Starting phenix.real_space_refine
on Fri Feb 14 09:49:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qki_18463/02_2025/8qki_18463_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qki_18463/02_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_18463/02_2025/8qki_18463.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qki_18463/02_2025/8qki_18463.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qki_18463/02_2025/8qki_18463_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qki_18463/02_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.88, per 1000 atoms: 0.48
  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=3, 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

  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: 2.64
  Conformation dependent library (CDL) restraints added in 1.1 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: 0.84
  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: 2.90

  Time building geometry restraints manager: 3.07 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: 5473
       11.70 -    23.40: 545
       23.40 -    35.11: 240
       35.11 -    46.81: 81
       46.81 -    58.51: 36
  Dihedral angle restraints: 6375
    sinusoidal: 2703
      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 6372 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:
        2.03 -     2.60: 53
        2.60 -     3.18: 8922
        3.18 -     3.75: 17051
        3.75 -     4.33: 21042
        4.33 -     4.90: 36036
  Nonbonded interactions: 83104
  Sorted by model distance:
  nonbonded pdb=" SG  CYS C  64 "
            pdb=" SG  CYS C 168 "
     model   vdw
     2.031 3.760
  nonbonded pdb=" SG  CYS B  60 "
            pdb=" SG  CYS B 173 "
     model   vdw
     2.031 3.760
  nonbonded pdb=" SG  CYS B  64 "
            pdb=" SG  CYS B 168 "
     model   vdw
     2.031 3.760
  nonbonded pdb=" SG  CYS F  64 "
            pdb=" SG  CYS F 168 "
     model   vdw
     2.031 3.760
  nonbonded pdb=" SG  CYS E  60 "
            pdb=" SG  CYS E 173 "
     model   vdw
     2.031 3.760
  ... (remaining 83099 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:             4.620
  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:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     23.590
  Find NCS groups from input model:        0.190
  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:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.040
-------------------------------------------------------------------------------
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  10476  Z= 0.238
  Angle     :  0.752   8.284  14304  Z= 0.354
  Chirality :  0.052   0.367   1704
  Planarity :  0.002   0.014   1674
  Dihedral  : 12.595  58.509   3978
  Min Nonbonded Distance : 2.031

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 

*********************** 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  : 1.169 
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: 0.2235
  time to fit residues: 98.7895
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  : 1.183 
-------------------------------------------------------------------------------
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:   10.0000
   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 = 0.3416 r_free = 0.3416 target = 0.076396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.067155 restraints weight = 30793.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 3.03
r_work: 0.3091 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10476  Z= 0.167
  Angle     :  0.562   6.057  14304  Z= 0.280
  Chirality :  0.037   0.123   1704
  Planarity :  0.003   0.017   1674
  Dihedral  :  5.014  53.612   1746
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 12.72 %
    Favored  : 85.48 %
  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:  3.13 (0.24), residues: 1218
  helix:  3.21 (0.16), residues: 894
  sheet: -0.65 (0.47), residues: 102
  loop : -1.66 (0.42), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D  24 
 HIS   0.002   0.001   HIS F  97 
 PHE   0.007   0.001   PHE F  31 
 TYR   0.013   0.001   TYR A 157 
 ARG   0.002   0.000   ARG D 142 

