Starting phenix.real_space_refine
on Wed Feb  4 03:43:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mkp_48333/02_2026/9mkp_48333.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mkp_48333/02_2026/9mkp_48333.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mkp_48333/02_2026/9mkp_48333.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mkp_48333/02_2026/9mkp_48333.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mkp_48333/02_2026/9mkp_48333.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mkp_48333/02_2026/9mkp_48333.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      65      5.16       5
     C    5265      2.51       5
     N    1560      2.21       5
     O    1605      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8495
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1699
          Classifications: {'peptide': 217}
          Link IDs: {'PTRANS': 10, 'TRANS': 206}
  Restraints were copied for chains:
    B, C, D, E
  Time building chain proxies: 1.23, per 1000 atoms: 0.14
  Number of scatterers: 8495
  At special positions: 0
  Unit cell: (104.94, 102.82, 80.56, 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      65     16.00
     O    1605      8.00
     N    1560      7.00
     C    5265      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 190 " - pdb=" SG  CYS A 214 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 190 " - pdb=" SG  CYS B 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 190 " - pdb=" SG  CYS C 214 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 190 " - pdb=" SG  CYS D 214 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 190 " - pdb=" SG  CYS E 214 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 317.9 milliseconds
  

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2050

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 5 sheets defined
      70.5% alpha, 1.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 30
    Processing helix  chain 'A' and resid 34 through 45
    Processing helix  chain 'A' and resid 49 through 60
    Processing helix  chain 'A' and resid 63 through 85
    Processing helix  chain 'A' and resid 95 through 100
    Processing helix  chain 'A' and resid 105 through 111
      removed outlier: 3.682A  pdb=" N   ALA A 110 " --> pdb=" O   ASN A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 136
      removed outlier: 3.629A  pdb=" N   GLN A 119 " --> pdb=" O   ASP A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 167
    Processing helix  chain 'A' and resid 170 through 185
      removed outlier: 4.181A  pdb=" N   TYR A 183 " --> pdb=" O   LEU A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 199
    Processing helix  chain 'A' and resid 200 through 202
      No H-bonds generated for 'chain 'A' and resid 200 through 202'
    Processing helix  chain 'A' and resid 206 through 212
    Processing helix  chain 'B' and resid 16 through 30
    Processing helix  chain 'B' and resid 34 through 45
    Processing helix  chain 'B' and resid 49 through 60
    Processing helix  chain 'B' and resid 63 through 85
    Processing helix  chain 'B' and resid 95 through 100
    Processing helix  chain 'B' and resid 105 through 111
      removed outlier: 3.682A  pdb=" N   ALA B 110 " --> pdb=" O   ASN B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 136
      removed outlier: 3.629A  pdb=" N   GLN B 119 " --> pdb=" O   ASP B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 167
    Processing helix  chain 'B' and resid 170 through 185
      removed outlier: 4.182A  pdb=" N   TYR B 183 " --> pdb=" O   LEU B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 199
    Processing helix  chain 'B' and resid 200 through 202
      No H-bonds generated for 'chain 'B' and resid 200 through 202'
    Processing helix  chain 'B' and resid 206 through 212
    Processing helix  chain 'C' and resid 16 through 30
    Processing helix  chain 'C' and resid 34 through 45
    Processing helix  chain 'C' and resid 49 through 60
    Processing helix  chain 'C' and resid 63 through 85
    Processing helix  chain 'C' and resid 95 through 100
    Processing helix  chain 'C' and resid 105 through 111
      removed outlier: 3.682A  pdb=" N   ALA C 110 " --> pdb=" O   ASN C 106 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 136
      removed outlier: 3.629A  pdb=" N   GLN C 119 " --> pdb=" O   ASP C 115 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 152 through 167
    Processing helix  chain 'C' and resid 170 through 185
      removed outlier: 4.181A  pdb=" N   TYR C 183 " --> pdb=" O   LEU C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 187 through 199
    Processing helix  chain 'C' and resid 200 through 202
      No H-bonds generated for 'chain 'C' and resid 200 through 202'
    Processing helix  chain 'C' and resid 206 through 212
    Processing helix  chain 'D' and resid 16 through 30
    Processing helix  chain 'D' and resid 34 through 45
    Processing helix  chain 'D' and resid 49 through 60
    Processing helix  chain 'D' and resid 63 through 85
    Processing helix  chain 'D' and resid 95 through 100
    Processing helix  chain 'D' and resid 105 through 111
      removed outlier: 3.683A  pdb=" N   ALA D 110 " --> pdb=" O   ASN D 106 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 114 through 136
      removed outlier: 3.629A  pdb=" N   GLN D 119 " --> pdb=" O   ASP D 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 152 through 167
    Processing helix  chain 'D' and resid 170 through 185
      removed outlier: 4.181A  pdb=" N   TYR D 183 " --> pdb=" O   LEU D 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 187 through 199
    Processing helix  chain 'D' and resid 200 through 202
      No H-bonds generated for 'chain 'D' and resid 200 through 202'
    Processing helix  chain 'D' and resid 206 through 212
    Processing helix  chain 'E' and resid 16 through 30
    Processing helix  chain 'E' and resid 34 through 45
    Processing helix  chain 'E' and resid 49 through 60
    Processing helix  chain 'E' and resid 63 through 85
    Processing helix  chain 'E' and resid 95 through 100
    Processing helix  chain 'E' and resid 105 through 111
      removed outlier: 3.682A  pdb=" N   ALA E 110 " --> pdb=" O   ASN E 106 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 114 through 136
      removed outlier: 3.629A  pdb=" N   GLN E 119 " --> pdb=" O   ASP E 115 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 152 through 167
    Processing helix  chain 'E' and resid 170 through 185
      removed outlier: 4.181A  pdb=" N   TYR E 183 " --> pdb=" O   LEU E 179 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 187 through 199
    Processing helix  chain 'E' and resid 200 through 202
      No H-bonds generated for 'chain 'E' and resid 200 through 202'
    Processing helix  chain 'E' and resid 206 through 212
    Processing sheet with id=1, first strand: chain 'A' and resid 2 through 4
    Processing sheet with id=2, first strand: chain 'B' and resid 2 through 4
    Processing sheet with id=3, first strand: chain 'C' and resid 2 through 4
    Processing sheet with id=4, first strand: chain 'D' and resid 2 through 4
    Processing sheet with id=5, first strand: chain 'E' and resid 2 through 4

