Starting phenix.real_space_refine
on Wed May 14 07:03:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jbx_36148/05_2025/8jbx_36148_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jbx_36148/05_2025/8jbx_36148.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jbx_36148/05_2025/8jbx_36148.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jbx_36148/05_2025/8jbx_36148.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jbx_36148/05_2025/8jbx_36148_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jbx_36148/05_2025/8jbx_36148_neut.cif"
  }
  resolution = 3.35
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.028
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: 5
    Type Number    sf(0)   Gaussians
     P     288      5.49       5
     S      14      5.16       5
     C    6564      2.51       5
     N    2227      2.21       5
     O    2788      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11881
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 824
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 799
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 824
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 2952
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2952
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 6.57, per 1000 atoms: 0.55
  Number of scatterers: 11881
  At special positions: 0
  Unit cell: (75.26, 118.72, 117.66, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     288     15.00
     O    2788      8.00
     N    2227      7.00
     C    6564      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.52
  Conformation dependent library (CDL) restraints added in 799.5 milliseconds
  

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1400

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 9 sheets defined
      72.7% alpha, 2.7% beta
      142 base pairs and 240 stacking pairs defined.
    Time for finding SS restraints: 5.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.751A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.644A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.300A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.422A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.832A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 124
      removed outlier: 3.554A  pdb=" N   SER D 124 " --> pdb=" O   LYS D 120 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.522A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 3.692A  pdb=" N   GLY F  28 " --> pdb=" O   ASN F  25 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 25 through 29'
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.629A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 72
      removed outlier: 4.330A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'H' and resid 38 through 49
      removed outlier: 3.612A  pdb=" N   TYR H  42 " --> pdb=" O   SER H  38 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 83
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 123
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.422A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.602A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.390A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102
      removed outlier: 3.712A  pdb=" N   TYR F  98 " --> pdb=" O   THR C 101 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.252A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.525A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78

    403 hydrogen bonds defined for protein.
    1203 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      364 hydrogen bonds
      728 hydrogen bond angles
      0 basepair planarities
      142 basepair parallelities
      240 stacking parallelities
  Total time for adding SS restraints: 3.98

  Time building geometry restraints manager: 3.03 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2342
        1.33 -     1.45: 4166
        1.45 -     1.57: 5576
        1.57 -     1.69: 576
        1.69 -     1.81: 24
  Bond restraints: 12684
  Sorted by residual:
  bond pdb=" C1'  DA I  72 "
       pdb=" N9   DA I  72 "
    ideal  model  delta    sigma   weight residual
    1.460  1.388  0.072 2.00e-02 2.50e+03 1.30e+01
  bond pdb=" CA  ASP F  85 "
       pdb=" C   ASP F  85 "
    ideal  model  delta    sigma   weight residual
    1.524  1.481  0.043 1.26e-02 6.30e+03 1.14e+01
  bond pdb=" CA  SER E  57 "
       pdb=" C   SER E  57 "
    ideal  model  delta    sigma   weight residual
    1.528  1.493  0.035 1.35e-02 5.49e+03 6.57e+00
  bond pdb=" CA  ASP F  85 "
       pdb=" CB  ASP F  85 "
    ideal  model  delta    sigma   weight residual
    1.529  1.493  0.036 1.58e-02 4.01e+03 5.06e+00
  bond pdb=" C   ASP F  85 "
       pdb=" N   VAL F  86 "
    ideal  model  delta    sigma   weight residual
    1.335  1.312  0.023 1.26e-02 6.30e+03 3.36e+00
  ... (remaining 12679 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 17871
        1.64 -     3.29: 459
        3.29 -     4.93: 32
        4.93 -     6.57: 8
        6.57 -     8.21: 3
  Bond angle restraints: 18373
  Sorted by residual:
  angle pdb=" N   ASP F  85 "
        pdb=" CA  ASP F  85 "
        pdb=" C   ASP F  85 "
      ideal   model   delta    sigma   weight residual
     111.14  104.13    7.01 1.08e+00 8.57e-01 4.21e+01
  angle pdb=" C   THR E  80 "
        pdb=" N   ASP E  81 "
        pdb=" CA  ASP E  81 "
      ideal   model   delta    sigma   weight residual
     121.54  126.83   -5.29 1.91e+00 2.74e-01 7.67e+00
  angle pdb=" CB  MET F  84 "
        pdb=" CG  MET F  84 "
        pdb=" SD  MET F  84 "
      ideal   model   delta    sigma   weight residual
     112.70  120.91   -8.21 3.00e+00 1.11e-01 7.50e+00
  angle pdb=" C   THR A  80 "
        pdb=" N   ASP A  81 "
        pdb=" CA  ASP A  81 "
      ideal   model   delta    sigma   weight residual
     121.54  126.48   -4.94 1.91e+00 2.74e-01 6.70e+00
  angle pdb=" CB  MET E  90 "
        pdb=" CG  MET E  90 "
        pdb=" SD  MET E  90 "
      ideal   model   delta    sigma   weight residual
     112.70  120.33   -7.63 3.00e+00 1.11e-01 6.47e+00
  ... (remaining 18368 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.60: 5445
       35.60 -    71.19: 1419
       71.19 -   106.78: 11
      106.78 -   142.38: 3
      142.38 -   177.97: 1