*********************** 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
  269 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 249
  time to evaluate  : 1.119 
Fit side-chains
REVERT: A  146 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8907 (tp30)
REVERT: B   98 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8229 (mm-40)
REVERT: B  150 MET cc_start: 0.9221 (mmp) cc_final: 0.7456 (tmm)
REVERT: C   14 ASN cc_start: 0.8196 (t0) cc_final: 0.7985 (t0)
REVERT: C   54 ASN cc_start: 0.9237 (t0) cc_final: 0.8943 (t0)
REVERT: C   66 ASP cc_start: 0.8814 (t0) cc_final: 0.8606 (t0)
REVERT: C   94 HIS cc_start: 0.8162 (OUTLIER) cc_final: 0.7842 (t-90)
REVERT: C  144 LEU cc_start: 0.8807 (mm) cc_final: 0.8476 (mm)
REVERT: C  150 MET cc_start: 0.9209 (mmp) cc_final: 0.7446 (tmm)
REVERT: D   14 ASN cc_start: 0.8410 (t0) cc_final: 0.8203 (t0)
REVERT: D   54 ASN cc_start: 0.9258 (t0) cc_final: 0.8904 (t0)
REVERT: D   66 ASP cc_start: 0.8828 (t0) cc_final: 0.8626 (t0)
REVERT: D   98 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8129 (mm-40)
REVERT: D  144 LEU cc_start: 0.8799 (mm) cc_final: 0.8457 (mm)
REVERT: D  150 MET cc_start: 0.9118 (mmp) cc_final: 0.7426 (tmm)
REVERT: E   14 ASN cc_start: 0.8224 (t0) cc_final: 0.8014 (t0)
REVERT: E   54 ASN cc_start: 0.9283 (t0) cc_final: 0.8976 (t0)
REVERT: E   98 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8177 (mm-40)
REVERT: E  150 MET cc_start: 0.9232 (mmp) cc_final: 0.7461 (tmm)
REVERT: F   14 ASN cc_start: 0.8168 (t0) cc_final: 0.7944 (t0)
REVERT: F   48 LYS cc_start: 0.8503 (tmmt) cc_final: 0.8252 (mptt)
REVERT: F   54 ASN cc_start: 0.9298 (t0) cc_final: 0.9024 (t0)
REVERT: F   66 ASP cc_start: 0.8775 (t0) cc_final: 0.8555 (t0)
REVERT: F  144 LEU cc_start: 0.8775 (mm) cc_final: 0.8434 (mm)
REVERT: F  150 MET cc_start: 0.9186 (mmp) cc_final: 0.7412 (tmm)
  outliers start: 20
  outliers final: 14
  residues processed: 257
  average time/residue: 0.2340
  time to fit residues: 83.1749
Evaluate side-chains
  238 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 223
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 93 optimal weight:    7.9990
   chunk 47 optimal weight:    0.1980
   chunk 68 optimal weight:    5.9990
   chunk 85 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 105 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3355 r_free = 0.3355 target = 0.073291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.063768 restraints weight = 31519.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3144 rms_B_bonded: 3.04
r_work: 0.3017 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
moved from start:          0.3159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  10476  Z= 0.156
  Angle     :  0.524   8.553  14304  Z= 0.259
  Chirality :  0.037   0.153   1704
  Planarity :  0.002   0.018   1674
  Dihedral  :  4.953  55.959   1746
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.89 %
    Favored  : 83.87 %
  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:  3.54 (0.24), residues: 1218
  helix:  3.43 (0.16), residues: 894
  sheet: -0.11 (0.57), residues: 72
  loop : -1.23 (0.39), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  44 
 HIS   0.003   0.001   HIS F 123 
 PHE   0.007   0.001   PHE E  68 
 TYR   0.007   0.001   TYR A 157 
 ARG   0.003   0.000   ARG A 183 

*********************** 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
  241 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 216
  time to evaluate  : 1.207 
Fit side-chains
REVERT: A   41 GLU cc_start: 0.6745 (tt0) cc_final: 0.6376 (tt0)
REVERT: A   48 LYS cc_start: 0.9209 (tppp) cc_final: 0.8928 (mmtp)
REVERT: A  105 MET cc_start: 0.8493 (mtt) cc_final: 0.8131 (mtm)
REVERT: B  144 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8726 (mm)
REVERT: C   14 ASN cc_start: 0.8434 (t0) cc_final: 0.8219 (t0)
REVERT: C   48 LYS cc_start: 0.8789 (tppp) cc_final: 0.8442 (mmmm)
REVERT: C   94 HIS cc_start: 0.8583 (OUTLIER) cc_final: 0.8310 (t-90)
REVERT: C  144 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8689 (mm)
REVERT: D   14 ASN cc_start: 0.8598 (t0) cc_final: 0.8371 (t0)
REVERT: D   48 LYS cc_start: 0.8819 (tppp) cc_final: 0.8436 (mmmm)
REVERT: D   54 ASN cc_start: 0.9372 (t0) cc_final: 0.9101 (t0)
REVERT: D  102 GLU cc_start: 0.8891 (tp30) cc_final: 0.8564 (tp30)
REVERT: D  144 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8726 (mm)
REVERT: E   14 ASN cc_start: 0.8447 (t0) cc_final: 0.8221 (t0)
REVERT: E   98 GLN cc_start: 0.8598 (mm-40) cc_final: 0.8319 (mp10)
REVERT: E  102 GLU cc_start: 0.8926 (tp30) cc_final: 0.8623 (tp30)
REVERT: E  144 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8733 (mm)
REVERT: F   14 ASN cc_start: 0.8429 (t0) cc_final: 0.8206 (t0)
REVERT: F   98 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8390 (mp10)
REVERT: F  144 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8653 (mm)
  outliers start: 25
  outliers final: 16
  residues processed: 231
  average time/residue: 0.2370
  time to fit residues: 76.2591
Evaluate side-chains
  223 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 201
  time to evaluate  : 1.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ASP
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   61 ASN
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   91 VAL
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 D residue  144 LEU
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  144 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 95 optimal weight:    0.5980
   chunk 33 optimal weight:    5.9990
   chunk 47 optimal weight:    8.9990
   chunk 1 optimal weight:    0.9980
   chunk 113 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 10 optimal weight:    9.9990
   chunk 82 optimal weight:   10.0000
   chunk 75 optimal weight:    1.9990
   overall best weight:    1.9186