    525 hydrogen bonds defined for protein.
    1575 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.25

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1706
        1.32 -     1.45: 1879
        1.45 -     1.57: 4940
        1.57 -     1.70: 0
        1.70 -     1.82: 115
  Bond restraints: 8640
  Sorted by residual:
  bond pdb=" CA  ALA E  45 "
       pdb=" CB  ALA E  45 "
    ideal  model  delta    sigma   weight residual
    1.529  1.467  0.061 1.40e-02 5.10e+03 1.92e+01
  bond pdb=" CA  ALA B  45 "
       pdb=" CB  ALA B  45 "
    ideal  model  delta    sigma   weight residual
    1.529  1.468  0.061 1.40e-02 5.10e+03 1.91e+01
  bond pdb=" CA  ALA A  45 "
       pdb=" CB  ALA A  45 "
    ideal  model  delta    sigma   weight residual
    1.529  1.468  0.061 1.40e-02 5.10e+03 1.90e+01
  bond pdb=" CA  ALA D  45 "
       pdb=" CB  ALA D  45 "
    ideal  model  delta    sigma   weight residual
    1.529  1.468  0.061 1.40e-02 5.10e+03 1.90e+01
  bond pdb=" CA  ALA C  45 "
       pdb=" CB  ALA C  45 "
    ideal  model  delta    sigma   weight residual
    1.529  1.468  0.061 1.40e-02 5.10e+03 1.88e+01
  ... (remaining 8635 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 7635
        1.67 -     3.34: 3231
        3.34 -     5.01: 674
        5.01 -     6.68: 130
        6.68 -     8.35: 25
  Bond angle restraints: 11695
  Sorted by residual:
  angle pdb=" N   ARG E  64 "
        pdb=" CA  ARG E  64 "
        pdb=" C   ARG E  64 "
      ideal   model   delta    sigma   weight residual
     112.54  104.80    7.74 1.22e+00 6.72e-01 4.03e+01
  angle pdb=" N   ARG B  64 "
        pdb=" CA  ARG B  64 "
        pdb=" C   ARG B  64 "
      ideal   model   delta    sigma   weight residual
     112.54  104.80    7.74 1.22e+00 6.72e-01 4.02e+01
  angle pdb=" N   ARG D  64 "
        pdb=" CA  ARG D  64 "
        pdb=" C   ARG D  64 "
      ideal   model   delta    sigma   weight residual
     112.54  104.81    7.73 1.22e+00 6.72e-01 4.01e+01
  angle pdb=" N   ARG A  64 "
        pdb=" CA  ARG A  64 "
        pdb=" C   ARG A  64 "
      ideal   model   delta    sigma   weight residual
     112.54  104.81    7.73 1.22e+00 6.72e-01 4.01e+01
  angle pdb=" N   ARG C  64 "
        pdb=" CA  ARG C  64 "
        pdb=" C   ARG C  64 "
      ideal   model   delta    sigma   weight residual
     112.54  104.81    7.73 1.22e+00 6.72e-01 4.01e+01
  ... (remaining 11690 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.85: 5090
       12.85 -    25.70: 120
       25.70 -    38.55: 95
       38.55 -    51.40: 0
       51.40 -    64.25: 65
  Dihedral angle restraints: 5370
    sinusoidal: 2215
      harmonic: 3155
  Sorted by residual:
  dihedral pdb=" CB  CYS B 190 "
           pdb=" SG  CYS B 190 "
           pdb=" SG  CYS B 214 "
           pdb=" CB  CYS B 214 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -60.74  -25.26     1      1.00e+01 1.00e-02 9.18e+00
  dihedral pdb=" CB  CYS D 190 "
           pdb=" SG  CYS D 190 "
           pdb=" SG  CYS D 214 "
           pdb=" CB  CYS D 214 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -60.74  -25.26     1      1.00e+01 1.00e-02 9.18e+00
  dihedral pdb=" CB  CYS E 190 "
           pdb=" SG  CYS E 190 "
           pdb=" SG  CYS E 214 "
           pdb=" CB  CYS E 214 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -60.74  -25.26     1      1.00e+01 1.00e-02 9.18e+00
  ... (remaining 5367 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 874
       0.098 -    0.196: 322
       0.196 -    0.294: 79
       0.294 -    0.392: 5
       0.392 -    0.490: 5
  Chirality restraints: 1285
  Sorted by residual:
  chirality pdb=" CG  LEU B 144 "
            pdb=" CB  LEU B 144 "
            pdb=" CD1 LEU B 144 "
            pdb=" CD2 LEU B 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.10   -0.49 2.00e-01 2.50e+01 6.01e+00
  chirality pdb=" CG  LEU C 144 "
            pdb=" CB  LEU C 144 "
            pdb=" CD1 LEU C 144 "
            pdb=" CD2 LEU C 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.10   -0.49 2.00e-01 2.50e+01 5.97e+00
  chirality pdb=" CG  LEU A 144 "
            pdb=" CB  LEU A 144 "
            pdb=" CD1 LEU A 144 "
            pdb=" CD2 LEU A 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.10   -0.49 2.00e-01 2.50e+01 5.96e+00
  ... (remaining 1282 not shown)

  Planarity restraints: 1560
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 210 "   -0.017 2.00e-02 2.50e+03   3.37e-02 1.14e+01
        pdb=" C   LYS B 210 "    0.058 2.00e-02 2.50e+03
        pdb=" O   LYS B 210 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   MET B 211 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 210 "   -0.017 2.00e-02 2.50e+03   3.37e-02 1.14e+01
        pdb=" C   LYS C 210 "    0.058 2.00e-02 2.50e+03
        pdb=" O   LYS C 210 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   MET C 211 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 210 "   -0.017 2.00e-02 2.50e+03   3.37e-02 1.13e+01
        pdb=" C   LYS A 210 "    0.058 2.00e-02 2.50e+03
        pdb=" O   LYS A 210 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   MET A 211 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1557 not shown)