  Dihedral angle restraints: 6879
    sinusoidal: 4707
      harmonic: 2172
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   37.97 -177.97     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC J  34 "
           pdb=" C3'  DC J  34 "
           pdb=" O3'  DC J  34 "
           pdb=" P    DT J  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   87.58  132.42     1      3.50e+01 8.16e-04 1.31e+01
  dihedral pdb=" C4'  DA J -38 "
           pdb=" C3'  DA J -38 "
           pdb=" O3'  DA J -38 "
           pdb=" P    DG J -37 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   92.19  127.81     1      3.50e+01 8.16e-04 1.26e+01
  ... (remaining 6876 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1540
       0.033 -    0.066: 443
       0.066 -    0.099: 72
       0.099 -    0.132: 30
       0.132 -    0.164: 5
  Chirality restraints: 2090
  Sorted by residual:
  chirality pdb=" CA  ASP E  81 "
            pdb=" N   ASP E  81 "
            pdb=" C   ASP E  81 "
            pdb=" CB  ASP E  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.76e-01
  chirality pdb=" CA  ILE D  89 "
            pdb=" N   ILE D  89 "
            pdb=" C   ILE D  89 "
            pdb=" CB  ILE D  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.72e-01
  chirality pdb=" CB  ILE A 112 "
            pdb=" CA  ILE A 112 "
            pdb=" CG1 ILE A 112 "
            pdb=" CG2 ILE A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.47e-01
  ... (remaining 2087 not shown)

  Planarity restraints: 1320
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET F  84 "    0.015 2.00e-02 2.50e+03   3.12e-02 9.76e+00
        pdb=" C   MET F  84 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   MET F  84 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ASP F  85 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS D  49 "   -0.046 5.00e-02 4.00e+02   7.01e-02 7.87e+00
        pdb=" N   PRO D  50 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO D  50 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO D  50 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F  88 "   -0.001 2.00e-02 2.50e+03   1.28e-02 3.28e+00
        pdb=" CG  TYR F  88 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR F  88 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 TYR F  88 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR F  88 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR F  88 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  TYR F  88 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR F  88 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1317 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2028
        2.77 -     3.31: 10993
        3.31 -     3.84: 24017
        3.84 -     4.37: 26289
        4.37 -     4.90: 38419
  Nonbonded interactions: 101746
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG C  81 "
            pdb=" O   GLY C 106 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" NH2 ARG F  92 "
            pdb=" OE1 GLU H  76 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" O   SER D 124 "
            pdb=" OG  SER D 124 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" NH2 ARG C  20 "
            pdb=" OP1  DT I -42 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" OH  TYR E  99 "
            pdb=" OE2 GLU E 133 "
     model   vdw
     2.279 3.040
  ... (remaining 101741 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and resid 38 through 133)
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 32 through 124)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.580
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     29.200
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:2.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  12684  Z= 0.181
  Angle     :  0.584   8.214  18373  Z= 0.347
  Chirality :  0.033   0.164   2090
  Planarity :  0.004   0.070   1320
  Dihedral  : 28.645 177.973   5479
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  : 30.83 %
    Favored  : 68.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.32), residues: 734
  helix:  1.91 (0.22), residues: 539
  sheet:  None (None), residues: 0
  loop : -1.08 (0.45), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.001   HIS D  82 
 PHE   0.007   0.001   PHE E  78 
 TYR   0.024   0.002   TYR D 121 
 ARG   0.007   0.000   ARG B  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09436 (  767)
  hydrogen bonds       : angle       3.58959 ( 1931)
  covalent geometry    : bond        0.00387 (12684)
  covalent geometry    : angle       0.58389 (18373)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  272 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 269
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   76 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8619 (tm-30)
REVERT: A   87 SER cc_start: 0.9548 (p) cc_final: 0.9231 (t)
REVERT: A   94 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8435 (tp30)
REVERT: A  125 GLN cc_start: 0.9096 (mt0) cc_final: 0.8830 (mt0)
REVERT: D   42 TYR cc_start: 0.7666 (t80) cc_final: 0.7155 (t80)
REVERT: D   68 ASP cc_start: 0.9156 (t0) cc_final: 0.8905 (t0)
REVERT: D   89 ILE cc_start: 0.9181 (mm) cc_final: 0.8864 (mm)
REVERT: E   74 ILE cc_start: 0.9535 (tt) cc_final: 0.9303 (tt)
REVERT: E   76 GLN cc_start: 0.9055 (pp30) cc_final: 0.8822 (pp30)
REVERT: E  108 ASN cc_start: 0.9476 (t0) cc_final: 0.9140 (t0)
REVERT: F   63 GLU cc_start: 0.8866 (tt0) cc_final: 0.8620 (mt-10)
REVERT: F   80 THR cc_start: 0.9432 (t) cc_final: 0.8985 (p)
REVERT: G   35 ARG cc_start: 0.9079 (mtm110) cc_final: 0.8756 (mtm-85)
REVERT: G   59 THR cc_start: 0.9519 (m) cc_final: 0.9303 (t)
REVERT: G   71 ARG cc_start: 0.9184 (ttp-110) cc_final: 0.8769 (ttp-110)
REVERT: G  100 VAL cc_start: 0.9353 (t) cc_final: 0.9109 (p)
REVERT: G  101 THR cc_start: 0.9279 (m) cc_final: 0.8910 (t)
REVERT: H   45 LEU cc_start: 0.9633 (tp) cc_final: 0.9383 (tt)
REVERT: H  113 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8180 (tm-30)
  outliers start: 3
  outliers final: 0
  residues processed: 270
  average time/residue: 0.3033
  time to fit residues: 106.7577
Evaluate side-chains
  222 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    8.9990
   chunk 74 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9980