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.064980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.056026 restraints weight = 31888.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 2.81
r_work: 0.2831 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8793
moved from start:          0.4541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10476  Z= 0.239
  Angle     :  0.570   8.074  14304  Z= 0.283
  Chirality :  0.039   0.146   1704
  Planarity :  0.003   0.019   1674
  Dihedral  :  5.576  59.428   1746
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 12.99 %
    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:  3.34 (0.24), residues: 1218
  helix:  3.30 (0.15), residues: 888
  sheet: -0.26 (0.52), residues: 102
  loop : -1.34 (0.44), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E  44 
 HIS   0.004   0.001   HIS C  16 
 PHE   0.011   0.001   PHE A 149 
 TYR   0.008   0.001   TYR F   7 
 ARG   0.003   0.000   ARG B 183 

*********************** 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
  255 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 214
  time to evaluate  : 1.319 
Fit side-chains
REVERT: A   57 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8557 (tm-30)
REVERT: A   94 HIS cc_start: 0.8967 (t70) cc_final: 0.8559 (t-90)
REVERT: A  123 HIS cc_start: 0.8320 (t70) cc_final: 0.7873 (t70)
REVERT: B   48 LYS cc_start: 0.9073 (tppp) cc_final: 0.8795 (mmmm)
REVERT: B   66 ASP cc_start: 0.8921 (t0) cc_final: 0.8712 (t0)
REVERT: B   94 HIS cc_start: 0.8868 (t-90) cc_final: 0.8655 (t-90)
REVERT: B  144 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8963 (mm)
REVERT: C   14 ASN cc_start: 0.8760 (t0) cc_final: 0.8537 (t0)
REVERT: C   48 LYS cc_start: 0.9105 (tppp) cc_final: 0.8894 (mmmm)
REVERT: C  102 GLU cc_start: 0.8965 (tp30) cc_final: 0.8548 (mm-30)
REVERT: C  144 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8930 (mm)
REVERT: D   14 ASN cc_start: 0.8791 (t0) cc_final: 0.8543 (t0)
REVERT: D   48 LYS cc_start: 0.9070 (tppp) cc_final: 0.8827 (mmmm)
REVERT: D  102 GLU cc_start: 0.9028 (tp30) cc_final: 0.8620 (mm-30)
REVERT: D  144 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8942 (mm)
REVERT: E   14 ASN cc_start: 0.8726 (t0) cc_final: 0.8495 (t0)
REVERT: E   48 LYS cc_start: 0.9162 (tppp) cc_final: 0.8910 (mmmm)
REVERT: E   66 ASP cc_start: 0.8939 (t0) cc_final: 0.8713 (t0)
REVERT: E   98 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8477 (mp10)
REVERT: E  102 GLU cc_start: 0.9032 (tp30) cc_final: 0.8795 (tp30)
REVERT: E  144 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9007 (mm)
REVERT: F   14 ASN cc_start: 0.8728 (t0) cc_final: 0.8511 (t0)
REVERT: F   57 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8468 (tm-30)
REVERT: F   94 HIS cc_start: 0.8910 (t-90) cc_final: 0.8587 (t-90)
REVERT: F   98 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8657 (mp10)
REVERT: F  102 GLU cc_start: 0.8974 (tp30) cc_final: 0.8557 (mm-30)
REVERT: F  144 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8925 (mm)
  outliers start: 41
  outliers final: 19
  residues processed: 243
  average time/residue: 0.2242
  time to fit residues: 76.1082
Evaluate side-chains
  219 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 195
  time to evaluate  : 1.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ASP
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  123 HIS
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   90 LEU
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain D residue   46 ASP
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue   56 LEU
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   46 ASP
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 70 optimal weight:    0.5980
   chunk 14 optimal weight:    6.9990
   chunk 99 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9980
   chunk 60 optimal weight:    9.9990
   chunk 109 optimal weight:   10.0000
   chunk 20 optimal weight:    9.9990
   chunk 30 optimal weight:    0.0010
   chunk 33 optimal weight:    7.9990
   chunk 101 optimal weight:    0.7980
   overall best weight:    1.2788