  Histogram of nonbonded interaction distances:
        1.00 -     1.78: 10
        1.78 -     2.56: 85
        2.56 -     3.34: 12128
        3.34 -     4.12: 20504
        4.12 -     4.90: 37196
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 69923
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP C 216 "
            pdb=" ND1 HIS D 137 "
     model   vdw
     0.998 3.120
  nonbonded pdb=" OD1 ASP A 216 "
            pdb=" ND1 HIS B 137 "
     model   vdw
     0.998 3.120
  nonbonded pdb=" OD1 ASP D 216 "
            pdb=" ND1 HIS E 137 "
     model   vdw
     0.998 3.120
  nonbonded pdb=" ND1 HIS A 137 "
            pdb=" OD1 ASP E 216 "
     model   vdw
     0.998 3.120
  nonbonded pdb=" OD1 ASP B 216 "
            pdb=" ND1 HIS C 137 "
     model   vdw
     0.999 3.120
  ... (remaining 69918 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.410
  Find NCS groups from input model:        0.070
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
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      :  0.013   0.061   8645  Z= 0.933
  Angle     :  1.854   8.352  11705  Z= 1.410
  Chirality :  0.106   0.490   1285
  Planarity :  0.008   0.069   1560
  Dihedral  : 10.881  64.248   3305
  Min Nonbonded Distance : 0.998

Molprobity Statistics.
  All-atom Clashscore : 20.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  4.47 %
    Favored  : 94.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.26), residues: 1075
  helix:  0.78 (0.20), residues: 680
  sheet:  0.71 (0.67), residues: 45
  loop :  0.32 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.002   ARG B 133 
 TYR   0.017   0.003   TYR C  43 
 PHE   0.015   0.003   PHE E 156 
 TRP   0.030   0.006   TRP C 124 
 HIS   0.009   0.002   HIS C 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.01254 ( 8640)
  covalent geometry    : angle       1.85138 (11695)
  SS BOND              : bond        0.00464 (    5)
  SS BOND              : angle       3.64345 (   10)
  hydrogen bonds       : bond        0.21074 (  525)
  hydrogen bonds       : angle       8.15264 ( 1575)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 212
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 PRO cc_start: 0.8632 (OUTLIER) cc_final: 0.8367 (Cg_exo)
REVERT: A   13 LYS cc_start: 0.8292 (pttt) cc_final: 0.8038 (pttt)
REVERT: B    1 PRO cc_start: 0.8742 (OUTLIER) cc_final: 0.8309 (Cg_endo)
REVERT: B   13 LYS cc_start: 0.8203 (pttt) cc_final: 0.7194 (pttt)
REVERT: B  114 MET cc_start: 0.8085 (mmt) cc_final: 0.7754 (mmt)
REVERT: B  182 SER cc_start: 0.7735 (m) cc_final: 0.7519 (t)
REVERT: C    1 PRO cc_start: 0.8786 (OUTLIER) cc_final: 0.8357 (Cg_endo)
REVERT: C   13 LYS cc_start: 0.8267 (pttt) cc_final: 0.7392 (pttt)
REVERT: C   73 LYS cc_start: 0.9148 (mmmt) cc_final: 0.8899 (mmmm)
REVERT: C   85 ASN cc_start: 0.8437 (m-40) cc_final: 0.8186 (m110)
REVERT: D    1 PRO cc_start: 0.8727 (OUTLIER) cc_final: 0.8499 (Cg_exo)
REVERT: D   13 LYS cc_start: 0.8094 (pttt) cc_final: 0.7732 (pttt)
REVERT: D   20 PHE cc_start: 0.7992 (m-10) cc_final: 0.7764 (m-10)
REVERT: D   73 LYS cc_start: 0.9177 (mmmt) cc_final: 0.8945 (mmmm)
REVERT: D  114 MET cc_start: 0.8079 (mmt) cc_final: 0.7823 (mmt)
REVERT: D  153 TYR cc_start: 0.6930 (t80) cc_final: 0.6424 (t80)
REVERT: E    1 PRO cc_start: 0.8725 (OUTLIER) cc_final: 0.8372 (Cg_endo)
REVERT: E   13 LYS cc_start: 0.8056 (pttt) cc_final: 0.7115 (pttt)
REVERT: E  153 TYR cc_start: 0.6788 (t80) cc_final: 0.6386 (t80)
  outliers start: 5
  outliers final: 0
  residues processed: 217
  average time/residue: 0.1262
  time to fit residues: 35.0720
Evaluate side-chains
  113 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 PRO
Chi-restraints excluded: chain B residue    1 PRO
Chi-restraints excluded: chain C residue    1 PRO
Chi-restraints excluded: chain D residue    1 PRO
Chi-restraints excluded: chain E residue    1 PRO
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   chunk 100 optimal weight:    9.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   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  22 GLN
A  40 GLN
A 111 GLN
A 137 HIS
A 185 ASN
A 212 GLN
** B  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  85 ASN
B 111 GLN
B 137 HIS
B 185 ASN
B 212 GLN
** C  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 ASN
C 111 GLN
C 137 HIS
** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 212 GLN
D  22 GLN
D  40 GLN
D 111 GLN
D 137 HIS
** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 212 GLN
E  22 GLN
E  40 GLN
E  85 ASN
E 111 GLN
E 137 HIS
** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 212 GLN