   chunk 25 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9980
   chunk 39 optimal weight:    7.9990
   chunk 76 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   chunk 57 optimal weight:    8.9990
   chunk 88 optimal weight:    7.9990
   overall best weight:    3.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 ASN
D  63 ASN
E  55 GLN
E  68 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.057517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.042179 restraints weight = 46095.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.2766 rms_B_bonded: 2.44
r_work: 0.2605 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  12684  Z= 0.241
  Angle     :  0.620   7.909  18373  Z= 0.360
  Chirality :  0.036   0.169   2090
  Planarity :  0.004   0.055   1320
  Dihedral  : 30.837 177.943   3997
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 27.00 %
    Favored  : 68.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.31), residues: 734
  helix:  2.01 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -1.08 (0.44), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.010   0.001   PHE B 100 
 TYR   0.013   0.002   TYR C  39 
 ARG   0.005   0.001   ARG H  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04183 (  767)
  hydrogen bonds       : angle       3.04888 ( 1931)
  covalent geometry    : bond        0.00541 (12684)
  covalent geometry    : angle       0.62015 (18373)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 232
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8412 (pm20) cc_final: 0.8184 (pm20)
REVERT: A   76 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8791 (tm-30)
REVERT: A   87 SER cc_start: 0.9418 (p) cc_final: 0.9212 (t)
REVERT: A   94 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8668 (tp30)
REVERT: B   27 GLN cc_start: 0.8641 (pt0) cc_final: 0.8352 (pm20)
REVERT: B   31 LYS cc_start: 0.9441 (tttt) cc_final: 0.9123 (tttp)
REVERT: B   53 GLU cc_start: 0.8804 (tp30) cc_final: 0.8079 (tp30)
REVERT: B   84 MET cc_start: 0.8997 (tpp) cc_final: 0.8430 (tpt)
REVERT: B   92 ARG cc_start: 0.9430 (ttp80) cc_final: 0.9013 (ttp80)
REVERT: C   99 ARG cc_start: 0.8904 (tpp80) cc_final: 0.8702 (tpp80)
REVERT: D   42 TYR cc_start: 0.7889 (t80) cc_final: 0.7508 (t80)
REVERT: D   47 GLN cc_start: 0.9149 (tm-30) cc_final: 0.8880 (tm-30)
REVERT: D   68 ASP cc_start: 0.9122 (t0) cc_final: 0.8763 (t0)
REVERT: D   79 ARG cc_start: 0.9362 (mtm180) cc_final: 0.9159 (ttp-110)
REVERT: D   89 ILE cc_start: 0.8973 (mm) cc_final: 0.8667 (mm)
REVERT: D  105 GLU cc_start: 0.8943 (tp30) cc_final: 0.8152 (tp30)
REVERT: E   42 ARG cc_start: 0.8269 (ttm-80) cc_final: 0.7935 (ttm110)
REVERT: E   74 ILE cc_start: 0.9161 (tt) cc_final: 0.8939 (tt)
REVERT: E   76 GLN cc_start: 0.9197 (pp30) cc_final: 0.8867 (pp30)
REVERT: E  108 ASN cc_start: 0.9517 (t0) cc_final: 0.9243 (t0)
REVERT: F   63 GLU cc_start: 0.9166 (tt0) cc_final: 0.8820 (mt-10)
REVERT: G   35 ARG cc_start: 0.9437 (mtm110) cc_final: 0.8789 (mtm-85)
REVERT: G   59 THR cc_start: 0.9299 (m) cc_final: 0.9023 (t)
REVERT: G   73 ASN cc_start: 0.9318 (OUTLIER) cc_final: 0.8971 (t0)
REVERT: G  100 VAL cc_start: 0.9667 (t) cc_final: 0.9146 (p)
REVERT: G  101 THR cc_start: 0.9092 (m) cc_final: 0.8589 (t)
REVERT: H   40 TYR cc_start: 0.9197 (m-80) cc_final: 0.8947 (m-80)
REVERT: H  105 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8065 (mm-30)
REVERT: H  113 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8388 (tm-30)
  outliers start: 28
  outliers final: 16
  residues processed: 247
  average time/residue: 0.2918
  time to fit residues: 95.6563
Evaluate side-chains
  233 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 216
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   40 SER
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   98 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 91 optimal weight:    6.9990
   chunk 11 optimal weight:    0.8980
   chunk 2 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   chunk 52 optimal weight:    7.9990
   chunk 92 optimal weight:    7.9990
   chunk 97 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.055425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.040383 restraints weight = 48396.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.2683 rms_B_bonded: 2.70
r_work: 0.2513 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077  12684  Z= 0.271
  Angle     :  0.645   7.395  18373  Z= 0.371
  Chirality :  0.037   0.164   2090
  Planarity :  0.004   0.042   1320
  Dihedral  : 30.995 177.376   3997
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  5.91 %
    Allowed  : 28.12 %
    Favored  : 65.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.83 (0.31), residues: 734
  helix:  1.97 (0.22), residues: 537
  sheet:  None (None), residues: 0
  loop : -0.93 (0.44), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.008   0.001   PHE B 100 
 TYR   0.045   0.002   TYR D  40 
 ARG   0.009   0.001   ARG D  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04270 (  767)
  hydrogen bonds       : angle       3.12267 ( 1931)
  covalent geometry    : bond        0.00614 (12684)
  covalent geometry    : angle       0.64461 (18373)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 219
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8620 (pm20) cc_final: 0.8323 (pm20)
REVERT: A   68 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8914 (tt0)
REVERT: A   76 GLN cc_start: 0.9106 (tm-30) cc_final: 0.8771 (tm-30)
REVERT: A   94 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8741 (tp30)
REVERT: B   27 GLN cc_start: 0.8704 (pt0) cc_final: 0.8420 (pm20)
REVERT: B   31 LYS cc_start: 0.9457 (tttt) cc_final: 0.9168 (tttp)
REVERT: B   53 GLU cc_start: 0.8877 (tp30) cc_final: 0.8157 (tp30)
REVERT: B   84 MET cc_start: 0.8927 (tpp) cc_final: 0.8471 (tpt)
REVERT: B   92 ARG cc_start: 0.9440 (ttp80) cc_final: 0.8976 (ttp80)
REVERT: C   61 GLU cc_start: 0.8992 (tp30) cc_final: 0.8588 (tp30)
REVERT: C   64 GLU cc_start: 0.9373 (pp20) cc_final: 0.9046 (pp20)
REVERT: D   42 TYR cc_start: 0.7966 (t80) cc_final: 0.7564 (t80)
REVERT: D   47 GLN cc_start: 0.9218 (tm-30) cc_final: 0.8954 (tm-30)
REVERT: D   68 ASP cc_start: 0.9130 (t0) cc_final: 0.8777 (t0)
REVERT: D   89 ILE cc_start: 0.8950 (mm) cc_final: 0.8640 (mm)