-------------------------------------------------------------------------------
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  67 GLN
** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  94 HIS
** 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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.065948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.056866 restraints weight = 31600.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 2.83
r_work: 0.2845 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8787
moved from start:          0.4790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10476  Z= 0.180
  Angle     :  0.552   7.333  14304  Z= 0.277
  Chirality :  0.038   0.138   1704
  Planarity :  0.003   0.020   1674
  Dihedral  :  5.390  58.638   1746
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 14.43 %
    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:  3.46 (0.24), residues: 1218
  helix:  3.36 (0.16), residues: 888
  sheet: -0.35 (0.52), residues: 102
  loop : -1.07 (0.44), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  44 
 HIS   0.003   0.001   HIS F 123 
 PHE   0.007   0.001   PHE C  68 
 TYR   0.009   0.001   TYR B 171 
 ARG   0.002   0.000   ARG A 183 

*********************** 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
  246 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 219
  time to evaluate  : 1.108 
Fit side-chains
REVERT: A   41 GLU cc_start: 0.7309 (tt0) cc_final: 0.6993 (tt0)
REVERT: A   47 GLU cc_start: 0.8078 (tp30) cc_final: 0.7690 (tp30)
REVERT: A  123 HIS cc_start: 0.8222 (t70) cc_final: 0.7901 (t70)
REVERT: B   41 GLU cc_start: 0.7623 (tt0) cc_final: 0.7410 (tt0)
REVERT: B   66 ASP cc_start: 0.8938 (t70) cc_final: 0.8723 (t0)
REVERT: B   94 HIS cc_start: 0.8866 (t-90) cc_final: 0.8600 (t-90)
REVERT: B  144 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8975 (mm)
REVERT: C   14 ASN cc_start: 0.8726 (t0) cc_final: 0.8492 (t0)
REVERT: C   66 ASP cc_start: 0.8870 (t0) cc_final: 0.8430 (t0)
REVERT: C  102 GLU cc_start: 0.9009 (tp30) cc_final: 0.8618 (mm-30)
REVERT: C  144 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.8943 (mm)
REVERT: D   14 ASN cc_start: 0.8736 (t0) cc_final: 0.8504 (t0)
REVERT: D  102 GLU cc_start: 0.9034 (tp30) cc_final: 0.8561 (mm-30)
REVERT: E   14 ASN cc_start: 0.8697 (t0) cc_final: 0.8490 (t0)
REVERT: E   47 GLU cc_start: 0.7984 (tp30) cc_final: 0.7669 (tp30)
REVERT: E   98 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8541 (mp10)
REVERT: E  102 GLU cc_start: 0.9013 (tp30) cc_final: 0.8779 (tp30)
REVERT: E  144 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8998 (mm)
REVERT: F   14 ASN cc_start: 0.8722 (t0) cc_final: 0.8492 (t0)
REVERT: F   66 ASP cc_start: 0.8822 (t0) cc_final: 0.8568 (t0)
REVERT: F  102 GLU cc_start: 0.8995 (tp30) cc_final: 0.8593 (mm-30)
REVERT: F  144 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8940 (mm)
  outliers start: 27
  outliers final: 16
  residues processed: 237
  average time/residue: 0.2309
  time to fit residues: 75.4914
Evaluate side-chains
  220 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 200
  time to evaluate  : 1.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 ASP
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 B residue  178 ASP
Chi-restraints excluded: chain C residue   46 ASP
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  178 ASP
Chi-restraints excluded: chain E residue   46 ASP
Chi-restraints excluded: chain E residue   90 LEU
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  144 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 80 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 101 optimal weight:    0.0770
   chunk 39 optimal weight:    3.9990
   chunk 76 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 78 optimal weight:    0.0980
   chunk 106 optimal weight:    7.9990
   overall best weight:    2.6344

-------------------------------------------------------------------------------
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**
C  94 HIS
** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 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 = 0.3138 r_free = 0.3138 target = 0.063383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.054599 restraints weight = 31621.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 2.70
r_work: 0.2773 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8869
moved from start:          0.5368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10476  Z= 0.286
  Angle     :  0.591   8.137  14304  Z= 0.298
  Chirality :  0.040   0.132   1704
  Planarity :  0.003   0.023   1674
  Dihedral  :  5.818  57.722   1746
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 14.87 %
    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:  3.40 (0.24), residues: 1218
  helix:  3.27 (0.16), residues: 888
  sheet: -0.37 (0.52), residues: 102
  loop : -0.92 (0.45), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  44 
 HIS   0.003   0.001   HIS B  16 
 PHE   0.009   0.001   PHE E 149 
 TYR   0.009   0.001   TYR F 151 
 ARG   0.005   0.000   ARG F 183 

