_start: 0.8036 (tp30) cc_final: 0.7767 (tp30)
REVERT: E   57 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8371 (tm-30)
REVERT: E   98 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8240 (mp10)
REVERT: E  144 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9003 (mm)
REVERT: E  167 LYS cc_start: 0.9338 (mmtp) cc_final: 0.9135 (mmtm)
REVERT: F   14 ASN cc_start: 0.8697 (t0) cc_final: 0.8488 (t0)
REVERT: F   47 GLU cc_start: 0.8190 (tp30) cc_final: 0.7702 (tp30)
REVERT: F   57 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8280 (tm-30)
REVERT: F   94 HIS cc_start: 0.8850 (t70) cc_final: 0.8609 (t-90)
REVERT: F  102 GLU cc_start: 0.9024 (tp30) cc_final: 0.8640 (mm-30)
REVERT: F  144 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8916 (mm)
  outliers start: 24
  outliers final: 8
  residues processed: 238
  average time/residue: 0.2314
  time to fit residues: 76.3957
Evaluate side-chains
  215 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 202
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ASP
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain B residue   46 ASP
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue   91 VAL
Chi-restraints excluded: chain E residue  144 LEU
Chi-restraints excluded: chain F residue  144 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 116 optimal weight:    7.9990
   chunk 90 optimal weight:    6.9990
   chunk 60 optimal weight:    9.9990
   chunk 75 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9980
   chunk 104 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 73 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  94 HIS
A  98 GLN
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  94 HIS
** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 123 HIS
** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.062321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.053098 restraints weight = 31801.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 2.71
r_work: 0.2748 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8901
moved from start:          0.5639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040  10494  Z= 0.253
  Angle     :  0.645   8.800  14340  Z= 0.330
  Chirality :  0.041   0.187   1704
  Planarity :  0.003   0.025   1674
  Dihedral  :  6.148  58.802   1746
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.95 %
    Favored  : 81.81 %
  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:  3.36 (0.24), residues: 1218
  helix:  3.28 (0.16), residues: 888
  sheet: -0.64 (0.50), residues: 102
  loop : -0.97 (0.46), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  44 
 HIS   0.004   0.001   HIS C  16 
 PHE   0.011   0.002   PHE A 149 
 TYR   0.013   0.002   TYR F 151 
 ARG   0.005   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03112 (  780)
  hydrogen bonds       : angle       3.24360 ( 2304)
  SS BOND              : bond        0.00303 (   18)
  SS BOND              : angle       0.37138 (   36)
  covalent geometry    : bond        0.00561 (10476)
  covalent geometry    : angle       0.64556 (14304)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 208
  time to evaluate  : 1.127 
Fit side-chains
REVERT: A   47 GLU cc_start: 0.8034 (tp30) cc_final: 0.7812 (tp30)
REVERT: A   57 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8414 (tm-30)
REVERT: A   94 HIS cc_start: 0.9039 (t70) cc_final: 0.8612 (t-90)
REVERT: A  123 HIS cc_start: 0.8277 (t70) cc_final: 0.7879 (t70)
REVERT: B   47 GLU cc_start: 0.8225 (tp30) cc_final: 0.7850 (tp30)
REVERT: B  102 GLU cc_start: 0.9036 (tp30) cc_final: 0.8817 (mm-30)
REVERT: B  144 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9183 (mm)
REVERT: C   57 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8426 (tm-30)
REVERT: C   94 HIS cc_start: 0.8958 (t-90) cc_final: 0.8286 (t-90)
REVERT: C  102 GLU cc_start: 0.9094 (tp30) cc_final: 0.8722 (mm-30)
REVERT: D   47 GLU cc_start: 0.8216 (tp30) cc_final: 0.7872 (tp30)
REVERT: D  102 GLU cc_start: 0.9014 (tp30) cc_final: 0.8618 (mm-30)
REVERT: E  144 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9186 (mm)
REVERT: F   47 GLU cc_start: 0.8326 (tp30) cc_final: 0.7765 (tp30)
REVERT: F   57 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8402 (tm-30)
REVERT: F   94 HIS cc_start: 0.8951 (t70) cc_final: 0.8394 (t-90)
REVERT: F  102 GLU cc_start: 0.9077 (tp30) cc_final: 0.8685 (mm-30)
  outliers start: 25
  outliers final: 20
  residues processed: 224
  average time/residue: 0.2242
  time to fit residues: 69.9438
Evaluate side-chains
  222 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 200
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 VAL
Chi-restraints excluded: chain A residue   46 ASP
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain B residue   46 ASP
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue   90 LEU
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue  144 LEU