REVERT: D  105 GLU cc_start: 0.8984 (tp30) cc_final: 0.8433 (tp30)
REVERT: E   72 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7986 (mtt90)
REVERT: E   76 GLN cc_start: 0.9185 (pp30) cc_final: 0.8829 (pp30)
REVERT: F   53 GLU cc_start: 0.9244 (tp30) cc_final: 0.8979 (tp30)
REVERT: F   84 MET cc_start: 0.8862 (mmm) cc_final: 0.8585 (tmm)
REVERT: F   85 ASP cc_start: 0.8994 (m-30) cc_final: 0.8593 (m-30)
REVERT: G   59 THR cc_start: 0.9289 (m) cc_final: 0.8950 (t)
REVERT: G   73 ASN cc_start: 0.9349 (OUTLIER) cc_final: 0.9121 (t0)
REVERT: G   91 GLU cc_start: 0.8857 (tp30) cc_final: 0.8617 (tp30)
REVERT: G   92 GLU cc_start: 0.9366 (mp0) cc_final: 0.8987 (tt0)
REVERT: G  100 VAL cc_start: 0.9687 (t) cc_final: 0.9209 (p)
REVERT: G  101 THR cc_start: 0.9232 (m) cc_final: 0.8755 (t)
REVERT: H  113 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8427 (tm-30)
  outliers start: 37
  outliers final: 23
  residues processed: 243
  average time/residue: 0.2848
  time to fit residues: 92.1511
Evaluate side-chains
  234 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 208
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   72 ARG
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   40 SER
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   98 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 88 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   chunk 96 optimal weight:    8.9990
   chunk 84 optimal weight:    8.9990
   chunk 3 optimal weight:    2.9990
   chunk 72 optimal weight:    8.9990
   chunk 37 optimal weight:    8.9990
   chunk 61 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 86 optimal weight:    7.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  63 ASN
E  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.053924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.039192 restraints weight = 48617.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.2651 rms_B_bonded: 2.69
r_work: 0.2482 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.2482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8753
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059  12684  Z= 0.314
  Angle     :  0.667   7.943  18373  Z= 0.386
  Chirality :  0.038   0.164   2090
  Planarity :  0.004   0.044   1320
  Dihedral  : 31.181 177.244   3997
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  7.67 %
    Allowed  : 26.68 %
    Favored  : 65.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.31), residues: 734
  helix:  1.93 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.94 (0.44), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.010   0.001   PHE B 100 
 TYR   0.052   0.003   TYR D  40 
 ARG   0.009   0.001   ARG D  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04706 (  767)
  hydrogen bonds       : angle       3.25692 ( 1931)
  covalent geometry    : bond        0.00711 (12684)
  covalent geometry    : angle       0.66701 (18373)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 215
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8776 (pm20) cc_final: 0.8406 (pm20)
REVERT: A   68 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8915 (tp40)
REVERT: A   76 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8755 (tm-30)
REVERT: A   94 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8821 (tp30)
REVERT: A  133 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7632 (pm20)
REVERT: B   27 GLN cc_start: 0.8745 (pt0) cc_final: 0.8431 (pm20)
REVERT: B   31 LYS cc_start: 0.9478 (tttt) cc_final: 0.9205 (tttp)
REVERT: B   53 GLU cc_start: 0.9008 (tp30) cc_final: 0.8226 (tp30)
REVERT: B   84 MET cc_start: 0.8822 (tpp) cc_final: 0.8034 (tpp)
REVERT: B   88 TYR cc_start: 0.8889 (OUTLIER) cc_final: 0.8183 (m-80)
REVERT: B   92 ARG cc_start: 0.9424 (ttp80) cc_final: 0.9063 (ttp80)
REVERT: C   61 GLU cc_start: 0.9068 (tp30) cc_final: 0.8704 (tp30)
REVERT: C   64 GLU cc_start: 0.9377 (OUTLIER) cc_final: 0.9021 (pp20)
REVERT: C   84 GLN cc_start: 0.9553 (tp-100) cc_final: 0.9334 (tp-100)
REVERT: D   42 TYR cc_start: 0.7990 (t80) cc_final: 0.7640 (t80)
REVERT: D   47 GLN cc_start: 0.9236 (tm-30) cc_final: 0.8895 (tm-30)
REVERT: D   68 ASP cc_start: 0.9147 (t0) cc_final: 0.8754 (t0)
REVERT: D   89 ILE cc_start: 0.8954 (mm) cc_final: 0.8647 (mm)
REVERT: D  105 GLU cc_start: 0.8986 (tp30) cc_final: 0.8585 (tp30)
REVERT: E   76 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8848 (pp30)
REVERT: F   53 GLU cc_start: 0.9272 (tp30) cc_final: 0.9027 (tp30)
REVERT: F   84 MET cc_start: 0.9032 (mmm) cc_final: 0.8582 (tmm)
REVERT: F   85 ASP cc_start: 0.9033 (m-30) cc_final: 0.8608 (m-30)
REVERT: G   73 ASN cc_start: 0.9357 (OUTLIER) cc_final: 0.9006 (t0)
REVERT: G   75 LYS cc_start: 0.8952 (mmmm) cc_final: 0.8731 (mmmm)
REVERT: G  100 VAL cc_start: 0.9714 (t) cc_final: 0.9212 (p)
REVERT: G  101 THR cc_start: 0.9304 (m) cc_final: 0.8848 (t)
REVERT: H  113 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8486 (tm-30)
  outliers start: 48
  outliers final: 32
  residues processed: 242
  average time/residue: 0.2776
  time to fit residues: 90.4988
Evaluate side-chains
  244 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 206
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   71 THR
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   88 TYR
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  102 ILE
Chi-restraints excluded: chain C residue  104 GLN
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   25 ASN
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   30 VAL
Chi-restraints excluded: chain G residue   40 SER
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   73 ILE
Chi-restraints excluded: chain H residue   98 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 92 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 81 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 79 optimal weight:    8.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 ASN
E  93 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  64 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.057124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.042201 restraints weight = 46338.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.2760 rms_B_bonded: 2.48