*********************** 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
  247 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 210
  time to evaluate  : 1.206 
Fit side-chains
REVERT: A   41 GLU cc_start: 0.7475 (tt0) cc_final: 0.7232 (tt0)
REVERT: A   47 GLU cc_start: 0.7989 (tp30) cc_final: 0.7767 (tp30)
REVERT: A   57 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8389 (tm-30)
REVERT: A  123 HIS cc_start: 0.8247 (t70) cc_final: 0.7885 (t70)
REVERT: B   41 GLU cc_start: 0.7699 (tt0) cc_final: 0.7484 (tt0)
REVERT: B   57 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8316 (tm-30)
REVERT: B   94 HIS cc_start: 0.8946 (t-90) cc_final: 0.8659 (t-90)
REVERT: B  144 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9057 (mm)
REVERT: C   57 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8342 (tm-30)
REVERT: C  102 GLU cc_start: 0.9063 (tp30) cc_final: 0.8674 (mm-30)
REVERT: D   14 ASN cc_start: 0.8828 (t0) cc_final: 0.8627 (t0)
REVERT: D   57 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8364 (tm-30)
REVERT: D  102 GLU cc_start: 0.9045 (tp30) cc_final: 0.8661 (mm-30)
REVERT: E   14 ASN cc_start: 0.8776 (t0) cc_final: 0.8570 (t0)
REVERT: E   57 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8339 (tm-30)
REVERT: E  144 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9121 (mm)
REVERT: F   57 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8406 (tm-30)
REVERT: F   66 ASP cc_start: 0.8809 (t0) cc_final: 0.8603 (t0)
REVERT: F   94 HIS cc_start: 0.8949 (t70) cc_final: 0.8417 (t-90)
REVERT: F  102 GLU cc_start: 0.9058 (tp30) cc_final: 0.8652 (mm-30)
REVERT: F  144 LEU cc_start: 0.9456 (OUTLIER) cc_final: 0.9071 (mm)
  outliers start: 37
  outliers final: 25
  residues processed: 234
  average time/residue: 0.2289
  time to fit residues: 74.5776
Evaluate side-chains
  226 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 198
  time to evaluate  : 1.582 
-------------------------------------------------------------------------------
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   56 LEU
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  144 LEU
Chi-restraints excluded: chain B residue  178 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   56 LEU
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  162 MET
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   66 ASP
Chi-restraints excluded: chain E residue  144 LEU
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  178 ASP
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 116 optimal weight:    4.9990
   chunk 90 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   chunk 75 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   chunk 104 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 73 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 123 HIS
C  94 HIS
D  94 HIS
** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  94 HIS
E  98 GLN
** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.061978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.053194 restraints weight = 32286.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.2887 rms_B_bonded: 2.74
r_work: 0.2742 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8893
moved from start:          0.5716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  10476  Z= 0.333
  Angle     :  0.625   6.782  14304  Z= 0.319
  Chirality :  0.040   0.170   1704
  Planarity :  0.003   0.023   1674
  Dihedral  :  6.074  59.178   1746
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 16.22 %
    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:  3.32 (0.24), residues: 1218
  helix:  3.19 (0.16), residues: 888
  sheet: -0.25 (0.51), residues: 102
  loop : -0.89 (0.46), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  44 
 HIS   0.003   0.001   HIS C  16 
 PHE   0.010   0.001   PHE F 193 
 TYR   0.011   0.002   TYR F 151 
 ARG   0.004   0.000   ARG C 183 

*********************** 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
  241 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 204
  time to evaluate  : 1.197 
Fit side-chains
REVERT: A   47 GLU cc_start: 0.7993 (tp30) cc_final: 0.7763 (tp30)
REVERT: A   94 HIS cc_start: 0.9124 (t70) cc_final: 0.8651 (t-90)
REVERT: A  123 HIS cc_start: 0.8278 (t70) cc_final: 0.7895 (t70)
REVERT: B   47 GLU cc_start: 0.8175 (tp30) cc_final: 0.7652 (tp30)
REVERT: B   65 TYR cc_start: 0.9108 (t80) cc_final: 0.8794 (t80)
REVERT: B   94 HIS cc_start: 0.8985 (t-90) cc_final: 0.8770 (t-90)
REVERT: B  102 GLU cc_start: 0.9127 (tp30) cc_final: 0.8908 (mm-30)
REVERT: B  144 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9181 (mm)
REVERT: C   47 GLU cc_start: 0.8439 (tp30) cc_final: 0.8149 (tp30)
REVERT: C   60 CYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8480 (t)
REVERT: C   94 HIS cc_start: 0.9056 (t70) cc_final: 0.8784 (t-90)
REVERT: C  102 GLU cc_start: 0.9115 (tp30) cc_final: 0.8748 (mm-30)
REVERT: C  173 CYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8123 (m)
REVERT: D   47 GLU cc_start: 0.8160 (tp30) cc_final: 0.7906 (tp30)
REVERT: D   60 CYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8645 (t)
REVERT: D   94 HIS cc_start: 0.9008 (t70) cc_final: 0.8730 (t-90)
REVERT: D  102 GLU cc_start: 0.9094 (tp30) cc_final: 0.8717 (mm-30)
REVERT: E   60 CYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8594 (t)
REVERT: E  144 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9203 (mm)
REVERT: F   47 GLU cc_start: 0.8357 (tp30) cc_final: 0.7870 (tp30)
REVERT: F   94 HIS cc_start: 0.8959 (t70) cc_final: 0.8400 (t-90)
REVERT: F  102 GLU cc_start: 0.9116 (tp30) cc_final: 0.8727 (mm-30)
  outliers start: 37
  outliers final: 26
  residues processed: 233
  average time/residue: 0.2178
  time to fit residues: 70.6141
Evaluate side-chains
  227 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 195
  time to evaluate  : 1.338 
-------------------------------------------------------------------------------
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  123 HIS
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   60 CYS
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   91 VAL
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  173 CYS
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain D residue   56 LEU
Chi-restraints excluded: chain D residue   60 CYS
Chi-restraints excluded: chain D residue   91 VAL
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  162 MET
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   60 CYS
Chi-restraints excluded: chain E residue  144 LEU
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  178 ASP
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:    8.9990
   chunk 94 optimal weight:    5.9990
   chunk 97 optimal weight:    0.8980
   chunk 98 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 5 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 112 optimal weight:    0.0270
   chunk 13 optimal weight:    5.9990
   chunk 101 optimal weight:    0.0010
   overall best weight:    0.7846