Total number of N/Q/H flips: 26

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.077809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.054722 restraints weight = 25675.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.057788 restraints weight = 11302.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.059764 restraints weight = 6986.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.060988 restraints weight = 5160.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.061702 restraints weight = 4299.680|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7599
moved from start:          0.3514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   8645  Z= 0.164
  Angle     :  0.594   5.552  11705  Z= 0.316
  Chirality :  0.039   0.139   1285
  Planarity :  0.004   0.042   1560
  Dihedral  :  4.161  18.220   1190
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  :  9.39 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.25), residues: 1075
  helix:  1.07 (0.18), residues: 760
  sheet:  0.04 (0.68), residues: 45
  loop :  0.52 (0.41), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  83 
 TYR   0.022   0.002   TYR C 153 
 PHE   0.012   0.001   PHE E  20 
 TRP   0.029   0.003   TRP D 124 
 HIS   0.010   0.003   HIS D 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 8640)
  covalent geometry    : angle       0.59166 (11695)
  SS BOND              : bond        0.00310 (    5)
  SS BOND              : angle       1.77196 (   10)
  hydrogen bonds       : bond        0.04910 (  525)
  hydrogen bonds       : angle       4.79323 ( 1575)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 134
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 MET cc_start: 0.9007 (mmt) cc_final: 0.8759 (mmt)
REVERT: A  113 ASN cc_start: 0.7582 (p0) cc_final: 0.7365 (p0)
REVERT: A  135 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8075 (tmm)
REVERT: A  181 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7423 (tp)
REVERT: A  182 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8422 (p)
REVERT: B   19 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6749 (ttm)
REVERT: B  100 MET cc_start: 0.9115 (mmt) cc_final: 0.8418 (mmt)
REVERT: B  148 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8490 (mmtt)
REVERT: B  153 TYR cc_start: 0.6537 (t80) cc_final: 0.6119 (t80)
REVERT: C   10 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7970 (mtp85)
REVERT: C   73 LYS cc_start: 0.9091 (mmmt) cc_final: 0.8743 (mmmm)
REVERT: C  181 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7516 (tp)
REVERT: D   73 LYS cc_start: 0.9186 (mmmt) cc_final: 0.8853 (mmmm)
REVERT: E  100 MET cc_start: 0.9133 (mmt) cc_final: 0.8903 (mmt)
  outliers start: 20
  outliers final: 3
  residues processed: 141
  average time/residue: 0.0985
  time to fit residues: 18.5461
Evaluate side-chains
  114 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain B residue   19 MET
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain C residue   10 ARG
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain C residue  182 SER
Chi-restraints excluded: chain D residue   22 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 10 optimal weight:   10.0000
   chunk 77 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 104 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 81 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 70 optimal weight:    9.9990
   chunk 41 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
B  21 GLN
** B  22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 ASN
C  22 GLN
C  40 GLN
C  75 ASN
D  22 GLN
** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  21 GLN
** E  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  66 GLN
** E 185 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 = 0.3477 r_free = 0.3477 target = 0.075739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.052137 restraints weight = 25907.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.055047 restraints weight = 12194.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.056866 restraints weight = 7758.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.058005 restraints weight = 5862.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.058656 restraints weight = 4944.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.4308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8645  Z= 0.176
  Angle     :  0.557   8.079  11705  Z= 0.284
  Chirality :  0.037   0.105   1285
  Planarity :  0.004   0.034   1560
  Dihedral  :  3.853  19.279   1175
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 11.06 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.77 (0.26), residues: 1075
  helix:  1.52 (0.19), residues: 735
  sheet:  0.68 (0.81), residues: 45
  loop :  0.60 (0.39), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  83 
 TYR   0.014   0.001   TYR E 153 
 PHE   0.009   0.001   PHE A  20 
 TRP   0.019   0.002   TRP B 124 
 HIS   0.007   0.002   HIS E 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 8640)
  covalent geometry    : angle       0.55595 (11695)
  SS BOND              : bond        0.00068 (    5)
  SS BOND              : angle       1.29539 (   10)
  hydrogen bonds       : bond        0.04241 (  525)
  hydrogen bonds       : angle       4.39143 ( 1575)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 105
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.8179 (m-80) cc_final: 0.7559 (t80)
REVERT: A  100 MET cc_start: 0.9061 (mmt) cc_final: 0.8803 (mmt)
REVERT: A  113 ASN cc_start: 0.7702 (p0) cc_final: 0.7443 (p0)
REVERT: A  135 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8141 (tmm)
REVERT: B   20 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7724 (t80)
REVERT: B   75 ASN cc_start: 0.9341 (OUTLIER) cc_final: 0.9081 (m-40)
REVERT: C   10 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8144 (mtm-85)
REVERT: C   20 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.8016 (t80)
REVERT: C   22 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7508 (tt0)
REVERT: C  135 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7990 (tmm)
REVERT: C  181 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7541 (tp)
REVERT: D   20 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7635 (t80)
REVERT: E   20 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7578 (t80)
REVERT: E  100 MET cc_start: 0.9193 (mmt) cc_final: 0.8931 (mmt)
  outliers start: 31
  outliers final: 11
  residues processed: 125
  average time/residue: 0.1017
  time to fit residues: 17.2899
Evaluate side-chains
  116 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   75 ASN
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain C residue   10 ARG
Chi-restraints excluded: chain C residue   20 PHE
Chi-restraints excluded: chain C residue   22 GLN
Chi-restraints excluded: chain C residue  135 MET
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain D residue   20 PHE
Chi-restraints excluded: chain D residue   57 LEU
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  182 SER
Chi-restraints excluded: chain E residue   20 PHE
Chi-restraints excluded: chain E residue  169 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 74 optimal weight:   20.0000
   chunk 97 optimal weight:    0.2980
   chunk 104 optimal weight:   20.0000
   chunk 44 optimal weight:    2.9990
   chunk 57 optimal weight:   10.0000
   chunk 38 optimal weight:    8.9990
   chunk 9 optimal weight:   10.0000
   chunk 86 optimal weight:    0.7980
   chunk 28 optimal weight:    9.9990
   chunk 73 optimal weight:    9.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    3.2186