r_work: 0.2597 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.2317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12684  Z= 0.177
  Angle     :  0.602   6.553  18373  Z= 0.353
  Chirality :  0.034   0.171   2090
  Planarity :  0.004   0.046   1320
  Dihedral  : 30.963 177.842   3997
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 30.67 %
    Favored  : 65.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.31), residues: 734
  helix:  2.09 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.87 (0.44), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS E  39 
 PHE   0.008   0.001   PHE B 100 
 TYR   0.011   0.002   TYR G  57 
 ARG   0.011   0.001   ARG B  95 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03739 (  767)
  hydrogen bonds       : angle       2.92990 ( 1931)
  covalent geometry    : bond        0.00395 (12684)
  covalent geometry    : angle       0.60232 (18373)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 231
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8660 (pm20) cc_final: 0.8296 (pm20)
REVERT: A   76 GLN cc_start: 0.9075 (tm-30) cc_final: 0.8688 (tm-30)
REVERT: A   94 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8667 (tp30)
REVERT: B   27 GLN cc_start: 0.8752 (pt0) cc_final: 0.8418 (pm20)
REVERT: B   31 LYS cc_start: 0.9457 (tttt) cc_final: 0.9159 (tttp)
REVERT: B   53 GLU cc_start: 0.8812 (tp30) cc_final: 0.8148 (tp30)
REVERT: B   84 MET cc_start: 0.8860 (tpp) cc_final: 0.8230 (tpp)
REVERT: B   88 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.8114 (m-80)
REVERT: B   92 ARG cc_start: 0.9366 (ttp80) cc_final: 0.8880 (ttp80)
REVERT: C   61 GLU cc_start: 0.8992 (tp30) cc_final: 0.8569 (tp30)
REVERT: C   64 GLU cc_start: 0.9365 (OUTLIER) cc_final: 0.8997 (pp20)
REVERT: D   42 TYR cc_start: 0.7877 (t80) cc_final: 0.7563 (t80)
REVERT: D   47 GLN cc_start: 0.9238 (tm-30) cc_final: 0.8891 (tm-30)
REVERT: D   68 ASP cc_start: 0.9131 (t0) cc_final: 0.8778 (t0)
REVERT: D   83 TYR cc_start: 0.8430 (t80) cc_final: 0.8062 (t80)
REVERT: D  105 GLU cc_start: 0.8918 (tp30) cc_final: 0.8358 (tp30)
REVERT: E   76 GLN cc_start: 0.9184 (pp30) cc_final: 0.8843 (pp30)
REVERT: F   53 GLU cc_start: 0.9227 (tp30) cc_final: 0.8952 (tp30)
REVERT: F   63 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8857 (mt-10)
REVERT: F   74 GLU cc_start: 0.9458 (tp30) cc_final: 0.9226 (tp30)
REVERT: F   84 MET cc_start: 0.8932 (mmm) cc_final: 0.8444 (tmm)
REVERT: F   85 ASP cc_start: 0.8918 (m-30) cc_final: 0.8522 (m-30)
REVERT: G   35 ARG cc_start: 0.9427 (mtm110) cc_final: 0.8767 (mtm-85)
REVERT: G   59 THR cc_start: 0.9271 (m) cc_final: 0.8967 (t)
REVERT: G   73 ASN cc_start: 0.9339 (OUTLIER) cc_final: 0.9133 (t0)
REVERT: G   75 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8163 (mmmm)
REVERT: G   91 GLU cc_start: 0.8778 (tp30) cc_final: 0.8552 (tp30)
REVERT: G   92 GLU cc_start: 0.9380 (mp0) cc_final: 0.9057 (mt-10)
REVERT: G  100 VAL cc_start: 0.9672 (t) cc_final: 0.9226 (p)
REVERT: H  113 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8444 (tm-30)
  outliers start: 27
  outliers final: 16
  residues processed: 245
  average time/residue: 0.2900
  time to fit residues: 94.8244
Evaluate side-chains
  239 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 219
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   62 ILE
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   88 TYR
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain D residue  108 LYS
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   98 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 92 optimal weight:    7.9990
   chunk 83 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 95 optimal weight:    8.9990
   chunk 64 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 90 optimal weight:    7.9990
   chunk 30 optimal weight:    6.9990
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
E  93 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  64 ASN
G  38 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.054874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.039917 restraints weight = 48233.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.2679 rms_B_bonded: 2.68
r_work: 0.2510 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.2510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8741
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  12684  Z= 0.251
  Angle     :  0.634   6.490  18373  Z= 0.369
  Chirality :  0.036   0.165   2090
  Planarity :  0.004   0.036   1320
  Dihedral  : 31.108 177.526   3997
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 29.55 %
    Favored  : 64.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.31), residues: 734
  helix:  1.99 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.72 (0.46), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  75 
 PHE   0.009   0.001   PHE B 100 
 TYR   0.036   0.002   TYR D  40 
 ARG   0.008   0.001   ARG H  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04282 (  767)
  hydrogen bonds       : angle       3.09259 ( 1931)
  covalent geometry    : bond        0.00568 (12684)
  covalent geometry    : angle       0.63364 (18373)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 218
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8682 (pm20) cc_final: 0.8324 (pm20)
REVERT: A   68 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8921 (tp40)
REVERT: A   76 GLN cc_start: 0.9103 (tm-30) cc_final: 0.8716 (tm-30)
REVERT: A   94 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8682 (tp30)
REVERT: A  133 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7533 (pm20)
REVERT: B   27 GLN cc_start: 0.8760 (pt0) cc_final: 0.8408 (pm20)
REVERT: B   31 LYS cc_start: 0.9487 (tttt) cc_final: 0.9170 (tttp)
REVERT: B   53 GLU cc_start: 0.8959 (tp30) cc_final: 0.8212 (tp30)
REVERT: B   84 MET cc_start: 0.8883 (tpp) cc_final: 0.8190 (tpp)
REVERT: B   88 TYR cc_start: 0.8889 (OUTLIER) cc_final: 0.8216 (m-80)
REVERT: B   92 ARG cc_start: 0.9368 (ttp80) cc_final: 0.9026 (ttp80)
REVERT: C   61 GLU cc_start: 0.9033 (tp30) cc_final: 0.8623 (tp30)
REVERT: C   64 GLU cc_start: 0.9382 (pp20) cc_final: 0.9033 (pp20)
REVERT: C   84 GLN cc_start: 0.9482 (tp-100) cc_final: 0.9134 (tp-100)
REVERT: C   88 ARG cc_start: 0.9087 (mmt90) cc_final: 0.8734 (mmt90)
REVERT: D   42 TYR cc_start: 0.7965 (t80) cc_final: 0.7639 (t80)