Chi-restraints excluded: chain F residue   56 LEU
Chi-restraints excluded: chain F residue  144 LEU
Chi-restraints excluded: chain F residue  178 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   chunk 98 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 27 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 112 optimal weight:    0.8980
   chunk 13 optimal weight:    6.9990
   chunk 101 optimal weight:    2.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  94 HIS
B  98 GLN
** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  94 HIS
E  98 GLN
** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.065112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.055770 restraints weight = 31304.053|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 2.85
r_work: 0.2828 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8824
moved from start:          0.5614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10494  Z= 0.124
  Angle     :  0.604   8.119  14340  Z= 0.303
  Chirality :  0.037   0.123   1704
  Planarity :  0.003   0.028   1674
  Dihedral  :  5.376  55.491   1746
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 17.56 %
    Favored  : 81.36 %
  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:  3.48 (0.24), residues: 1218
  helix:  3.39 (0.16), residues: 888
  sheet: -0.66 (0.50), residues: 102
  loop : -0.95 (0.46), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  44 
 HIS   0.004   0.001   HIS B 123 
 PHE   0.007   0.001   PHE A 149 
 TYR   0.007   0.001   TYR F 157 
 ARG   0.004   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02678 (  780)
  hydrogen bonds       : angle       3.07267 ( 2304)
  SS BOND              : bond        0.00155 (   18)
  SS BOND              : angle       0.17448 (   36)
  covalent geometry    : bond        0.00268 (10476)
  covalent geometry    : angle       0.60421 (14304)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 209
  time to evaluate  : 1.173 
Fit side-chains
REVERT: A   57 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8286 (tm-30)
REVERT: A   94 HIS cc_start: 0.9036 (t70) cc_final: 0.8487 (t-90)
REVERT: A   98 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8822 (mm110)
REVERT: A  123 HIS cc_start: 0.8274 (t70) cc_final: 0.7920 (t70)
REVERT: B   47 GLU cc_start: 0.8115 (tp30) cc_final: 0.7827 (tp30)
REVERT: B  144 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9115 (mm)
REVERT: C   57 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8276 (tm-30)
REVERT: C   94 HIS cc_start: 0.8969 (t-90) cc_final: 0.8607 (t-90)
REVERT: C  102 GLU cc_start: 0.9082 (tp30) cc_final: 0.8730 (mm-30)
REVERT: D   47 GLU cc_start: 0.8019 (tp30) cc_final: 0.7776 (tp30)
REVERT: D   94 HIS cc_start: 0.8940 (t-90) cc_final: 0.8672 (t-90)
REVERT: D  102 GLU cc_start: 0.9052 (tp30) cc_final: 0.8684 (mm-30)
REVERT: E   47 GLU cc_start: 0.8279 (tp30) cc_final: 0.7956 (tp30)
REVERT: E   57 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8393 (tm-30)
REVERT: E  144 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9103 (mm)
REVERT: F   47 GLU cc_start: 0.8167 (tp30) cc_final: 0.7855 (tp30)
REVERT: F   57 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8278 (tm-30)
REVERT: F   94 HIS cc_start: 0.8946 (t70) cc_final: 0.8369 (t-90)
REVERT: F  102 GLU cc_start: 0.9066 (tp30) cc_final: 0.8675 (mm-30)
REVERT: F  105 MET cc_start: 0.8419 (mtt) cc_final: 0.8205 (mtm)
REVERT: F  144 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9045 (mm)
  outliers start: 12
  outliers final: 9
  residues processed: 221
  average time/residue: 0.2301
  time to fit residues: 70.3362
Evaluate side-chains
  214 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 202
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ASP
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain B residue   46 ASP
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue  144 LEU
Chi-restraints excluded: chain F residue  144 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 119 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9980
   chunk 88 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 13 optimal weight:    7.9990
   chunk 93 optimal weight:    4.9990
   chunk 81 optimal weight:    9.9990
   chunk 45 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 56 optimal weight:   10.0000
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  94 HIS
B  98 GLN
** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  94 HIS
** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.065676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.056486 restraints weight = 31191.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.2980 rms_B_bonded: 2.84
r_work: 0.2845 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8817
moved from start:          0.5684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10494  Z= 0.125