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

Flipped N/Q/H residues before XYZ refinement:
A  21 GLN
A  66 GLN
B  22 GLN
B  40 GLN
B  75 ASN
D  40 GLN
E  40 GLN
** E 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.074653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.051064 restraints weight = 26598.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.053911 restraints weight = 12368.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.055750 restraints weight = 7835.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.056897 restraints weight = 5895.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.057592 restraints weight = 4956.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.4707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8645  Z= 0.175
  Angle     :  0.536   5.962  11705  Z= 0.274
  Chirality :  0.037   0.105   1285
  Planarity :  0.005   0.048   1560
  Dihedral  :  3.761  19.745   1175
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 11.51 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.26), residues: 1075
  helix:  1.39 (0.19), residues: 760
  sheet:  0.67 (0.82), residues: 45
  loop :  0.29 (0.40), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  83 
 TYR   0.023   0.001   TYR D 153 
 PHE   0.008   0.001   PHE C  20 
 TRP   0.012   0.001   TRP B 124 
 HIS   0.006   0.002   HIS E 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 8640)
  covalent geometry    : angle       0.53553 (11695)
  SS BOND              : bond        0.00034 (    5)
  SS BOND              : angle       1.20840 (   10)
  hydrogen bonds       : bond        0.03904 (  525)
  hydrogen bonds       : angle       4.27064 ( 1575)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7496 (t80)
REVERT: A  100 MET cc_start: 0.9175 (mmt) cc_final: 0.8861 (mmt)
REVERT: A  113 ASN cc_start: 0.7783 (p0) cc_final: 0.7535 (p0)
REVERT: A  135 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8196 (tmm)
REVERT: A  148 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8617 (mmtt)
REVERT: A  181 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7520 (tt)
REVERT: B  135 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8370 (tmm)
REVERT: B  178 LYS cc_start: 0.8265 (ttpt) cc_final: 0.8019 (mtmm)
REVERT: C   10 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8201 (mtm-85)
REVERT: C   73 LYS cc_start: 0.9207 (mmmm) cc_final: 0.8849 (mmtp)
REVERT: C  181 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7442 (tp)
REVERT: D   20 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.7559 (t80)
REVERT: D  182 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8754 (p)
REVERT: E   20 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7687 (t80)
REVERT: E  100 MET cc_start: 0.9233 (mmt) cc_final: 0.8975 (mmt)
REVERT: E  135 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8353 (tmm)
REVERT: E  181 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7556 (tp)
  outliers start: 27
  outliers final: 11
  residues processed: 117
  average time/residue: 0.1045
  time to fit residues: 16.6713
Evaluate side-chains
  117 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  182 SER
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain C residue   10 ARG
Chi-restraints excluded: chain C residue  135 MET
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain D residue   20 PHE
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  135 MET
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  182 SER
Chi-restraints excluded: chain E residue   20 PHE
Chi-restraints excluded: chain E residue  135 MET
Chi-restraints excluded: chain E residue  169 VAL
Chi-restraints excluded: chain E residue  181 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 51 optimal weight:    0.1980
   chunk 34 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 76 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9980
   chunk 98 optimal weight:    0.0370
   chunk 42 optimal weight:   10.0000
   chunk 101 optimal weight:    0.8980
   chunk 19 optimal weight:    7.9990
   chunk 68 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
B 116 GLN
D 134 HIS
D 185 ASN
E 134 HIS
E 185 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.076955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.053659 restraints weight = 26444.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.056688 restraints weight = 12096.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.058619 restraints weight = 7530.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.059816 restraints weight = 5581.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.060553 restraints weight = 4649.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.5242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8645  Z= 0.100
  Angle     :  0.477   7.218  11705  Z= 0.241
  Chirality :  0.035   0.120   1285
  Planarity :  0.004   0.043   1560
  Dihedral  :  3.517  18.044   1175
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 12.74 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.01 (0.26), residues: 1075
  helix:  1.79 (0.19), residues: 735
  sheet:  0.95 (0.81), residues: 45
  loop :  0.40 (0.39), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  83 
 TYR   0.019   0.001   TYR A 153 
 PHE   0.005   0.001   PHE A 156 
 TRP   0.011   0.001   TRP C 124 
 HIS   0.003   0.001   HIS C 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 8640)
  covalent geometry    : angle       0.47585 (11695)
  SS BOND              : bond        0.00259 (    5)
  SS BOND              : angle       1.31735 (   10)
  hydrogen bonds       : bond        0.03241 (  525)
  hydrogen bonds       : angle       3.92590 ( 1575)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7264 (t80)
REVERT: A  100 MET cc_start: 0.9142 (mmt) cc_final: 0.8900 (mmt)
REVERT: A  113 ASN cc_start: 0.7419 (p0) cc_final: 0.7219 (p0)
REVERT: A  135 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8191 (tmm)
REVERT: B  135 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8362 (tmm)
REVERT: B  178 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7979 (mtmm)
REVERT: C   10 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8209 (mtp85)
REVERT: C   73 LYS cc_start: 0.9196 (mmmm) cc_final: 0.8833 (mmtp)
REVERT: C  135 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8014 (tmm)
REVERT: C  181 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7690 (tp)
REVERT: D   20 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7124 (t80)
REVERT: D   21 GLN cc_start: 0.8290 (mm110) cc_final: 0.7955 (tp-100)
REVERT: D  181 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7369 (tp)
REVERT: E  100 MET cc_start: 0.9211 (mmt) cc_final: 0.9008 (mmt)
REVERT: E  135 MET cc_start: 0.8764 (ttm) cc_final: 0.8460 (tmm)
REVERT: E  181 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7539 (tp)
  outliers start: 25
  outliers final: 13
  residues processed: 127
  average time/residue: 0.1031
  time to fit residues: 17.8500
Evaluate side-chains
  123 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  151 GLU
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain C residue   10 ARG
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain C residue   20 PHE
Chi-restraints excluded: chain C residue  135 MET
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain D residue   20 PHE
Chi-restraints excluded: chain D residue  151 GLU
Chi-restraints excluded: chain D residue  169 VAL
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain E residue   20 PHE
Chi-restraints excluded: chain E residue  169 VAL
Chi-restraints excluded: chain E residue  181 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 73 optimal weight:    0.0570
   chunk 104 optimal weight:   10.0000
   chunk 94 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   chunk 64 optimal weight:    8.9990
   chunk 100 optimal weight:    6.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    4.0106