REVERT: D   47 GLN cc_start: 0.9247 (tm-30) cc_final: 0.8929 (tm-30)
REVERT: D   68 ASP cc_start: 0.9133 (t0) cc_final: 0.8774 (t0)
REVERT: D   83 TYR cc_start: 0.8618 (t80) cc_final: 0.8033 (t80)
REVERT: D  105 GLU cc_start: 0.8995 (tp30) cc_final: 0.8538 (tp30)
REVERT: E   76 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8880 (pp30)
REVERT: F   53 GLU cc_start: 0.9261 (tp30) cc_final: 0.9007 (tp30)
REVERT: F   63 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.8608 (mt-10)
REVERT: F   84 MET cc_start: 0.9006 (mmm) cc_final: 0.8592 (mmm)
REVERT: F   85 ASP cc_start: 0.8973 (m-30) cc_final: 0.8526 (m-30)
REVERT: G   73 ASN cc_start: 0.9355 (OUTLIER) cc_final: 0.9155 (t0)
REVERT: G   75 LYS cc_start: 0.8949 (mmmm) cc_final: 0.8183 (mmmm)
REVERT: G  100 VAL cc_start: 0.9699 (t) cc_final: 0.9199 (p)
REVERT: G  101 THR cc_start: 0.9301 (m) cc_final: 0.8820 (t)
REVERT: H  113 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8516 (tm-30)
  outliers start: 36
  outliers final: 22
  residues processed: 238
  average time/residue: 0.2784
  time to fit residues: 89.3442
Evaluate side-chains
  237 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 209
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   68 GLN
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   88 TYR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain H residue   98 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 63 optimal weight:    8.9990
   chunk 95 optimal weight:    8.9990
   chunk 72 optimal weight:    8.9990
   chunk 78 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.057926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.043112 restraints weight = 46371.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.2793 rms_B_bonded: 2.51
r_work: 0.2631 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8695
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12684  Z= 0.160
  Angle     :  0.602   8.044  18373  Z= 0.351
  Chirality :  0.034   0.163   2090
  Planarity :  0.004   0.035   1320
  Dihedral  : 30.913 177.874   3997
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 32.91 %
    Favored  : 64.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.31), residues: 734
  helix:  2.01 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.67 (0.46), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E  39 
 PHE   0.008   0.001   PHE B 100 
 TYR   0.032   0.002   TYR D  40 
 ARG   0.007   0.000   ARG H  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03617 (  767)
  hydrogen bonds       : angle       2.90009 ( 1931)
  covalent geometry    : bond        0.00354 (12684)
  covalent geometry    : angle       0.60175 (18373)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 236
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8608 (pm20) cc_final: 0.8262 (pm20)
REVERT: A   94 GLU cc_start: 0.9066 (mm-30) cc_final: 0.8742 (tp30)
REVERT: B   27 GLN cc_start: 0.8744 (pt0) cc_final: 0.8421 (pm20)
REVERT: B   31 LYS cc_start: 0.9457 (tttt) cc_final: 0.9156 (tttp)
REVERT: B   53 GLU cc_start: 0.8799 (tp30) cc_final: 0.8129 (tp30)
REVERT: B   84 MET cc_start: 0.8883 (tpp) cc_final: 0.8193 (tpp)
REVERT: B   88 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.8118 (m-80)
REVERT: B   92 ARG cc_start: 0.9327 (ttp80) cc_final: 0.8986 (ttp80)
REVERT: C   61 GLU cc_start: 0.8989 (tp30) cc_final: 0.8533 (tp30)
REVERT: C   64 GLU cc_start: 0.9375 (OUTLIER) cc_final: 0.8990 (pp20)
REVERT: C   84 GLN cc_start: 0.9465 (tp-100) cc_final: 0.9202 (tp-100)
REVERT: C   88 ARG cc_start: 0.9094 (mmt90) cc_final: 0.8794 (mmt90)
REVERT: D   42 TYR cc_start: 0.7916 (t80) cc_final: 0.7618 (t80)
REVERT: D   47 GLN cc_start: 0.9257 (tm-30) cc_final: 0.8912 (tm-30)
REVERT: D   68 ASP cc_start: 0.9109 (t0) cc_final: 0.8750 (t0)
REVERT: D   83 TYR cc_start: 0.8421 (t80) cc_final: 0.8089 (t80)
REVERT: D  105 GLU cc_start: 0.8876 (tp30) cc_final: 0.8256 (tp30)
REVERT: E   76 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8859 (pp30)
REVERT: F   53 GLU cc_start: 0.9201 (tp30) cc_final: 0.8943 (tp30)
REVERT: F   63 GLU cc_start: 0.9219 (tt0) cc_final: 0.8887 (mt-10)
REVERT: F   84 MET cc_start: 0.8963 (mmm) cc_final: 0.8215 (mmm)
REVERT: G   24 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8865 (mm-40)
REVERT: G   73 ASN cc_start: 0.9322 (OUTLIER) cc_final: 0.9058 (t0)
REVERT: G   75 LYS cc_start: 0.8910 (mmmm) cc_final: 0.8177 (mmmm)
REVERT: G   90 ASP cc_start: 0.8060 (t0) cc_final: 0.7783 (t0)
REVERT: G   91 GLU cc_start: 0.8693 (tp30) cc_final: 0.8401 (tp30)
REVERT: G   92 GLU cc_start: 0.9338 (mp0) cc_final: 0.8972 (tt0)
REVERT: G  100 VAL cc_start: 0.9666 (t) cc_final: 0.9222 (p)
REVERT: H   62 MET cc_start: 0.9387 (mmm) cc_final: 0.9040 (mmm)
REVERT: H  113 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8524 (tm-30)
  outliers start: 16
  outliers final: 9
  residues processed: 241
  average time/residue: 0.2664
  time to fit residues: 87.0725
Evaluate side-chains
  233 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 220
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   88 TYR
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 18 optimal weight:    9.9990
   chunk 74 optimal weight:    8.9990
   chunk 32 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 90 optimal weight:    7.9990
   chunk 15 optimal weight:    0.8980
   chunk 76 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 85 optimal weight:   10.0000
   chunk 63 optimal weight:    4.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  55 GLN
E  93 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  64 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.056404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.041416 restraints weight = 47586.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.2752 rms_B_bonded: 2.56
r_work: 0.2587 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.2587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  12684  Z= 0.213
  Angle     :  0.627   7.663  18373  Z= 0.363
  Chirality :  0.035   0.178   2090
  Planarity :  0.004   0.035   1320
  Dihedral  : 31.015 177.579   3997
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 32.59 %
    Favored  : 64.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.31), residues: 734