  Angle     :  0.593   9.366  14340  Z= 0.297
  Chirality :  0.037   0.136   1704
  Planarity :  0.003   0.025   1674
  Dihedral  :  5.276  55.171   1746
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 17.03 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.49 (0.24), residues: 1218
  helix:  3.39 (0.16), residues: 888
  sheet: -0.72 (0.49), residues: 102
  loop : -0.91 (0.46), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  44 
 HIS   0.004   0.001   HIS B 123 
 PHE   0.007   0.001   PHE C 149 
 TYR   0.007   0.001   TYR A 171 
 ARG   0.003   0.000   ARG E 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02575 (  780)
  hydrogen bonds       : angle       3.04936 ( 2304)
  SS BOND              : bond        0.00120 (   18)
  SS BOND              : angle       0.18958 (   36)
  covalent geometry    : bond        0.00273 (10476)
  covalent geometry    : angle       0.59319 (14304)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 212
  time to evaluate  : 1.273 
Fit side-chains
REVERT: A   57 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8263 (tm-30)
REVERT: A   94 HIS cc_start: 0.9027 (t70) cc_final: 0.8450 (t-90)
REVERT: A   98 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8819 (mm110)
REVERT: A  123 HIS cc_start: 0.8244 (t70) cc_final: 0.7917 (t70)
REVERT: B    7 TYR cc_start: 0.8878 (t80) cc_final: 0.8563 (t80)
REVERT: B  105 MET cc_start: 0.8372 (mtt) cc_final: 0.8165 (mtm)
REVERT: B  144 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9108 (mm)
REVERT: C   57 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8241 (tm-30)
REVERT: C   94 HIS cc_start: 0.8950 (t-90) cc_final: 0.8582 (t-90)
REVERT: C  102 GLU cc_start: 0.9115 (tp30) cc_final: 0.8756 (mm-30)
REVERT: C  105 MET cc_start: 0.8494 (mtt) cc_final: 0.8272 (mtm)
REVERT: D   94 HIS cc_start: 0.8954 (t-90) cc_final: 0.8707 (t-90)
REVERT: D  102 GLU cc_start: 0.9092 (tp30) cc_final: 0.8692 (mm-30)
REVERT: E   47 GLU cc_start: 0.8256 (tp30) cc_final: 0.7983 (tp30)
REVERT: E  144 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9095 (mm)
REVERT: F   47 GLU cc_start: 0.8188 (tp30) cc_final: 0.7940 (tp30)
REVERT: F   57 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8241 (tm-30)
REVERT: F   94 HIS cc_start: 0.8944 (t70) cc_final: 0.8382 (t-90)
REVERT: F  102 GLU cc_start: 0.9073 (tp30) cc_final: 0.8691 (mm-30)
REVERT: F  105 MET cc_start: 0.8424 (mtt) cc_final: 0.8218 (mtm)
REVERT: F  144 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9047 (mm)
  outliers start: 16
  outliers final: 11
  residues processed: 225
  average time/residue: 0.2266
  time to fit residues: 71.1035
Evaluate side-chains
  218 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 204
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ASP
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain B residue   46 ASP
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue   48 LYS
Chi-restraints excluded: chain E residue  144 LEU
Chi-restraints excluded: chain F residue  144 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 5 optimal weight:    7.9990
   chunk 13 optimal weight:    3.9990
   chunk 110 optimal weight:    3.9990
   chunk 109 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 35 optimal weight:    9.9990
   chunk 61 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  94 HIS
B  98 GLN
** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  94 HIS
** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.064190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.054863 restraints weight = 31379.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 3.00
r_work: 0.2824 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8811
moved from start:          0.5758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10494  Z= 0.144
  Angle     :  0.629  10.117  14340  Z= 0.316
  Chirality :  0.038   0.140   1704
  Planarity :  0.003   0.023   1674
  Dihedral  :  5.346  56.895   1746
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 17.65 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.49 (0.24), residues: 1218
  helix:  3.41 (0.16), residues: 888
  sheet: -0.75 (0.48), residues: 102
  loop : -0.96 (0.46), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  44 
 HIS   0.003   0.001   HIS B 123 
 PHE   0.008   0.001   PHE A  31 
 TYR   0.007   0.001   TYR B  65 
 ARG   0.003   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02676 (  780)
  hydrogen bonds       : angle       3.04956 ( 2304)
  SS BOND              : bond        0.00162 (   18)
  SS BOND              : angle       0.28353 (   36)
  covalent geometry    : bond        0.00320 (10476)
  covalent geometry    : angle       0.62963 (14304)

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

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

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2436 Ramachandran restraints generated.