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

Flipped N/Q/H residues before XYZ refinement:
A  66 GLN
A  75 ASN
A 147 GLN
B  66 GLN
B 116 GLN
C  66 GLN
D  66 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.073801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.049867 restraints weight = 26616.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.052674 restraints weight = 12726.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.054461 restraints weight = 8155.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.055506 restraints weight = 6205.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.056255 restraints weight = 5272.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.5254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8645  Z= 0.205
  Angle     :  0.561   6.846  11705  Z= 0.282
  Chirality :  0.037   0.129   1285
  Planarity :  0.004   0.054   1560
  Dihedral  :  3.683  19.314   1175
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 14.08 %
    Favored  : 82.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.26), residues: 1075
  helix:  1.63 (0.19), residues: 720
  sheet:  0.80 (0.83), residues: 45
  loop :  0.35 (0.38), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 159 
 TYR   0.022   0.001   TYR D 153 
 PHE   0.005   0.001   PHE B  20 
 TRP   0.004   0.001   TRP C 124 
 HIS   0.005   0.002   HIS C 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 8640)
  covalent geometry    : angle       0.55950 (11695)
  SS BOND              : bond        0.00101 (    5)
  SS BOND              : angle       1.44042 (   10)
  hydrogen bonds       : bond        0.03853 (  525)
  hydrogen bonds       : angle       4.08569 ( 1575)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 96
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7458 (t80)
REVERT: A  100 MET cc_start: 0.9245 (mmt) cc_final: 0.8993 (mmt)
REVERT: A  135 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8211 (tmm)
REVERT: A  181 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7497 (tt)
REVERT: B   20 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7603 (t80)
REVERT: B  135 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8442 (tmm)
REVERT: B  178 LYS cc_start: 0.8219 (ttpt) cc_final: 0.7975 (mtmm)
REVERT: C   10 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8179 (mtm-85)
REVERT: C   59 MET cc_start: 0.8618 (ptp) cc_final: 0.8404 (ptp)
REVERT: C   73 LYS cc_start: 0.9216 (mmmm) cc_final: 0.8744 (mmtp)
REVERT: C  181 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7586 (tp)
REVERT: C  194 MET cc_start: 0.8925 (mtm) cc_final: 0.8686 (mtm)
REVERT: D   20 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7443 (t80)
REVERT: D   21 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8206 (tp40)
REVERT: D   60 MET cc_start: 0.8630 (mmm) cc_final: 0.8193 (mmm)
REVERT: D  181 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7358 (tp)
REVERT: E   20 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7647 (t80)
REVERT: E  100 MET cc_start: 0.9255 (mmt) cc_final: 0.8962 (mmt)
REVERT: E  135 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8377 (tmm)
REVERT: E  181 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7416 (tp)
REVERT: E  194 MET cc_start: 0.8889 (mtp) cc_final: 0.8622 (mpp)
  outliers start: 31
  outliers final: 10
  residues processed: 115
  average time/residue: 0.1102
  time to fit residues: 17.2646
Evaluate side-chains
  118 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain C residue   10 ARG
Chi-restraints excluded: chain C residue  135 MET
Chi-restraints excluded: chain C residue  151 GLU
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain D residue   20 PHE
Chi-restraints excluded: chain D residue   21 GLN
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain E residue    2 ILE
Chi-restraints excluded: chain E residue   20 PHE
Chi-restraints excluded: chain E residue  135 MET
Chi-restraints excluded: chain E residue  169 VAL
Chi-restraints excluded: chain E residue  181 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 84 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 95 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 38 optimal weight:    9.9990
   chunk 54 optimal weight:    0.8980
   chunk 43 optimal weight:    7.9990
   chunk 18 optimal weight:   10.0000
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  75 ASN
B 134 HIS
D  75 ASN
E  71 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.073986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.050042 restraints weight = 27072.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.052845 restraints weight = 12928.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.054602 restraints weight = 8290.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.055750 restraints weight = 6315.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.056446 restraints weight = 5320.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.5445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8645  Z= 0.177
  Angle     :  0.532   7.325  11705  Z= 0.269
  Chirality :  0.036   0.117   1285
  Planarity :  0.004   0.039   1560
  Dihedral  :  3.681  18.623   1175
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 14.08 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.69 (0.26), residues: 1075
  helix:  1.60 (0.19), residues: 725
  sheet:  0.49 (0.82), residues: 45
  loop :  0.21 (0.39), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  83 
 TYR   0.008   0.001   TYR D 153 
 PHE   0.004   0.001   PHE C  20 
 TRP   0.005   0.001   TRP C 124 
 HIS   0.005   0.001   HIS C 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8640)
  covalent geometry    : angle       0.53096 (11695)
  SS BOND              : bond        0.00124 (    5)
  SS BOND              : angle       1.38932 (   10)
  hydrogen bonds       : bond        0.03623 (  525)
  hydrogen bonds       : angle       4.02808 ( 1575)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 96
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.7370 (t80)
REVERT: A  100 MET cc_start: 0.9253 (mmt) cc_final: 0.9043 (mmt)
REVERT: A  135 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8200 (tmm)
REVERT: A  181 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7561 (tp)
REVERT: B  100 MET cc_start: 0.9076 (mmt) cc_final: 0.8650 (mmt)
REVERT: B  135 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8384 (tmm)
REVERT: B  178 LYS cc_start: 0.8281 (ttpt) cc_final: 0.8040 (mtmm)
REVERT: C   10 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8202 (mtm-85)
REVERT: C   20 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7768 (t80)
REVERT: C   73 LYS cc_start: 0.9213 (mmmm) cc_final: 0.8846 (mmtp)
REVERT: C  181 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7635 (tp)
REVERT: D   20 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7375 (t80)
REVERT: D   21 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8044 (tp-100)
REVERT: D  100 MET cc_start: 0.9108 (mmt) cc_final: 0.8790 (mmt)
REVERT: D  135 MET cc_start: 0.8755 (ttm) cc_final: 0.8013 (tmm)
REVERT: D  181 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7384 (tp)
REVERT: E   20 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7704 (t80)
REVERT: E  100 MET cc_start: 0.9263 (mmt) cc_final: 0.8989 (mmt)
REVERT: E  135 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8362 (tmm)
REVERT: E  181 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7385 (tp)
REVERT: E  194 MET cc_start: 0.8878 (mtp) cc_final: 0.8610 (mpp)
  outliers start: 30
  outliers final: 13
  residues processed: 112
  average time/residue: 0.1064
  time to fit residues: 16.2275
Evaluate side-chains
  121 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   19 MET
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain C residue   10 ARG
Chi-restraints excluded: chain C residue   20 PHE
Chi-restraints excluded: chain C residue  135 MET
Chi-restraints excluded: chain C residue  151 GLU
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain D residue   20 PHE
Chi-restraints excluded: chain D residue   21 GLN
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain D residue  181 LEU
Chi-restraints excluded: chain E residue    2 ILE
Chi-restraints excluded: chain E residue   20 PHE
Chi-restraints excluded: chain E residue  135 MET
Chi-restraints excluded: chain E residue  169 VAL
Chi-restraints excluded: chain E residue  181 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 20 optimal weight:    8.9990
   chunk 100 optimal weight:    8.9990
   chunk 26 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 88 optimal weight:    4.9990
   chunk 63 optimal weight:   10.0000