-------------------------------------------------------------------------------
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**
C  98 GLN
** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  94 HIS
E  98 GLN
E 123 HIS
** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3185 r_free = 0.3185 target = 0.065100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.056294 restraints weight = 32033.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 2.85
r_work: 0.2839 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8805
moved from start:          0.5706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10476  Z= 0.169
  Angle     :  0.605   8.673  14304  Z= 0.302
  Chirality :  0.037   0.181   1704
  Planarity :  0.003   0.032   1674
  Dihedral  :  5.354  53.709   1746
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 16.31 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.40 (0.24), residues: 1218
  helix:  3.28 (0.16), residues: 888
  sheet: -0.38 (0.51), residues: 102
  loop : -0.91 (0.46), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E  44 
 HIS   0.003   0.001   HIS B 123 
 PHE   0.007   0.001   PHE E 153 
 TYR   0.008   0.001   TYR C  65 
 ARG   0.003   0.000   ARG A 183 

*********************** 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
  241 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 211
  time to evaluate  : 1.123 
Fit side-chains
REVERT: A   57 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8298 (tm-30)
REVERT: A   94 HIS cc_start: 0.9088 (t70) cc_final: 0.8535 (t-90)
REVERT: A  123 HIS cc_start: 0.8237 (t70) cc_final: 0.7869 (t70)
REVERT: B    7 TYR cc_start: 0.8865 (t80) cc_final: 0.8565 (t80)
REVERT: B   47 GLU cc_start: 0.8015 (tp30) cc_final: 0.7533 (tp30)
REVERT: B   57 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8247 (tm-30)
REVERT: B   65 TYR cc_start: 0.8918 (t80) cc_final: 0.8554 (t80)
REVERT: B   94 HIS cc_start: 0.8954 (t-90) cc_final: 0.8651 (t-90)
REVERT: B  144 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9056 (mm)
REVERT: C   57 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8249 (tm-30)
REVERT: C   60 CYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8271 (t)
REVERT: C  102 GLU cc_start: 0.9079 (tp30) cc_final: 0.8700 (mm-30)
REVERT: C  105 MET cc_start: 0.8456 (mtt) cc_final: 0.8227 (mtm)
REVERT: D   47 GLU cc_start: 0.8099 (tp30) cc_final: 0.7735 (tp30)
REVERT: D   57 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8186 (tm-30)
REVERT: D  102 GLU cc_start: 0.9089 (tp30) cc_final: 0.8690 (mm-30)
REVERT: D  124 LYS cc_start: 0.9267 (mmmm) cc_final: 0.9058 (mmmm)
REVERT: E   57 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8168 (tm-30)
REVERT: E   60 CYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8540 (t)
REVERT: E  144 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9081 (mm)
REVERT: F   47 GLU cc_start: 0.8267 (tp30) cc_final: 0.7904 (tp30)
REVERT: F   57 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8104 (tm-30)
REVERT: F   94 HIS cc_start: 0.8962 (t70) cc_final: 0.8387 (t-90)
REVERT: F  102 GLU cc_start: 0.9080 (tp30) cc_final: 0.8679 (mm-30)
REVERT: F  105 MET cc_start: 0.8439 (mtt) cc_final: 0.8218 (mtm)
  outliers start: 30
  outliers final: 20
  residues processed: 239
  average time/residue: 0.2278
  time to fit residues: 75.7270
Evaluate side-chains
  223 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 199
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
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   74 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  123 HIS
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain C residue   34 MET
Chi-restraints excluded: chain C residue   60 CYS
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain D residue   74 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   60 CYS
Chi-restraints excluded: chain E residue  144 LEU
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain F residue   74 VAL
Chi-restraints excluded: chain F residue  144 LEU
Chi-restraints excluded: chain F residue  178 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 119 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 88 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 13 optimal weight:    0.3980
   chunk 93 optimal weight:    5.9990
   chunk 81 optimal weight:   10.0000
   chunk 45 optimal weight:    0.0870
   chunk 49 optimal weight:    2.9990
   chunk 80 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.6962