    1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 205
  time to evaluate  : 1.291 
Fit side-chains
REVERT: A   94 HIS cc_start: 0.9056 (t70) cc_final: 0.8553 (t-90)
REVERT: A  123 HIS cc_start: 0.8255 (t70) cc_final: 0.7918 (t70)
REVERT: B   47 GLU cc_start: 0.8143 (tp30) cc_final: 0.7779 (tm-30)
REVERT: B  105 MET cc_start: 0.8343 (mtt) cc_final: 0.8127 (mtm)
REVERT: B  144 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9083 (mm)
REVERT: C   57 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8171 (tm-30)
REVERT: C   94 HIS cc_start: 0.8975 (t-90) cc_final: 0.8299 (t-90)
REVERT: C  102 GLU cc_start: 0.9155 (tp30) cc_final: 0.8801 (mm-30)
REVERT: C  105 MET cc_start: 0.8482 (mtt) cc_final: 0.8269 (mtm)
REVERT: D   94 HIS cc_start: 0.8981 (t-90) cc_final: 0.8736 (t-90)
REVERT: D  102 GLU cc_start: 0.9127 (tp30) cc_final: 0.8764 (mm-30)
REVERT: D  150 MET cc_start: 0.9326 (mmm) cc_final: 0.8975 (tpp)
REVERT: E   47 GLU cc_start: 0.8309 (tp30) cc_final: 0.8035 (tp30)
REVERT: E   57 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8294 (tm-30)
REVERT: E  144 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9056 (mm)
REVERT: E  194 MET cc_start: 0.9447 (mmp) cc_final: 0.9216 (mmt)
REVERT: F   57 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8144 (tm-30)
REVERT: F   94 HIS cc_start: 0.8980 (t70) cc_final: 0.8395 (t-90)
REVERT: F  102 GLU cc_start: 0.9130 (tp30) cc_final: 0.8753 (mm-30)
REVERT: F  105 MET cc_start: 0.8415 (mtt) cc_final: 0.8214 (mtm)
REVERT: F  144 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9110 (mm)
  outliers start: 14
  outliers final: 11
  residues processed: 217
  average time/residue: 0.2220
  time to fit residues: 67.4347
Evaluate side-chains
  216 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 202
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ASP
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain B residue   46 ASP
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain E residue   34 MET
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue  144 LEU
Chi-restraints excluded: chain F residue  144 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 111 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   chunk 112 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 77 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9980
   chunk 32 optimal weight:    7.9990
   chunk 119 optimal weight:    1.9990
   chunk 81 optimal weight:    9.9990
   chunk 90 optimal weight:    9.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  94 HIS
B  98 GLN
** B 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  94 HIS
** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.065120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.055860 restraints weight = 31103.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.2995 rms_B_bonded: 3.02
r_work: 0.2850 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8793
moved from start:          0.5793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10494  Z= 0.130
  Angle     :  0.631  10.230  14340  Z= 0.316
  Chirality :  0.037   0.145   1704
  Planarity :  0.003   0.024   1674
  Dihedral  :  5.282  56.881   1746
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 18.01 %
    Favored  : 80.47 %
  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:  3.50 (0.24), residues: 1218
  helix:  3.42 (0.16), residues: 888
  sheet: -0.74 (0.48), residues: 102
  loop : -1.00 (0.45), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  44 
 HIS   0.004   0.001   HIS B 123 
 PHE   0.007   0.001   PHE B  31 
 TYR   0.009   0.001   TYR C 171 
 ARG   0.003   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02549 (  780)
  hydrogen bonds       : angle       3.04297 ( 2304)
  SS BOND              : bond        0.00109 (   18)
  SS BOND              : angle       0.25935 (   36)
  covalent geometry    : bond        0.00284 (10476)
  covalent geometry    : angle       0.63141 (14304)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4289.38 seconds
wall clock time: 76 minutes 7.67 seconds (4567.67 seconds total)