  helix:  2.07 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.66 (0.46), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS E  39 
 PHE   0.009   0.001   PHE B 100 
 TYR   0.041   0.002   TYR D  40 
 ARG   0.007   0.000   ARG H  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03885 (  767)
  hydrogen bonds       : angle       3.00347 ( 1931)
  covalent geometry    : bond        0.00485 (12684)
  covalent geometry    : angle       0.62692 (18373)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 216
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8598 (pm20) cc_final: 0.8250 (pm20)
REVERT: A   94 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8758 (tp30)
REVERT: B   27 GLN cc_start: 0.8741 (pt0) cc_final: 0.8427 (pm20)
REVERT: B   31 LYS cc_start: 0.9464 (tttt) cc_final: 0.9124 (tttp)
REVERT: B   53 GLU cc_start: 0.8823 (tp30) cc_final: 0.8155 (tp30)
REVERT: B   84 MET cc_start: 0.8874 (tpp) cc_final: 0.8155 (tpp)
REVERT: B   88 TYR cc_start: 0.8887 (OUTLIER) cc_final: 0.8301 (m-80)
REVERT: B   92 ARG cc_start: 0.9341 (ttp80) cc_final: 0.8992 (ttp80)
REVERT: C   61 GLU cc_start: 0.9013 (tp30) cc_final: 0.8573 (tp30)
REVERT: C   64 GLU cc_start: 0.9383 (OUTLIER) cc_final: 0.9008 (pp20)
REVERT: D   42 TYR cc_start: 0.7961 (t80) cc_final: 0.7663 (t80)
REVERT: D   47 GLN cc_start: 0.9259 (tm-30) cc_final: 0.8917 (tm-30)
REVERT: D   57 LYS cc_start: 0.8658 (mmtt) cc_final: 0.8363 (mmmm)
REVERT: D   68 ASP cc_start: 0.9116 (t0) cc_final: 0.8732 (t0)
REVERT: D   83 TYR cc_start: 0.8581 (t80) cc_final: 0.8040 (t80)
REVERT: D  105 GLU cc_start: 0.8940 (tp30) cc_final: 0.8451 (tp30)
REVERT: E   76 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8839 (pp30)
REVERT: F   53 GLU cc_start: 0.9240 (tp30) cc_final: 0.8949 (tp30)
REVERT: F   63 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8909 (mt-10)
REVERT: F   84 MET cc_start: 0.8960 (mmm) cc_final: 0.8468 (mmm)
REVERT: G   24 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8917 (mm-40)
REVERT: G   73 ASN cc_start: 0.9325 (OUTLIER) cc_final: 0.9067 (t0)
REVERT: G   75 LYS cc_start: 0.8953 (mmmm) cc_final: 0.8223 (mmmm)
REVERT: G   90 ASP cc_start: 0.8123 (t0) cc_final: 0.7824 (t0)
REVERT: G   91 GLU cc_start: 0.8787 (tp30) cc_final: 0.8515 (tp30)
REVERT: G   92 GLU cc_start: 0.9330 (mp0) cc_final: 0.9005 (tt0)
REVERT: G  100 VAL cc_start: 0.9688 (t) cc_final: 0.9247 (p)
REVERT: H  113 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8476 (tm-30)
  outliers start: 19
  outliers final: 13
  residues processed: 224
  average time/residue: 0.2735
  time to fit residues: 82.0123
Evaluate side-chains
  228 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 210
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain B residue   88 TYR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 95 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 70 optimal weight:   10.0000
   chunk 22 optimal weight:    1.9990
   chunk 78 optimal weight:    7.9990
   chunk 50 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 83 optimal weight:   10.0000
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.057091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.042300 restraints weight = 47308.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.2770 rms_B_bonded: 2.53
r_work: 0.2606 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.2606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.2569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12684  Z= 0.192
  Angle     :  0.628   8.474  18373  Z= 0.361
  Chirality :  0.034   0.161   2090
  Planarity :  0.004   0.033   1320
  Dihedral  : 30.984 177.630   3997
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 33.23 %
    Favored  : 63.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.31), residues: 734
  helix:  2.14 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.80 (0.45), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H  82 
 PHE   0.009   0.001   PHE B 100 
 TYR   0.029   0.002   TYR H  40 
 ARG   0.007   0.000   ARG H  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03735 (  767)
  hydrogen bonds       : angle       2.98391 ( 1931)
  covalent geometry    : bond        0.00435 (12684)
  covalent geometry    : angle       0.62764 (18373)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 220
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8626 (pm20) cc_final: 0.8276 (pm20)
REVERT: A   94 GLU cc_start: 0.9103 (mm-30) cc_final: 0.8779 (tp30)
REVERT: B   27 GLN cc_start: 0.8701 (pt0) cc_final: 0.8407 (pm20)
REVERT: B   31 LYS cc_start: 0.9463 (tttt) cc_final: 0.9146 (tttp)
REVERT: B   53 GLU cc_start: 0.8820 (tp30) cc_final: 0.8183 (tp30)
REVERT: B   84 MET cc_start: 0.8868 (tpp) cc_final: 0.8090 (tpp)
REVERT: B   88 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.8177 (m-80)
REVERT: B   92 ARG cc_start: 0.9364 (ttp80) cc_final: 0.9005 (ttp80)
REVERT: C   61 GLU cc_start: 0.9025 (tp30) cc_final: 0.8581 (tp30)
REVERT: C   64 GLU cc_start: 0.9382 (OUTLIER) cc_final: 0.9004 (pp20)
REVERT: C   84 GLN cc_start: 0.9444 (tp-100) cc_final: 0.9132 (tp-100)
REVERT: C   88 ARG cc_start: 0.9152 (mmt90) cc_final: 0.8778 (mmt90)
REVERT: D   42 TYR cc_start: 0.7935 (t80) cc_final: 0.7639 (t80)
REVERT: D   47 GLN cc_start: 0.9268 (tm-30) cc_final: 0.9066 (tm-30)
REVERT: D   57 LYS cc_start: 0.8691 (mmtt) cc_final: 0.8413 (mmmm)
REVERT: D   68 ASP cc_start: 0.9143 (t0) cc_final: 0.8780 (t0)
REVERT: D   83 TYR cc_start: 0.8548 (t80) cc_final: 0.8074 (t80)
REVERT: D  105 GLU cc_start: 0.8921 (tp30) cc_final: 0.8610 (tp30)
REVERT: E   76 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8834 (pp30)
REVERT: F   63 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.8898 (mt-10)
REVERT: F   84 MET cc_start: 0.8926 (mmm) cc_final: 0.8400 (mmm)
REVERT: G   24 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8941 (mm-40)
REVERT: G   73 ASN cc_start: 0.9328 (OUTLIER) cc_final: 0.9065 (t0)
REVERT: G   75 LYS cc_start: 0.8953 (mmmm) cc_final: 0.8201 (mmmm)
REVERT: G   90 ASP cc_start: 0.8128 (t0) cc_final: 0.7782 (t0)
REVERT: G   91 GLU cc_start: 0.8770 (tp30) cc_final: 0.8480 (tp30)
REVERT: G   92 GLU cc_start: 0.9308 (mp0) cc_final: 0.8997 (tt0)
REVERT: G  100 VAL cc_start: 0.9684 (t) cc_final: 0.9241 (p)
REVERT: H  113 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8482 (tm-30)