-------------------------------------------------------------------------------
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**
** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  94 HIS
D  98 GLN
** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  94 HIS
E  98 GLN
** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3204 r_free = 0.3204 target = 0.065745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.056919 restraints weight = 31956.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 2.86
r_work: 0.2864 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8802
moved from start:          0.5757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10476  Z= 0.163
  Angle     :  0.597   8.961  14304  Z= 0.302
  Chirality :  0.037   0.137   1704
  Planarity :  0.003   0.029   1674
  Dihedral  :  5.243  54.615   1746
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.49 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.41 (0.24), residues: 1218
  helix:  3.29 (0.16), residues: 888
  sheet: -0.50 (0.50), residues: 102
  loop : -0.84 (0.46), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  44 
 HIS   0.004   0.001   HIS E 123 
 PHE   0.006   0.001   PHE A 149 
 TYR   0.012   0.001   TYR D  65 
 ARG   0.003   0.000   ARG A 183 

*********************** 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
  242 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 217
  time to evaluate  : 1.172 
Fit side-chains
REVERT: A   57 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8301 (tm-30)
REVERT: A   94 HIS cc_start: 0.9054 (t70) cc_final: 0.8403 (t-90)
REVERT: A   98 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8802 (mm110)
REVERT: A  123 HIS cc_start: 0.8205 (t70) cc_final: 0.7898 (t70)
REVERT: B    7 TYR cc_start: 0.8824 (t80) cc_final: 0.8560 (t80)
REVERT: B   47 GLU cc_start: 0.7941 (tp30) cc_final: 0.7704 (tp30)
REVERT: B   57 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8142 (tm-30)
REVERT: B   94 HIS cc_start: 0.8884 (OUTLIER) cc_final: 0.8494 (t-90)
REVERT: B  144 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9067 (mm)
REVERT: C   57 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8238 (tm-30)
REVERT: C   60 CYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8615 (t)
REVERT: C   94 HIS cc_start: 0.9004 (t70) cc_final: 0.8508 (t-90)
REVERT: C  102 GLU cc_start: 0.9091 (tp30) cc_final: 0.8731 (mm-30)
REVERT: C  105 MET cc_start: 0.8467 (mtt) cc_final: 0.8239 (mtm)
REVERT: D   57 GLN cc_start: 0.8381 (tm-30) cc_final: 0.8048 (tm-30)
REVERT: D  102 GLU cc_start: 0.9089 (tp30) cc_final: 0.8699 (mm-30)
REVERT: E   57 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8096 (tm-30)
REVERT: E   60 CYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8486 (t)
REVERT: E  144 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9080 (mm)
REVERT: F   57 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7968 (tm-30)
REVERT: F   94 HIS cc_start: 0.8929 (t70) cc_final: 0.8344 (t-90)
REVERT: F  102 GLU cc_start: 0.9089 (tp30) cc_final: 0.8708 (mm-30)
REVERT: F  105 MET cc_start: 0.8416 (mtt) cc_final: 0.8196 (mtm)
  outliers start: 25
  outliers final: 17
  residues processed: 238
  average time/residue: 0.2195
  time to fit residues: 72.9746
Evaluate side-chains
  226 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 204
  time to evaluate  : 1.302 
-------------------------------------------------------------------------------
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   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   94 HIS
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain C residue   60 CYS
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain D residue   74 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   60 CYS
Chi-restraints excluded: chain E residue  144 LEU
Chi-restraints excluded: chain F residue   34 MET
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:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 5 optimal weight:    0.2980
   chunk 13 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 35 optimal weight:    0.5980
   chunk 61 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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**
C  98 GLN
** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  94 HIS
** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  94 HIS
E  98 GLN
** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3203 r_free = 0.3203 target = 0.064745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.056035 restraints weight = 32255.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.2995 rms_B_bonded: 2.99
r_work: 0.2863 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
moved from start:          0.5808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10476  Z= 0.184
  Angle     :  0.649  10.175  14304  Z= 0.321
  Chirality :  0.037   0.137   1704
  Planarity :  0.003   0.025   1674
  Dihedral  :  5.215  55.511   1746
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 17.29 %
    Favored  : 80.65 %
  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:  3.46 (0.24), residues: 1218
  helix:  3.34 (0.16), residues: 888
  sheet: -0.61 (0.49), residues: 102
  loop : -0.82 (0.46), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  44 
 HIS   0.004   0.001   HIS E 123 
 PHE   0.007   0.001   PHE E  31 
 TYR   0.015   0.001   TYR D  65 
 ARG   0.003   0.000   ARG A 183 