   chunk 68 optimal weight:    5.9990
   chunk 50 optimal weight:    8.9990
   chunk 102 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 77 optimal weight:    9.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  75 ASN
B  40 GLN
B 116 GLN
C  40 GLN
E  71 GLN
E  75 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.072798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.048810 restraints weight = 27038.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.051490 restraints weight = 13216.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.053228 restraints weight = 8588.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.054337 restraints weight = 6543.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.055029 restraints weight = 5534.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.5428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   8645  Z= 0.253
  Angle     :  0.607   7.464  11705  Z= 0.305
  Chirality :  0.038   0.126   1285
  Planarity :  0.004   0.041   1560
  Dihedral  :  3.852  19.621   1175
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 14.75 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.26), residues: 1075
  helix:  1.45 (0.19), residues: 720
  sheet:  0.19 (0.83), residues: 45
  loop :  0.08 (0.38), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 118 
 TYR   0.008   0.001   TYR A  43 
 PHE   0.005   0.001   PHE C  20 
 TRP   0.005   0.001   TRP C 124 
 HIS   0.007   0.002   HIS E 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00581 ( 8640)
  covalent geometry    : angle       0.60597 (11695)
  SS BOND              : bond        0.00141 (    5)
  SS BOND              : angle       1.44140 (   10)
  hydrogen bonds       : bond        0.04014 (  525)
  hydrogen bonds       : angle       4.23487 ( 1575)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 91
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7503 (t80)
REVERT: A  100 MET cc_start: 0.9278 (mmt) cc_final: 0.9070 (mmt)
REVERT: A  181 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7356 (tp)
REVERT: A  194 MET cc_start: 0.9049 (mtp) cc_final: 0.8519 (mpp)
REVERT: B  135 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8349 (tmm)
REVERT: B  178 LYS cc_start: 0.8278 (ttpt) cc_final: 0.8016 (mtmm)
REVERT: C   10 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8425 (mtm-85)
REVERT: C   20 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7773 (t80)
REVERT: C   73 LYS cc_start: 0.9217 (mmmm) cc_final: 0.8748 (mmtp)
REVERT: C  181 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7679 (tp)
REVERT: C  194 MET cc_start: 0.8802 (mtm) cc_final: 0.8561 (mtm)
REVERT: D   20 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7542 (t80)
REVERT: D   21 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8211 (tp40)
REVERT: D   60 MET cc_start: 0.8642 (mmm) cc_final: 0.8197 (mmm)
REVERT: D  135 MET cc_start: 0.8821 (ttm) cc_final: 0.8016 (tmm)
REVERT: E   20 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7746 (t80)
REVERT: E  100 MET cc_start: 0.9281 (mmt) cc_final: 0.8998 (mmt)
REVERT: E  135 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8373 (tmm)
REVERT: E  181 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7377 (tp)
REVERT: E  194 MET cc_start: 0.8905 (mtp) cc_final: 0.8584 (mpp)
  outliers start: 28
  outliers final: 13
  residues processed: 108
  average time/residue: 0.1062
  time to fit residues: 15.6076
Evaluate side-chains
  113 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain B residue   19 MET
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain C residue   10 ARG
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain C residue   20 PHE
Chi-restraints excluded: chain C residue  135 MET
Chi-restraints excluded: chain C residue  151 GLU
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain D residue   20 PHE
Chi-restraints excluded: chain D residue   21 GLN
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain E residue    2 ILE
Chi-restraints excluded: chain E residue   20 PHE
Chi-restraints excluded: chain E residue  135 MET
Chi-restraints excluded: chain E residue  169 VAL
Chi-restraints excluded: chain E residue  181 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 40 optimal weight:    8.9990
   chunk 98 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 104 optimal weight:    9.9990
   chunk 17 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 134 HIS
B  40 GLN
C 134 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.075226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.051411 restraints weight = 26821.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.054307 restraints weight = 12720.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.056158 restraints weight = 8140.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.057341 restraints weight = 6144.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.058044 restraints weight = 5162.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.5649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8645  Z= 0.130
  Angle     :  0.511   7.821  11705  Z= 0.255
  Chirality :  0.035   0.116   1285
  Planarity :  0.004   0.038   1560
  Dihedral  :  3.646  18.092   1175
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 15.20 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.26), residues: 1075
  helix:  1.61 (0.19), residues: 725
  sheet:  0.31 (0.83), residues: 45
  loop :  0.06 (0.39), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 159 
 TYR   0.006   0.001   TYR D 153 
 PHE   0.003   0.001   PHE E 156 
 TRP   0.007   0.001   TRP C 124 
 HIS   0.004   0.001   HIS C 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 8640)
  covalent geometry    : angle       0.50954 (11695)
  SS BOND              : bond        0.00194 (    5)
  SS BOND              : angle       1.39313 (   10)
  hydrogen bonds       : bond        0.03364 (  525)
  hydrogen bonds       : angle       3.96453 ( 1575)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7283 (t80)
REVERT: A   44 TYR cc_start: 0.8527 (m-10) cc_final: 0.8292 (m-10)
REVERT: A  135 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8108 (tmm)
REVERT: A  181 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7431 (tp)
REVERT: A  194 MET cc_start: 0.9070 (mtp) cc_final: 0.8538 (mpp)
REVERT: B  135 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8323 (tmm)
REVERT: B  178 LYS cc_start: 0.8284 (ttpt) cc_final: 0.8063 (mtmm)
REVERT: C   10 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8402 (mtm-85)
REVERT: C   20 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7804 (t80)
REVERT: C   73 LYS cc_start: 0.9216 (mmmm) cc_final: 0.8879 (mmtp)
REVERT: C  181 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7641 (tp)
REVERT: C  194 MET cc_start: 0.8803 (mtm) cc_final: 0.8584 (mtm)
REVERT: D   20 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7373 (t80)
REVERT: D   21 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7963 (tp-100)
REVERT: D  135 MET cc_start: 0.8751 (ttm) cc_final: 0.8211 (tmm)
REVERT: D  194 MET cc_start: 0.9078 (mtp) cc_final: 0.8335 (mpp)
REVERT: E   13 LYS cc_start: 0.7907 (ptmm) cc_final: 0.7657 (ptmm)
REVERT: E   20 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7656 (t80)
REVERT: E  100 MET cc_start: 0.9255 (mmt) cc_final: 0.9031 (mmt)
REVERT: E  135 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8489 (tmm)
REVERT: E  181 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7347 (tp)
REVERT: E  194 MET cc_start: 0.8871 (mtp) cc_final: 0.8641 (mpp)
  outliers start: 29
  outliers final: 11
  residues processed: 112
  average time/residue: 0.0931
  time to fit residues: 14.0987
Evaluate side-chains
  117 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain C residue   10 ARG
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   20 PHE
Chi-restraints excluded: chain C residue  135 MET
Chi-restraints excluded: chain C residue  151 GLU
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain D residue   20 PHE
Chi-restraints excluded: chain D residue   21 GLN
Chi-restraints excluded: chain E residue   20 PHE
Chi-restraints excluded: chain E residue  135 MET
Chi-restraints excluded: chain E residue  169 VAL
Chi-restraints excluded: chain E residue  181 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 93 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 36 optimal weight:    6.9990
   chunk 43 optimal weight:   10.0000
   chunk 80 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 99 optimal weight:    6.9990
   chunk 79 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   overall best weight:    4.1188