  outliers start: 18
  outliers final: 13
  residues processed: 228
  average time/residue: 0.2870
  time to fit residues: 88.4091
Evaluate side-chains
  232 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 214
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   88 TYR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 73 optimal weight:    8.9990
   chunk 66 optimal weight:    5.9990
   chunk 46 optimal weight:    9.9990
   chunk 2 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 51 optimal weight:    6.9990
   chunk 37 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 25 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 97 optimal weight:   10.0000
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  55 GLN
E  93 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  64 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.054354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.039646 restraints weight = 48565.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.2669 rms_B_bonded: 2.67
r_work: 0.2500 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8749
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  12684  Z= 0.285
  Angle     :  0.684   8.996  18373  Z= 0.390
  Chirality :  0.037   0.167   2090
  Planarity :  0.004   0.034   1320
  Dihedral  : 31.257 177.216   3997
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 33.07 %
    Favored  : 63.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.31), residues: 734
  helix:  2.03 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.84 (0.44), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H  82 
 PHE   0.009   0.001   PHE B 100 
 TYR   0.041   0.003   TYR D  40 
 ARG   0.008   0.001   ARG H  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04561 (  767)
  hydrogen bonds       : angle       3.22150 ( 1931)
  covalent geometry    : bond        0.00648 (12684)
  covalent geometry    : angle       0.68428 (18373)

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

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

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1468 Ramachandran restraints generated.
    734 Oldfield, 0 Emsley, 734 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 211
  time to evaluate  : 0.873 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8698 (pm20) cc_final: 0.8358 (pm20)
REVERT: A   94 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8816 (tp30)
REVERT: B   27 GLN cc_start: 0.8683 (pt0) cc_final: 0.8366 (pm20)
REVERT: B   31 LYS cc_start: 0.9491 (tttt) cc_final: 0.9174 (tttp)
REVERT: B   53 GLU cc_start: 0.9009 (tp30) cc_final: 0.8274 (tp30)
REVERT: B   84 MET cc_start: 0.8908 (tpp) cc_final: 0.8013 (tpp)
REVERT: B   88 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.8366 (m-80)
REVERT: B   92 ARG cc_start: 0.9364 (ttp80) cc_final: 0.9004 (ttp80)
REVERT: C   61 GLU cc_start: 0.9057 (tp30) cc_final: 0.8636 (tp30)
REVERT: C   64 GLU cc_start: 0.9389 (OUTLIER) cc_final: 0.9021 (pp20)
REVERT: C   84 GLN cc_start: 0.9444 (tp-100) cc_final: 0.9215 (tp-100)
REVERT: D   42 TYR cc_start: 0.8002 (t80) cc_final: 0.7726 (t80)
REVERT: D   47 GLN cc_start: 0.9239 (tm-30) cc_final: 0.8884 (tm-30)
REVERT: D   57 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8438 (mmmm)
REVERT: D   68 ASP cc_start: 0.9139 (t0) cc_final: 0.8801 (t0)
REVERT: D   83 TYR cc_start: 0.8693 (t80) cc_final: 0.8042 (t80)
REVERT: D  105 GLU cc_start: 0.9006 (tp30) cc_final: 0.8565 (tp30)
REVERT: E   76 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8864 (pp30)
REVERT: F   63 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.8654 (mt-10)
REVERT: F   84 MET cc_start: 0.9013 (mmm) cc_final: 0.8456 (mmm)
REVERT: F   85 ASP cc_start: 0.9058 (m-30) cc_final: 0.8616 (m-30)
REVERT: G   73 ASN cc_start: 0.9342 (OUTLIER) cc_final: 0.9070 (t0)
REVERT: G   75 LYS cc_start: 0.8972 (mmmm) cc_final: 0.8213 (mmmm)
REVERT: G   90 ASP cc_start: 0.8249 (t0) cc_final: 0.7923 (t0)
REVERT: G   91 GLU cc_start: 0.8834 (tp30) cc_final: 0.8537 (tp30)
REVERT: G   92 GLU cc_start: 0.9320 (mp0) cc_final: 0.9020 (tt0)
REVERT: G  100 VAL cc_start: 0.9724 (t) cc_final: 0.9298 (p)
REVERT: H  113 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8462 (tm-30)
  outliers start: 21
  outliers final: 12
  residues processed: 221
  average time/residue: 0.2832
  time to fit residues: 83.8655
Evaluate side-chains
  224 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 207
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain B residue   88 TYR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   64 GLU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   78 SER
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 81 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 90 optimal weight:    6.9990
   chunk 74 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 37 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9990
   chunk 35 optimal weight:    8.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  55 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.056824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.041981 restraints weight = 46646.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.2759 rms_B_bonded: 2.50
r_work: 0.2596 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8720
moved from start:          0.2738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12684  Z= 0.188
  Angle     :  0.646   8.880  18373  Z= 0.368
  Chirality :  0.034   0.163   2090
  Planarity :  0.004   0.033   1320
  Dihedral  : 31.084 177.604   3997
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 33.55 %
    Favored  : 63.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.31), residues: 734
  helix:  2.04 (0.22), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.81 (0.45), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS H  82 
 PHE   0.009   0.001   PHE B 100 
 TYR   0.031   0.002   TYR H  40 
 ARG   0.009   0.000   ARG H  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03792 (  767)
  hydrogen bonds       : angle       3.06014 ( 1931)
  covalent geometry    : bond        0.00426 (12684)
  covalent geometry    : angle       0.64596 (18373)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4974.66 seconds
wall clock time: 86 minutes 42.86 seconds (5202.86 seconds total)