********************** 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
  228 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 205
  time to evaluate  : 1.187 
Fit side-chains
REVERT: A   47 GLU cc_start: 0.8094 (tp30) cc_final: 0.7615 (tm-30)
REVERT: A   57 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8209 (tm-30)
REVERT: A   94 HIS cc_start: 0.9059 (t70) cc_final: 0.8603 (t-90)
REVERT: A  123 HIS cc_start: 0.8229 (t70) cc_final: 0.7912 (t70)
REVERT: B   57 GLN cc_start: 0.8344 (tm-30) cc_final: 0.8079 (tm-30)
REVERT: B   65 TYR cc_start: 0.8914 (t80) cc_final: 0.8714 (t80)
REVERT: B   94 HIS cc_start: 0.8879 (OUTLIER) cc_final: 0.8459 (t-90)
REVERT: B  144 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9011 (mm)
REVERT: C   57 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8183 (tm-30)
REVERT: C   60 CYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8513 (t)
REVERT: C   94 HIS cc_start: 0.8992 (t70) cc_final: 0.8442 (t-90)
REVERT: C  102 GLU cc_start: 0.9131 (tp30) cc_final: 0.8780 (mm-30)
REVERT: C  105 MET cc_start: 0.8434 (mtt) cc_final: 0.8204 (mtm)
REVERT: D   57 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7935 (tm-30)
REVERT: D   94 HIS cc_start: 0.8967 (t70) cc_final: 0.8685 (t-90)
REVERT: D   98 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8601 (mp10)
REVERT: D  102 GLU cc_start: 0.9117 (tp30) cc_final: 0.8754 (mm-30)
REVERT: E   57 GLN cc_start: 0.8311 (tm-30) cc_final: 0.7985 (tm-30)
REVERT: E   60 CYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8449 (t)
REVERT: E  144 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9021 (mm)
REVERT: F    7 TYR cc_start: 0.8929 (t80) cc_final: 0.8702 (t80)
REVERT: F   47 GLU cc_start: 0.8115 (tp30) cc_final: 0.7826 (tp30)
REVERT: F   57 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7830 (tm-30)
REVERT: F   94 HIS cc_start: 0.8962 (t70) cc_final: 0.8351 (t-90)
REVERT: F  102 GLU cc_start: 0.9121 (tp30) cc_final: 0.8745 (mm-30)
REVERT: F  105 MET cc_start: 0.8396 (mtt) cc_final: 0.8189 (mtm)
REVERT: F  144 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9088 (mm)
  outliers start: 23
  outliers final: 15
  residues processed: 226
  average time/residue: 0.2210
  time to fit residues: 70.5245
Evaluate side-chains
  222 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 201
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
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   74 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   94 HIS
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain C residue   60 CYS
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain D residue   74 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   60 CYS
Chi-restraints excluded: chain E residue  144 LEU
Chi-restraints excluded: chain F residue   74 VAL
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:    6.9990
   chunk 64 optimal weight:    7.9990
   chunk 112 optimal weight:    0.9980
   chunk 51 optimal weight:    9.9990
   chunk 77 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 119 optimal weight:    0.7980
   chunk 81 optimal weight:    9.9990
   chunk 90 optimal weight:    0.7980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  94 HIS
E  98 GLN
** E 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3211 r_free = 0.3211 target = 0.065053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.056323 restraints weight = 32127.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 2.99
r_work: 0.2869 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8780
moved from start:          0.5830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10476  Z= 0.179
  Angle     :  0.649  10.064  14304  Z= 0.319
  Chirality :  0.037   0.139   1704
  Planarity :  0.003   0.024   1674
  Dihedral  :  5.219  56.108   1746
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 17.56 %
    Favored  : 80.29 %
  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:  3.37 (0.16), residues: 888
  sheet: -0.67 (0.49), residues: 102
  loop : -0.84 (0.46), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  44 
 HIS   0.004   0.001   HIS E 123 
 PHE   0.007   0.001   PHE B  31 
 TYR   0.021   0.001   TYR D   7 
 ARG   0.003   0.000   ARG A 183 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4063.01 seconds
wall clock time: 73 minutes 42.28 seconds (4422.28 seconds total)