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

Flipped N/Q/H residues before XYZ refinement:
** C 185 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 = 0.3431 r_free = 0.3431 target = 0.073458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.049394 restraints weight = 26824.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.052144 restraints weight = 12932.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.053915 restraints weight = 8341.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.055059 restraints weight = 6332.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.055758 restraints weight = 5331.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.5619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8645  Z= 0.207
  Angle     :  0.563   8.196  11705  Z= 0.281
  Chirality :  0.037   0.118   1285
  Planarity :  0.004   0.040   1560
  Dihedral  :  3.737  19.135   1175
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 15.31 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.54 (0.26), residues: 1075
  helix:  1.55 (0.19), residues: 720
  sheet: -0.16 (0.79), residues: 45
  loop :  0.10 (0.39), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  83 
 TYR   0.007   0.001   TYR A  43 
 PHE   0.005   0.001   PHE B  20 
 TRP   0.004   0.001   TRP C 124 
 HIS   0.006   0.002   HIS C 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 8640)
  covalent geometry    : angle       0.56191 (11695)
  SS BOND              : bond        0.00127 (    5)
  SS BOND              : angle       1.40679 (   10)
  hydrogen bonds       : bond        0.03749 (  525)
  hydrogen bonds       : angle       4.10554 ( 1575)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 PHE cc_start: 0.8082 (OUTLIER) cc_final: 0.7386 (t80)
REVERT: A  181 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7350 (tp)
REVERT: A  194 MET cc_start: 0.9064 (mtp) cc_final: 0.8555 (mpp)
REVERT: B   20 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7497 (t80)
REVERT: B  135 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8325 (tmm)
REVERT: B  178 LYS cc_start: 0.8239 (ttpt) cc_final: 0.8028 (mtmm)
REVERT: C   10 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8407 (mtm-85)
REVERT: C   20 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7768 (t80)
REVERT: C   73 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8746 (mmtp)
REVERT: C  181 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7629 (tp)
REVERT: C  194 MET cc_start: 0.8842 (mtm) cc_final: 0.8553 (mtm)
REVERT: D   20 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7505 (t80)
REVERT: D   21 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8137 (tp40)
REVERT: D  135 MET cc_start: 0.8783 (ttm) cc_final: 0.8213 (tmm)
REVERT: D  194 MET cc_start: 0.9044 (mtp) cc_final: 0.8261 (mpp)
REVERT: E   20 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7711 (t80)
REVERT: E  100 MET cc_start: 0.9245 (mmt) cc_final: 0.8993 (mmt)
REVERT: E  135 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8368 (tmm)
REVERT: E  181 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7339 (tp)
REVERT: E  194 MET cc_start: 0.8863 (mtp) cc_final: 0.8581 (mpp)
  outliers start: 25
  outliers final: 13
  residues processed: 107
  average time/residue: 0.0918
  time to fit residues: 13.5590
Evaluate side-chains
  116 residues out of total 895 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 91
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  211 MET
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  181 LEU
Chi-restraints excluded: chain C residue   10 ARG
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain C residue   18 VAL
Chi-restraints excluded: chain C residue   20 PHE
Chi-restraints excluded: chain C residue  135 MET
Chi-restraints excluded: chain C residue  151 GLU
Chi-restraints excluded: chain C residue  169 VAL
Chi-restraints excluded: chain C residue  181 LEU
Chi-restraints excluded: chain D residue   20 PHE
Chi-restraints excluded: chain D residue   21 GLN
Chi-restraints excluded: chain D residue  122 LEU
Chi-restraints excluded: chain E residue   20 PHE
Chi-restraints excluded: chain E residue  135 MET
Chi-restraints excluded: chain E residue  169 VAL
Chi-restraints excluded: chain E residue  181 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0060
   chunk 81 optimal weight:   20.0000
   chunk 57 optimal weight:   10.0000
   chunk 92 optimal weight:    8.9990
   chunk 63 optimal weight:   10.0000
   chunk 74 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0980
   chunk 40 optimal weight:    5.9990
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
B  66 GLN
B 116 GLN
C  22 GLN
C  40 GLN
** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  66 GLN
D 147 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.075817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.052869 restraints weight = 25831.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.055472 restraints weight = 12667.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.057215 restraints weight = 8221.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.058289 restraints weight = 6272.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.058894 restraints weight = 5313.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.5944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8645  Z= 0.097
  Angle     :  0.491   7.988  11705  Z= 0.242
  Chirality :  0.035   0.120   1285
  Planarity :  0.004   0.037   1560
  Dihedral  :  3.520  17.150   1175
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.64 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.74 (0.27), residues: 1075
  helix:  1.77 (0.20), residues: 725
  sheet: -0.15 (0.79), residues: 45
  loop : -0.02 (0.38), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 159 
 TYR   0.007   0.000   TYR A  44 
 PHE   0.003   0.001   PHE E 156 
 TRP   0.010   0.001   TRP E 124 
 HIS   0.003   0.001   HIS C 137 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 8640)
  covalent geometry    : angle       0.48957 (11695)
  SS BOND              : bond        0.00228 (    5)
  SS BOND              : angle       1.38174 (   10)
  hydrogen bonds       : bond        0.02993 (  525)
  hydrogen bonds       : angle       3.80511 ( 1575)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1462.29 seconds
wall clock time: 26 minutes 2.73 seconds (1562.73 seconds total)